151
|
Patel RA, Weiß CL, Zhu H, Mostafavi H, Simons YB, Spence JP, Pritchard JK. Conditional frequency spectra as a tool for studying selection on complex traits in biobanks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599126. [PMID: 38948697 PMCID: PMC11212903 DOI: 10.1101/2024.06.15.599126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. To account for GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insight into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.
Collapse
Affiliation(s)
- Roshni A. Patel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Clemens L. Weiß
- Stanford Cancer Institute Core, Stanford University School of Medicine, Stanford, CA
| | - Huisheng Zhu
- Department of Biology, Stanford University, Stanford, CA
| | - Hakhamanesh Mostafavi
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY
| | | | - Jeffrey P. Spence
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
| |
Collapse
|
152
|
Gordon H, Minozzi S, Kopylov U, Verstockt B, Chaparro M, Buskens C, Warusavitarne J, Agrawal M, Allocca M, Atreya R, Battat R, Bettenworth D, Bislenghi G, Brown SR, Burisch J, Casanova MJ, Czuber-Dochan W, de Groof J, El-Hussuna A, Ellul P, Fidalgo C, Fiorino G, Gisbert J, Sabino JG, Hanzel J, Holubar S, Iacucci M, Iqbal N, Kapizioni C, Karmiris K, Kobayashi T, Kotze PG, Luglio G, Maaser C, Moran G, Noor N, Papamichael K, Peros G, Reenaers C, Sica G, Sigall-Boneh R, Vavricka SR, Yanai H, Myrelid P, Adamina M, Raine T. ECCO Guidelines on Therapeutics in Crohn's Disease: Medical Treatment. J Crohns Colitis 2024:jjae091. [PMID: 38877997 DOI: 10.1093/ecco-jcc/jjae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Indexed: 07/28/2024]
Affiliation(s)
- Hannah Gordon
- Translational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK
| | - Silvia Minozzi
- Department of Epidemiology, Lazio Regional Health Service, Rome, Italy
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center, Ramat Gan, Israel
| | - Bram Verstockt
- Department Gastroenterology & Hepatology, University Hospitals Leuven, KU Leuven and Dpt. Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Maria Chaparro
- Gastroenterology Department. Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid; Spain
| | - Christianne Buskens
- Department of Surgery, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | | | - Manasi Agrawal
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Mariangela Allocca
- IRCCS Hospital San Raffaele and University Vita-Salute San Raffaele, Gastroenterology and Endoscopy, Milan, Italy
| | - Raja Atreya
- First Department of Medicine, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Battat
- Division of Gastroenterology, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
| | - Dominik Bettenworth
- CED Schwerpunktpraxis, Münster and Medical Faculty of the University of Münster, Münster, NRW, Germany
| | | | | | - Johan Burisch
- Gastrounit, Medical Division, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre; Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - María José Casanova
- Gastroenterology Department. Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid. Spain
| | - Wladyslawa Czuber-Dochan
- Florence Nightingale Faculty of Nursing- Midwifery and Palliative Care, King's College London, London, United Kingdom
| | - Joline de Groof
- Colorectal Surgery, Royal Surrey NHS Foundation Trust, Guildford, UK
| | - Alaa El-Hussuna
- OpenSourceResearch Organization (OSRC.Network), Aalborg, Denmark
| | - Pierre Ellul
- Division of Gastroenterology, Mater Dei Hospital, Malta
| | - Catarina Fidalgo
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Division of Gastroenterology, Hospital da Luz, Lisboa, Portugal
| | | | - Javier Gisbert
- Gastroenterology Department. Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - João Guedelha Sabino
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Jurij Hanzel
- Department of Gastroenterology, University Medical Centre Ljubljana, Ljubljana; Chair of Internal Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Stefan Holubar
- Department of Colon & Rectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Marietta Iacucci
- APC Microbiome Ireland, College of Medicine and Health, University College of Cork, Cork, Ireland
| | - Nusrat Iqbal
- Department of Surgery, Worcestershire Acute Hospitals NHS Trust, Worcester, UK
| | | | | | - Taku Kobayashi
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Paulo Gustavo Kotze
- Health Sciences Postgraduate Program, Pontificia Universidade Católica do Paraná (PUCPR), Curitiba, Brazil
| | - Gaetano Luglio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Christian Maaser
- Outpatients Department of Gastroenterology, University Teaching Hospital Lueneburg, Germany
| | - Gordon Moran
- National Institute of Health Research Nottingham Biomedical Research Centre, University of Nottingham and Nottingham University Hospitals, Nottingham
- Translational Medical Sciences, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham. NG7 2UH. United Kingdom
| | - Nurulamin Noor
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Konstantinos Papamichael
- Center for Inflammatory Bowel Diseases, Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Georgios Peros
- Department of Surgery, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | | | - Giuseppe Sica
- Department of Surgery, Università Tor Vergata, Roma, Italy
| | - Rotem Sigall-Boneh
- Pediatric Gastroenterology and Nutrition Unit, The E. Wolfson Medical Center, Holon, Israel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephan R Vavricka
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Henit Yanai
- IBD Center, Division of Gastroenterology, Rabin Medical Center, Petah Tikva; Faculty of Medicine, Tel Aviv University, Tel Aviv; Israel
| | - Pär Myrelid
- Department of Surgery and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Michel Adamina
- Department of Surgery, Cantonal Hospital of Fribourg & Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Tim Raine
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| |
Collapse
|
153
|
Deng W, Li ZY, Liu B. [Value of different endoscopic scoring methods in assessing disease activity in pediatric Crohn's disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:584-591. [PMID: 38926374 DOI: 10.7499/j.issn.1008-8830.2311103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
OBJECTIVES To explore the value of different endoscopic scoring methods in assessing disease activity in pediatric Crohn's disease (CD). METHODS A total of 70 children diagnosed with CD at the Children's Hospital of Chongqing Medical University from January 2018 to January 2023 were included. Clinical disease activity was assessed using the Pediatric Crohn's Disease Activity Index (PCDAI), while different endoscopic scores were assigned based on endoscopic findings. Spearman rank correlation analysis was used to evaluate the correlation between each endoscopic scoring method and PCDAI as well as laboratory indicators. Kappa test was used to assess the consistency between colonoscopy/capsule endoscopy scoring methods and PCDAI in determining CD activity. Receiver operating characteristic curve analysis was performed to assess the diagnostic efficacy of laboratory indicators in predicting endoscopic activity. RESULTS The PCDAI score showed a moderate positive correlation with the scores of Crohn's Disease Endoscopic Index of Severity (CDEIS) (rs=0.696, P<0.01), Simple Endoscopic Score for Crohn's Disease (SES-CD) (rs=0.680, P<0.01), Lewis Score (rs=0.540, P<0.01), and Capsule Endoscopy-Crohn's Disease Index (CE-CD) (rs=0.502, P<0.01). The consistency between all endoscopic scoring methods and PCDAI in determining CD activity was poor (Kappa=0.069-0.226). Erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), hematocrit (HCT), and serum albumin (ALB) levels showed a moderate correlation with the PCDAI score and the scores of colonoscopy scoring methods (CDEIS and SES-CD) (|rs|=0.581-0.725, P<0.01), but a weak correlation with the scores of capsule scoring methods (P<0.05). ESR and CRP had higher area under the curve (AUC) values in predicting disease activity based on PCDAI, CDEIS, SES-CD, and Lewis Score compared to HCT and ALB (P<0.05). CONCLUSIONS CDEIS, SES-CD, Lewis Score, and CE-CD can be used to evaluate disease activity in pediatric CD, but they do not fully correspond with disease activity assessed by PCDAI. Elevated levels of ESR and CRP can predict clinical and endoscopic disease activity in children with CD.
Collapse
Affiliation(s)
- Wen Deng
- Department of Gastroenterology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/China International Science and Technology Cooperation Base of Child Development and Critical Disorders/Chonging Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Zhong-Yue Li
- Department of Gastroenterology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/China International Science and Technology Cooperation Base of Child Development and Critical Disorders/Chonging Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Bo Liu
- Department of Gastroenterology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/China International Science and Technology Cooperation Base of Child Development and Critical Disorders/Chonging Key Laboratory of Pediatrics, Chongqing 400014, China
| |
Collapse
|
154
|
Lin J, Cheng Y, Gu S, Song S, Zhang H, Li J, Ling S. Mendelian randomization study and mediation analysis about the relation of inflammatory bowel disease and diabetic retinopathy: the further exploration of gut-retina axis. Front Endocrinol (Lausanne) 2024; 15:1382777. [PMID: 38948518 PMCID: PMC11211271 DOI: 10.3389/fendo.2024.1382777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
Background The concept of the gut-retinal axis proposed by previous scholars primarily focused on the relationship between intestinal microbiota and retinal diseases, and few further expanded the relationship between intestinal diseases and retinal diseases. To further substantiate the concept of the gut-retinal axis, we analyzed inflammatory bowel disease (IBD) and diabetic retinopathy (DR) using Mendelian randomization (MR), and use mediation analysis to further explore the potential substances that influence this causal relationship. Methods The genome-wide association study's (GWAS) summary statistics for genetic variations were utilized in a Mendelian randomization (MR) investigation. GWAS data on IBD (including ulcerative colitis (UC), Crohn's disease (CD), and IBD) for non-Finnish Europeans (NFE) were sourced from published articles. In contrast, data on DR (including DR and diabetic maculopathy (DMP)) were obtained from FinnGen R9. The causal relationship has been investigated using inverse variance weighted (IVW), MR-Egger, and weighted median and sensitivity analysis was applied to verify the stability of the results. In addition, we applied mediation analysis to investigate whether circulating inflammatory proteins and plasma lipids played a mediating role, and calculated its effect ratio. Results The causal relationship between IBD and DR was discovered by employing the inverse variance weighted (IVW) method and weighted median method. In forward MR, UC was significantly associated with lower risk of DR (IVW: OR=0.874; 95%CI= 0.835-0.916; P value= 1.28E-08) (Weighted median: OR=0.893; 95%CI= 0.837-0.954; P value= 7.40E-04). In reverse MR, it was shown that DR (IVW: OR=0.870; 95%CI= 0.828-0.914; P value= 2.79E-08)(Weighted median: OR=0.857; 95%CI= 0.801-0.916; P value= 6.40E-06) and DMP (IVW: OR=0.900; 95%CI= 0.865-0.937; P value= 3.34E-07)(Weighted median: OR=0.882; 95%CI= 0.841-0.924; P value= 1.82E-07) could reduce the risk of CD. What's more, DR is associated with a lower risk of IBD according to genetic prediction (IVW: OR=0.922; 95%CI= 0.873-0.972; P value= 0.002) (Weighted median: OR=0.924; 95%CI= 0.861-0.992; P value= 0.029). Fibroblast growth factor 21 (FGF21), phosphatidylcholine (PC), and triacylglycerol (TG) serve as mediators in these relationships. Conclusions Our research offers novel insights and sources for investigating the gut-retina axis in the genetic relationship between IBD and DR. We discover four mediators and more about the association between the intestine and retinal disorders and provide more evidence for the gut-retinal axis theory.
Collapse
Affiliation(s)
| | | | | | | | | | - Jianbing Li
- Department of Ophthalmology, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Shiqi Ling
- Department of Ophthalmology, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
155
|
Kotowski MJ, Ostrowski P, Sieńko J, Czerny B, Tejchman K, Machaliński B, Górska A, Mrozikiewicz AE, Bogacz A. The Importance of the FUT2 rs602662 Polymorphism in the Risk of Cardiovascular Complications in Patients after Kidney Transplantation. Int J Mol Sci 2024; 25:6562. [PMID: 38928269 PMCID: PMC11203847 DOI: 10.3390/ijms25126562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The FUT2 gene encodes an enzyme called α-1,2-fucosyltransferase, which is involved in the formation of blood group antigens AB0(H) and is also involved in the processes of vitamin B12 absorption and its transport between cells. FUT2 gene polymorphisms are associated with vitamin B12 levels in the body. Vitamin B12 deficiency associated with hyperhomocysteinemia is a major risk factor for cardiovascular diseases (CVDs), which are one of the main causes of death in patients after kidney transplantation. The aim of our study was to determine the impact of the rs602662 (G>A) polymorphism of the FUT2 gene on the functionality of transplanted kidneys and the risk of CVD in patients after kidney transplantation. The study included 402 patients treated with immunosuppression (183 patients taking cyclosporine (CsA) and 219 patients taking tacrolimus (TAC)). The analysis of the FUT2 rs602662 (G>A) polymorphism was performed using real-time PCR. Patients with CsA were more likely to be underweight (1.64% vs. 0.91%) and obese (27.87% vs. 15.98%), while those taking TAC were more likely to be of normal weight (39.27%) or overweight (43.84%). No statistically significant differences were observed comparing the mean blood pressure, both systolic and diastolic. The renal profile showed a higher median urea nitrogen concentration in patients with CsA (26.45 mg/dL (20.60-35.40) vs. 22.95 mg/dL (17.60-33.30), p = 0.004). The observed frequency of rs602662 alleles of the FUT2 gene was similar in the analyzed groups. The A allele was present in 43.7% of patients with CsA and 41.1% of those taking TAC (OR = 0.898; 95% CI: 0.678-1.189; p = 0.453). In the group with CsA, the GG genotype was present in 32.2% of patients, the GA in 48.1% and the AA in 19.7%. A similar distribution was obtained in the TAC group: GG-33.8%, GA-50.2%, and AA-16.0%. An association of genotypes containing the G allele with a higher incidence of hypertension was observed. The G allele was present in 65% of people with hypertension and in 56% of patients with normal blood pressure (p = 0.036). Moreover, the evaluation of the renal parameters showed no effect of the FUT2 polymorphism on the risk of organ rejection because the levels of creatinine, eGFR, potassium, and urea nitrogen were prognostic of successful transplantation. Our results suggest that the rs6022662 FUT2 polymorphism may influence the risk of cardiovascular diseases.
Collapse
Affiliation(s)
- Maciej Józef Kotowski
- Department of General Surgery and Transplantology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (M.J.K.); (P.O.); (K.T.)
| | - Piotr Ostrowski
- Department of General Surgery and Transplantology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (M.J.K.); (P.O.); (K.T.)
| | - Jerzy Sieńko
- Institute of Physical Culture Sciences, University of Szczecin, 70-453 Szczecin, Poland;
| | - Bogusław Czerny
- Department of Stem Cells and Regenerative Medicine, Institute of Natural Fibres and Medicinal Plants, Kolejowa 2, 62-064 Plewiska, Poland; (B.C.); (A.G.)
- Department of Pharmacology and Pharmacoeconomics, Pomeranian Medical University in Szczecin, Żołnierska 48, 71-230 Szczecin, Poland
| | - Karol Tejchman
- Department of General Surgery and Transplantology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (M.J.K.); (P.O.); (K.T.)
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland;
| | - Aleksandra Górska
- Department of Stem Cells and Regenerative Medicine, Institute of Natural Fibres and Medicinal Plants, Kolejowa 2, 62-064 Plewiska, Poland; (B.C.); (A.G.)
| | - Aleksandra E. Mrozikiewicz
- Department of Obstetrics and Women’s Diseases, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan, Poland;
| | - Anna Bogacz
- Department of Personalized Medicine and Cell Therapy, Regional Blood Center, Marcelińska 44, 60-354 Poznan, Poland
| |
Collapse
|
156
|
Zhang B, Sun C, Zhu Y, Qin H, Kong D, Zhang J, Shao B, Li X, Ren S, Wang H, Hao J, Wang H. Upregulation of TCPTP in Macrophages Is Involved in IL-35 Mediated Attenuation of Experimental Colitis. Mediators Inflamm 2024; 2024:3282679. [PMID: 38962170 PMCID: PMC11221972 DOI: 10.1155/2024/3282679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 04/11/2024] [Accepted: 06/01/2024] [Indexed: 07/05/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic intestinal inflammatory disease with complex etiology. Interleukin-35 (IL-35), as a cytokine with immunomodulatory function, has been shown to have therapeutic effects on UC, but its mechanism is not yet clear. Therefore, we constructed Pichia pastoris stably expressing IL-35 which enables the cytokines to reach the diseased mucosa, and explored whether upregulation of T-cell protein tyrosine phosphatase (TCPTP) in macrophages is involved in the mechanisms of IL-35-mediated attenuation of UC. After the successful construction of engineered bacteria expressing IL-35, a colitis model was successfully induced by giving BALB/c mice a solution containing 3% dextran sulfate sodium (DSS). Mice were treated with Pichia/IL-35, empty plasmid-transformed Pichia (Pichia/0), or PBS by gavage, respectively. The expression of TCPTP in macrophages (RAW264.7, BMDMs) and intestinal tissues after IL-35 treatment was detected. After administration of Pichia/IL-35, the mice showed significant improvement in weight loss, bloody stools, and shortened colon. Colon pathology also showed that the inflammatory condition of mice in the Pichia/IL-35 treatment group was alleviated. Notably, Pichia/IL-35 treatment not only increases local M2 macrophages but also decreases the expression of inflammatory cytokine IL-6 in the colon. With Pichia/IL-35 treatment, the proportion of M1 macrophages, Th17, and Th1 cells in mouse MLNs were markedly decreased, while Tregs were significantly increased. In vitro experiments, IL-35 significantly promoted the expression of TCPTP in macrophages stimulated with LPS. Similarly, the mice in the Pichia/IL-35 group also expressed more TCPTP than that of the untreated group and the Pichia/0 group.
Collapse
Affiliation(s)
- Baoren Zhang
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Chenglu Sun
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Yanglin Zhu
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Hong Qin
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Dejun Kong
- School of MedicineNankai University, Tianjin, China
| | - Jingyi Zhang
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Bo Shao
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Xiang Li
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Shaohua Ren
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Hongda Wang
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
| | - Jingpeng Hao
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
- Department of Anorectal SurgeryTianjin Medical University Second Hospital, Tianjin, China
| | - Hao Wang
- Department of General SurgeryTianjin Medical University General Hospital, Tianjin, China
- Tianjin General Surgery Institute, Tianjin, China
- Tianjin Key Laboratory of Precise Vascular Reconstruction and Organ Function Repair, Tianjin, China
| |
Collapse
|
157
|
Liu Q, Zheng Y, Sturmlechner I, Jain A, Own M, Yang Q, Zhang H, Pinto e Vairo F, Cerosaletti K, Buckner JH, Warrington KJ, Koster MJ, Weyand CM, Goronzy JJ. IKZF1 and UBR4 gene variants drive autoimmunity and Th2 polarization in IgG4-related disease. J Clin Invest 2024; 134:e178692. [PMID: 38885295 PMCID: PMC11324302 DOI: 10.1172/jci178692] [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: 12/26/2023] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
IgG4-related disease (IgG4-RD) is a systemic immune-mediated fibroinflammatory disease whose pathomechanisms remain poorly understood. Here, we identified gene variants in familial IgG4-RD and determined their functional consequences. All 3 affected members of the family shared variants of the transcription factor IKAROS, encoded by IKZF1, and the E3 ubiquitin ligase UBR4. The IKAROS variant increased binding to the FYN promoter, resulting in higher transcription of FYN in T cells. The UBR4 variant prevented the lysosomal degradation of the phosphatase CD45. In the presence of elevated FYN, CD45 functioned as a positive regulatory loop, lowering the threshold for T cell activation. Consequently, T cells from the affected family members were hyperresponsive to stimulation. When transduced with a low-avidity, autoreactive T cell receptor, their T cells responded to the autoantigenic peptide. In parallel, high expression of FYN in T cells biased their differentiation toward Th2 polarization by stabilizing the transcription factor JunB. This bias was consistent with the frequent atopic manifestations in patients with IgG4-RD, including the affected family members in the present study. Building on the functional consequences of these 2 variants, we propose a disease model that is not only instructive for IgG4-RD but also for atopic diseases and autoimmune diseases associated with an IKZF1 risk haplotype.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Filippo Pinto e Vairo
- Center for Individualized Medicine and Department of Clinical Genomics, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Karen Cerosaletti
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Jane H. Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | | | | | | | | |
Collapse
|
158
|
Cao G, Luo Q, Wu Y, Chen G. Inflammatory bowel disease and rheumatoid arthritis share a common genetic structure. Front Immunol 2024; 15:1359857. [PMID: 38938570 PMCID: PMC11208460 DOI: 10.3389/fimmu.2024.1359857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Background The comorbidity rate of inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) is high; nevertheless, the reasons behind this high rate remain unclear. Their similar genetic makeup probably contributes to this comorbidity. Methods Based on data obtained from the genome-wide association study of IBD and RA, we first assessed an overall genetic association by performing the linkage disequilibrium score regression (LDSC) analysis. Further, a local correlation analysis was performed by estimating the heritability in summary statistics. Next, the causality between the two diseases was analyzed by two-sample Mendelian randomization (MR). A genetic overlap was analyzed by the conditional/conjoint false discovery rate (cond/conjFDR) method.LDSC with specific expression of gene analysis was performed to identify related tissues between the two diseases. Finally, GWAS multi-trait analysis (MTAG) was also carried out. Results IBD and RA are correlated at the genomic level, both overall and locally. The MR results suggested that IBD induced RA. We identified 20 shared loci between IBD and RA on the basis of a conjFDR of <0.01. Additionally, we identified two tissues, namely spleen and small intestine terminal ileum, which were commonly associated with both IBD and RA. Conclusion Herein, we proved the presence of a polygenic overlap between the genetic makeup of IBD and RA and provided new insights into the genetic architecture and mechanisms underlying the high comorbidity between these two diseases.
Collapse
Affiliation(s)
- Guoling Cao
- Department of Anorectal Surgery, The People’s Hospital of Cangnan, Wenzhou, China
| | - Qinghua Luo
- Clinical Medical College, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yunxiang Wu
- Department of Anorectal Surgery, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| | - Guanghua Chen
- Department of Anorectal Surgery, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| |
Collapse
|
159
|
Fong A, Rochus CM, Shandilya UK, Muniz MMM, Sharma A, Schenkel FS, Karrow NA, Baes CF. The role of interleukin-10 receptor alpha (IL10Rα) in Mycobacterium avium subsp. paratuberculosis infection of a mammary epithelial cell line. BMC Genom Data 2024; 25:58. [PMID: 38867147 PMCID: PMC11167801 DOI: 10.1186/s12863-024-01234-w] [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: 01/29/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Johne's disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne's disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne's disease in dairy cattle. Our objective was to determine how IL10Rα affects the pathogenesis of MAP by examining the effect of a live MAP challenge on a mammary epithelial cell line (MAC-T) that had IL10Rα knocked out using CRISPR/cas9. The wild type and the IL10Rα knockout MAC-T cell lines were exposed to live MAP bacteria for 72 h. Thereafter, mRNA was extracted from infected and uninfected cells. Differentially expressed genes were compared between the wild type and the IL10Rα knockout cell lines. Gene ontology was performed based on the differentially expressed genes to determine which biological pathways were involved. RESULTS Immune system processes pathways were targeted to determine the effect of IL10Rα on the response to MAP infection. There was a difference in immune response between the wild type and IL10Rα knockout MAC-T cell lines, and less difference in immune response between infected and not infected IL10Rα knockout MAC-T cells, indicating IL10Rα plays an important role in the progression of MAP infection. Additionally, these comparisons allowed us to identify other genes involved in inflammation-mediated chemokine and cytokine signalling, interleukin signalling and toll-like receptor pathways. CONCLUSIONS Identifying differentially expressed genes in wild type and ILR10α knockout MAC-T cells infected with live MAP bacteria provided further evidence that IL10Rα contributes to mounting an immune response to MAP infection and allowed us to identify additional potential candidate genes involved in this process. We found there was a complex immune response during MAP infection that is controlled by many genes.
Collapse
Affiliation(s)
- Aisha Fong
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christina M Rochus
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Umesh K Shandilya
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Maria M M Muniz
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ankita Sharma
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christine F Baes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3002, Switzerland.
| |
Collapse
|
160
|
Fiz Benito E, Feito Rodríguez M, Souza RDM, López EPS, de Lucas Laguna R. Bowel-associated dermatosis-arthritis syndrome, a diagnostic challenge in a young child with very early-onset inflammatory bowel disease. Pediatr Dermatol 2024. [PMID: 38863220 DOI: 10.1111/pde.15637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/16/2024] [Indexed: 06/13/2024]
Abstract
A 14-month-old girl with very early-onset inflammatory bowel disease (VEO-IBD) was admitted with a flare of her bowel disease and subsequently developed high fevers, joint pain, and skin lesions during her hospitalization. Workup demonstrated bowel-associated dermatosis-arthritis syndrome in the setting of VEO-IBD, a neutrophilic dermatosis rarely reported in children that can be challenging to diagnose and treat, with limited literature for patients under 2 years of age.
Collapse
Affiliation(s)
- Esther Fiz Benito
- Department of Dermatology, La Paz University Hospital, Madrid, Spain
| | | | | | | | | |
Collapse
|
161
|
Babaei A, Pourmotabbed A, Talebi S, Mehrabani S, Bagheri R, Ghoreishy SM, Amirian P, Zarpoosh M, Mohammadi H, Kermani MAH, Fakhari H, Moradi S. The association of ultra-processed food consumption with adult inflammatory bowel disease risk: a systematic review and dose-response meta-analysis of 4 035 694 participants. Nutr Rev 2024; 82:861-871. [PMID: 37632227 DOI: 10.1093/nutrit/nuad101] [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] [Indexed: 08/27/2023] Open
Abstract
CONTEXT There is an inconsistency between the results obtained from observational studies regarding intake of ultra-processed foods (UPFs) and the risk of inflammatory bowel disease (IBD). OBJECTIVES A dose-response meta-analysis was performed to evaluate the relationship between UPF intake and the risk of IBD. DATA SOURCES Searches were performed in the PubMed, ISI Web of Science, and Scopus databases up to November 2, 2022. DATA EXTRACTION Data were available from 24 studies including a total of 4 035 694 participants from 20 countries. DATA ANALYSIS Risk ratios for IBD were analyzed by a random-effects model. Outcomes indicated that UPF intake was linked to an increased risk of IBD (relative risk [RR], 1.13; 95%CI, 1.06-1.21; P = 0.001; I2 = 73.2%; n = 59; N = 4 035 694). This association was significant, especially for the risk of Crohn's disease (CD) (RR, 1.19; 95%CI, 1.00-1.41; I2 = 78.2%; P = 0.046; n = 23; N = 2 167 160), unlike the risk of ulcerative colitis (UC) (RR = 1.11; 95%CI, 0.99-1.26; P = 0.085; I2 = 60.3%; n = 27; N = 2 167 918). Also, results revealed that each 10% enhancement in daily UPF intake was not related to the risk of IBD (RR, 1.05; 95%CI, 0.98-1.14; P = 0.168; I2 = 31.9%; n = 4) or the risk of UC (RR, 1.01; 95%CI, 0.92-1.11; P = 0.876; I2 = 34.7%; n = 2) in adults. However, results suggested that for every 10% increase in daily UPF intake, there was a 19% increase in the risk of CD (RR, 1.19; 95%CI, 1.01-1.32; P = 0.021; I2 = 0.0%; n = 2) among adults. In addition, the results showed a positive linear relation between UPF intake with CD risk (Pnonlinearity = 0.431; Pdose response = 0.049) but not risk of IBD or UC. CONCLUSION High intake of UPFs was linked with an enhanced IBD risk, a specific risk of CD. However, conducting more observational studies among several ethnicities and using specific tools that accurately assess the amount of UPF consumption, components of UPFs, and food additives may be necessary. Systematic Review Registration: PROSPERO registration no. CRD42023390258.
Collapse
Affiliation(s)
- Atefeh Babaei
- Department of Physiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Pourmotabbed
- Department of Physiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepide Talebi
- Department of Clinical Nutrition, School of Nutritional Science, Tehran University of Medical Science, Tehran, Iran
- Student Research Committee, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Sanaz Mehrabani
- Department of Clinical Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Bagheri
- Department of Exercise Physiology, University of Isfahan, Isfahan, Iran
| | - Seyed Mojtaba Ghoreishy
- Department of Clinical Nutrition, School of Nutritional Science, Tehran University of Medical Science, Tehran, Iran
- Student Research Committee, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Parsa Amirian
- General Practitioner, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mahsa Zarpoosh
- General Practitioner, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamed Mohammadi
- Department of Clinical Nutrition, School of Nutritional Science, Tehran University of Medical Science, Tehran, Iran
| | - Mohammad Ali Hojjati Kermani
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Fakhari
- Department of Exercise Physiology, University of Isfahan, Isfahan, Iran
| | - Sajjad Moradi
- Nutritional Sciences Department, School of Nutritional Sciences and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
162
|
Al-Beltagi M, Saeed NK, Bediwy AS, Elbeltagi R. Fecal calprotectin in pediatric gastrointestinal diseases: Pros and cons. World J Clin Pediatr 2024; 13:93341. [PMID: 38948001 PMCID: PMC11212754 DOI: 10.5409/wjcp.v13.i2.93341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/28/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Fecal calprotectin is a valuable biomarker for assessing intestinal inflammation in pediatric gastrointestinal diseases. However, its role, pros, and cons in various conditions must be comprehensively elucidated. AIM To explore the role of fecal calprotectin in pediatric gastrointestinal diseases, including its advantages and limitations. METHODS A comprehensive search was conducted on PubMed, PubMed Central, Google Scholar, and other scientific research engines until February 24, 2024. The review included 88 research articles, 56 review articles, six meta-analyses, two systematic reviews, two consensus papers, and two letters to the editors. RESULTS Fecal calprotectin is a non-invasive marker for detecting intestinal inflammation and monitoring disease activity in pediatric conditions such as functional gastrointestinal disorders, inflammatory bowel disease, coeliac disease, coronavirus disease 2019-induced gastrointestinal disorders, gastroenteritis, and cystic fibrosis-associated intestinal pathology. However, its lack of specificity and susceptibility to various confounding factors pose challenges in interpretation. Despite these limitations, fecal calprotectin offers significant advantages in diagnosing, monitoring, and managing pediatric gastrointestinal diseases. CONCLUSION Fecal calprotectin holds promise as a valuable tool in pediatric gastroenterology, offering insights into disease activity, treatment response, and prognosis. Standardized protocols and guidelines are needed to optimize its clinical utility and mitigate interpretation challenges. Further research is warranted to address the identified limitations and enhance our understanding of fecal calprotectin in pediatric gastrointestinal diseases.
Collapse
Affiliation(s)
- Mohammed Al-Beltagi
- Department of Pediatric, Faculty of Medicine, Tanta University, Tanta 31511, Alghrabia, Egypt
- Department of Pediatrics, University Medical Center, King Abdulla Medical City, Arabian Gulf University, Manama 26671, Manama, Bahrain
- Department of Pediatrics, University Medical Center, Dr. Sulaiman Al Habib Medical Group, Bahrain, Manama 26671, Manama, Bahrain
| | - Nermin Kamal Saeed
- Medical Microbiology Section, Department of Pathology, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 12, Manama, Bahrain
- Medical Microbiology Section, Department of Pathology, Irish Royal College of Surgeon, Bahrain, Busaiteen 15503, Muharraq, Bahrain
| | - Adel Salah Bediwy
- Department of Pulmonology, Faculty of Medicine, Tanta University, Tanta 31527, Alghrabia, Egypt
- Department of Pulmonology, University Medical Center, King Abdulla Medical City, Arabian Gulf University, Manama 26671, Manama, Bahrain
- Department of Pulmonology, University Medical Center, King Abdulla Medical City, Dr. Sulaiman Al Habib Medical Group, Manama 26671, Manama, Bahrain
| | - Reem Elbeltagi
- Department of Medicine, The Royal College of Surgeons in Ireland - Bahrain, Busiateen 15503, Muharraq, Bahrain
| |
Collapse
|
163
|
Guo Z, Xu C, Fang Z, Yu X, Yang K, Liu C, Ning X, Dong Z, Liu C. Inflammatory bowel disease and breast cancer: A two-sample bidirectional Mendelian randomization study. Medicine (Baltimore) 2024; 103:e38392. [PMID: 38847661 PMCID: PMC11155618 DOI: 10.1097/md.0000000000038392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 06/10/2024] Open
Abstract
There is a correlation between IBD and breast cancer according to previous observational studies. However, so far there is no evidence to support if there is a causal relationship between these 2 diseases. We acquired comprehensive Genome-Wide Association Study (GWAS) summary data on IBD (including ulcerative colitis [UC] and Crohn disease [CD]) as well as breast cancer of completely European descent from the IEU GWAS database. The estimation of bidirectional causality between IBD (including UC and CD) and breast cancer was achieved through the utilization of 2-sample Mendelian randomization (MR). The MR results were also assessed for any potential bias caused by heterogeneity and pleiotropy through sensitivity analyses. Our study found a bidirectional causal effect between IBD and breast cancer. Genetic susceptibility to IBD was associated with an increased risk of breast cancer (OR = 1.053, 95% CI: 1.016-1.090, P = .004). Similarly, the presence of breast cancer may increase the risk of IBD (OR = 1.111, 95% CI: 1.035-1.194, P = .004). Moreover, the bidirectional causal effect between IBD and breast cancer can be confirmed by another GWAS of IBD. Subtype analysis showed that CD was associated with breast cancer (OR = 1.050, 95% CI: 1.020-1.080, P < .001), but not UC and breast cancer. There was a suggestive association between breast cancer and UC (OR = 1.106, 95% CI: 1.011-1.209, P = .028), but not with CD. This study supports a bidirectional causal effect between IBD and breast cancer. There appear to be considerable differences in the specific associations of UC and CD with AD. Understanding that IBD including its specific subtypes and breast cancer constitute common risk factors can contribute to the clinical management of both diseases.
Collapse
Affiliation(s)
- Zihao Guo
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Changyu Xu
- Department of Ultrasound, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhihao Fang
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoxiao Yu
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kai Yang
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Changxu Liu
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinwei Ning
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhichao Dong
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chang Liu
- Department of General Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
164
|
Fu X, Wu H, Shu Y, Yang B, Deng C. Crohn disease but not ulcerative colitis increases the risk of acute pancreatitis: A 2-sample Mendelian randomization study. Medicine (Baltimore) 2024; 103:e38317. [PMID: 38847662 PMCID: PMC11155567 DOI: 10.1097/md.0000000000038317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/01/2024] [Indexed: 06/10/2024] Open
Abstract
Accumulating evidence has indicated an increased risk of acute pancreatitis in individuals with inflammatory bowel disease (IBD); however, the establishment of a clear and direct causal connection between IBD and acute pancreatitis remains uncertain. Utilizing genetic data from publicly accessible genome-wide association studies (GWAS), we conducted a 2-sample MR analysis to identify the associations between IBD, ulcerative colitis (UC), Crohn disease (CD), and acute pancreatitis risk. Rigorous quality control steps ensured the selection of eligible single nucleotide polymorphisms (SNPs) with strong associations to IBD. The primary estimation used the inverse-variance weighted method. We also assessed heterogeneity, potential pleiotropy, and conducted sensitivity analyses. The direction of causality was confirmed using the Steiger test. The MR analysis showed that IBD increased the risk of acute pancreatitis (IVW: OR = 1.032, 95% CI: 1.006-1.06, P = .015). Among the subgroup of IBD, CD (IVW: OR = 1.034, 95% CI: 1.008-1.06, P = .007) indicates a significant increase in the risk of acute pancreatitis compared to UC (IVW: OR = 1.02, 95% CI: 0.99-1.051, P = .189). The MR analysis assessing the association between CD and acute pancreatitis showed no evidence of heterogeneity or horizontal pleiotropy. Likewise, the leave-one-out (LOO) method indicated no significant influence of any individual SNP on the overall findings. In addition, the Steiger direction test revealed that CD was the cause for increased risk of acute pancreatitis, but not vice versa. In summary, this research pioneers in proposing a causal relationship between CD and acute pancreatitis among the European population.
Collapse
Affiliation(s)
- Xuewei Fu
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Hao Wu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Yufeng Shu
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Bocheng Yang
- Division of Plastic Surgery, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Chao Deng
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
165
|
Kelemen M, Vigorito E, Fachal L, Anderson CA, Wallace C. shaPRS: Leveraging shared genetic effects across traits or ancestries improves accuracy of polygenic scores. Am J Hum Genet 2024; 111:1006-1017. [PMID: 38703768 PMCID: PMC11179256 DOI: 10.1016/j.ajhg.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
We present shaPRS, a method that leverages widespread pleiotropy between traits or shared genetic effects across ancestries, to improve the accuracy of polygenic scores. The method uses genome-wide summary statistics from two diseases or ancestries to improve the genetic effect estimate and standard error at SNPs where there is homogeneity of effect between the two datasets. When there is significant evidence of heterogeneity, the genetic effect from the disease or population closest to the target population is maintained. We show via simulation and a series of real-world examples that shaPRS substantially enhances the accuracy of polygenic risk scores (PRSs) for complex diseases and greatly improves PRS performance across ancestries. shaPRS is a PRS pre-processing method that is agnostic to the actual PRS generation method, and as a result, it can be integrated into existing PRS generation pipelines and continue to be applied as more performant PRS methods are developed over time.
Collapse
Affiliation(s)
- Martin Kelemen
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK.
| | - Elena Vigorito
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Laura Fachal
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| |
Collapse
|
166
|
Ando T, Takazawa I, Spencer ZT, Ito R, Tomimori Y, Mikulski Z, Matsumoto K, Ishitani T, Denson LA, Kawakami Y, Kawakami Y, Kitaura J, Ahmed Y, Kawakami T. Ileal Crohn's Disease Exhibits Reduced Activity of Phospholipase C-β3-Dependent Wnt/β-Catenin Signaling Pathway. Cells 2024; 13:986. [PMID: 38891118 PMCID: PMC11171731 DOI: 10.3390/cells13110986] [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: 05/06/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Crohn's disease is a chronic, debilitating, inflammatory bowel disease. Here, we report a critical role of phospholipase C-β3 (PLC-β3) in intestinal homeostasis. In PLC-β3-deficient mice, exposure to oral dextran sodium sulfate induced lethality and severe inflammation in the small intestine. The lethality was due to PLC-β3 deficiency in multiple non-hematopoietic cell types. PLC-β3 deficiency resulted in reduced Wnt/β-catenin signaling, which is essential for homeostasis and the regeneration of the intestinal epithelium. PLC-β3 regulated the Wnt/β-catenin pathway in small intestinal epithelial cells (IECs) at transcriptional, epigenetic, and, potentially, protein-protein interaction levels. PLC-β3-deficient IECs were unable to respond to stimulation by R-spondin 1, an enhancer of Wnt/β-catenin signaling. Reduced expression of PLC-β3 and its signature genes was found in biopsies of patients with ileal Crohn's disease. PLC-β regulation of Wnt signaling was evolutionally conserved in Drosophila. Our data indicate that a reduction in PLC-β3-mediated Wnt/β-catenin signaling contributes to the pathogenesis of ileal Crohn's disease.
Collapse
Affiliation(s)
- Tomoaki Ando
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Ikuo Takazawa
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zachary T. Spencer
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Ryoji Ito
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Central Institute for Experimental Animals, Kawasaki 210-0821, Kanagawa, Japan
| | - Yoshiaki Tomimori
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zbigniew Mikulski
- Imaging Facility, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Tohru Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-0044, Gunma, Japan
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Yuko Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Jiro Kitaura
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Toshiaki Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| |
Collapse
|
167
|
Syed AH, Abujabal HAS, Ahmad S, Malebary SJ, Alromema N. Advances in Inflammatory Bowel Disease Diagnostics: Machine Learning and Genomic Profiling Reveal Key Biomarkers for Early Detection. Diagnostics (Basel) 2024; 14:1182. [PMID: 38893707 PMCID: PMC11172026 DOI: 10.3390/diagnostics14111182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/25/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
This study, utilizing high-throughput technologies and Machine Learning (ML), has identified gene biomarkers and molecular signatures in Inflammatory Bowel Disease (IBD). We could identify significant upregulated or downregulated genes in IBD patients by comparing gene expression levels in colonic specimens from 172 IBD patients and 22 healthy individuals using the GSE75214 microarray dataset. Our ML techniques and feature selection methods revealed six Differentially Expressed Gene (DEG) biomarkers (VWF, IL1RL1, DENND2B, MMP14, NAAA, and PANK1) with strong diagnostic potential for IBD. The Random Forest (RF) model demonstrated exceptional performance, with accuracy, F1-score, and AUC values exceeding 0.98. Our findings were rigorously validated with independent datasets (GSE36807 and GSE10616), further bolstering their credibility and showing favorable performance metrics (accuracy: 0.841, F1-score: 0.734, AUC: 0.887). Our functional annotation and pathway enrichment analysis provided insights into crucial pathways associated with these dysregulated genes. DENND2B and PANK1 were identified as novel IBD biomarkers, advancing our understanding of the disease. The validation in independent cohorts enhances the reliability of these findings and underscores their potential for early detection and personalized treatment of IBD. Further exploration of these genes is necessary to fully comprehend their roles in IBD pathogenesis and develop improved diagnostic tools and therapies. This study significantly contributes to IBD research with valuable insights, potentially greatly enhancing patient care.
Collapse
Affiliation(s)
- Asif Hassan Syed
- Department of Computer Science, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, Jeddah 22254, Saudi Arabia;
| | - Hamza Ali S. Abujabal
- Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
| | - Shakeel Ahmad
- Department of Computer Science, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, Jeddah 22254, Saudi Arabia;
| | - Sharaf J. Malebary
- Department of Information Technology, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, P.O. Box 344, Rabigh 21911, Saudi Arabia;
| | - Nashwan Alromema
- Department of Computer Science, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, P.O. Box 344, Rabigh 21911, Saudi Arabia;
| |
Collapse
|
168
|
Chang H, Liu Y, Wang Y, Li L, Mu Y, Zheng M, Liu J, Zhang J, Bai R, Li Y, Zuo X. Unveiling the Links Between Microbial Alteration and Host Gene Disarray in Crohn's Disease via TAHMC. Adv Biol (Weinh) 2024:e2400064. [PMID: 38837746 DOI: 10.1002/adbi.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/03/2024] [Indexed: 06/07/2024]
Abstract
A compelling correlation method linking microbial communities and host gene expression in tissues is currently absent. A novel pipeline is proposed, dubbed Transcriptome Analysis of Host-Microbiome Crosstalk (TAHMC), designed to concurrently restore both host gene expression and microbial quantification from bulk RNA-seq data. Employing this approach, it discerned associations between the tissue microbiome and host immunity in the context of Crohn's disease (CD). Further, machine learning is utilized to separately construct networks of associations among host mRNA, long non-coding RNA, and tissue microbes. Unique host genes and tissue microbes are extracted from these networks for potential utility in CD diagnosis. Experimental validation of the predicted host gene regulation by microbes from the association network is achieved through the co-culturing of Faecalibacterium prausnitzii with Caco-2 cells. Collectively, the TAHMC pipeline accurately recovers both host gene expression and microbial quantification from CD RNA-seq data, thereby illuminating potential causal links between shifts in microbial composition as well as diversity within CD mucosal tissues and aberrant host gene expression.
Collapse
Affiliation(s)
- Huijun Chang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yongshuai Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yijun Mu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Junfei Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jinghui Zhang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Runze Bai
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| |
Collapse
|
169
|
Nieva C, Pryor J, Williams GM, Hoedt EC, Burns GL, Eslick GD, Talley NJ, Duncanson K, Keely S. The Impact of Dietary Interventions on the Microbiota in Inflammatory Bowel Disease: A Systematic Review. J Crohns Colitis 2024; 18:920-942. [PMID: 38102104 PMCID: PMC11147801 DOI: 10.1093/ecco-jcc/jjad204] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND AND AIMS Diet plays an integral role in the modulation of the intestinal environment, with the potential to be modified for management of individuals with inflammatory bowel disease [IBD]. It has been hypothesised that poor 'Western-style' dietary patterns select for a microbiota that drives IBD inflammation and, that through dietary intervention, a healthy microbiota may be restored. This study aimed to systematically review the literature and assess current available evidence regarding the influence of diet on the intestinal microbiota composition in IBD patients, and how this may affect disease activity. METHODS MEDLINE, EMBASE, Scopus, Web of Science, and Cochrane Library were searched from January 2013 to June 2023, to identify studies investigating diet and microbiota in IBD. RESULTS Thirteen primary studies met the inclusion criteria and were selected for narrative synthesis. Reported associations between diet and microbiota in IBD were conflicting due to the considerable degree of heterogeneity between studies. Nine intervention studies trialled specific diets and did not demonstrate significant shifts in the diversity and abundance of intestinal microbial communities or improvement in disease outcomes. The remaining four cross-sectional studies did not find a specific microbial signature associated with habitual dietary patterns in IBD patients. CONCLUSIONS Diet modulates the gut microbiota, and this may have implications for IBD; however, the body of evidence does not currently support clear dietary patterns or food constituents that are associated with a specific microbiota profile or disease marker in IBD patients. Further research is required with a focus on robust and consistent methodology to achieve improved identification of associations.
Collapse
Affiliation(s)
- Cheenie Nieva
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jennifer Pryor
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Georgina M Williams
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Emily C Hoedt
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Grace L Burns
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Guy D Eslick
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J Talley
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Kerith Duncanson
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Simon Keely
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council [NHMRC], Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| |
Collapse
|
170
|
Shaw VR, Byun J, Pettit RW, Hou JK, Walsh KM, Han Y, Amos CI. An Atlas Characterizing the Shared Genetic Architecture of Inflammatory Bowel Disease with Clinical and Behavioral Traits. Inflamm Bowel Dis 2024; 30:884-893. [PMID: 37982439 PMCID: PMC11144996 DOI: 10.1093/ibd/izad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) development is a complex, multifactorial process that involves extrinsic and intrinsic factors such as host genetics, the immune system, the gut microbiome, and environmental risks. To help understand the genetic contribution of clinical, behavioral, psychiatric, and diet-related traits, we aim to provide a deep and comprehensive characterization of the shared genetic architecture between IBD and hundreds of potentially related traits. METHODS Utilizing publicly available summary statistics from a previously published IBD genome-wide association study and hundreds of traits from the United Kingdom BioBank (UKBB), we performed linkage disequilibrium score regression (LDSR) analysis to estimate cross-trait genetic correlations between Crohn's disease (CD), ulcerative colitis (UC), and IBD summary statistics with the UKBB traits of interest. RESULTS Nominally significant (P < .05) genetic correlations were observed for 181 traits in overall IBD, 239 traits in CD, and 94 traits in UC. We replicate the known association between smoking behavior and CD/UC, namely that current tobacco smoking has a positive genetic correlation with CD (rg = 0.12, P = 4.2 × 10-4), while "ever smoking" has a negative genetic correlation with UC (rg = -0.07, P = .042). Globally, all 3 strata (IBD, CD, and UC) demonstrated increased genetic correlations for psychiatric-related traits related to anxiety and depression. CONCLUSION The present analysis reveals the shared genetic architecture between multiple traits and IBD, CD, and UC. Understanding the relevance of joint occurrences of IBD with psychiatric diseases may moderate management of these diseases for individuals jointly affected by them.
Collapse
Affiliation(s)
- Vikram R Shaw
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jason K Hou
- Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | - Kyle M Walsh
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
171
|
Salihovic S, Nyström N, Mathisen CBW, Kruse R, Olbjørn C, Andersen S, Noble AJ, Dorn-Rasmussen M, Bazov I, Perminow G, Opheim R, Detlie TE, Huppertz-Hauss G, Hedin CRH, Carlson M, Öhman L, Magnusson MK, Keita ÅV, Söderholm JD, D'Amato M, Orešič M, Wewer V, Satsangi J, Lindqvist CM, Burisch J, Uhlig HH, Repsilber D, Hyötyläinen T, Høivik ML, Halfvarson J. Identification and validation of a blood- based diagnostic lipidomic signature of pediatric inflammatory bowel disease. Nat Commun 2024; 15:4567. [PMID: 38830848 PMCID: PMC11148148 DOI: 10.1038/s41467-024-48763-7] [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: 05/19/2023] [Accepted: 04/30/2024] [Indexed: 06/05/2024] Open
Abstract
Improved biomarkers are needed for pediatric inflammatory bowel disease. Here we identify a diagnostic lipidomic signature for pediatric inflammatory bowel disease by analyzing blood samples from a discovery cohort of incident treatment-naïve pediatric patients and validating findings in an independent inception cohort. The lipidomic signature comprising of only lactosyl ceramide (d18:1/16:0) and phosphatidylcholine (18:0p/22:6) improves the diagnostic prediction compared with high-sensitivity C-reactive protein. Adding high-sensitivity C-reactive protein to the signature does not improve its performance. In patients providing a stool sample, the diagnostic performance of the lipidomic signature and fecal calprotectin, a marker of gastrointestinal inflammation, does not substantially differ. Upon investigation in a third pediatric cohort, the findings of increased lactosyl ceramide (d18:1/16:0) and decreased phosphatidylcholine (18:0p/22:6) absolute concentrations are confirmed. Translation of the lipidomic signature into a scalable diagnostic blood test for pediatric inflammatory bowel disease has the potential to support clinical decision making.
Collapse
Affiliation(s)
- Samira Salihovic
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Niklas Nyström
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Charlotte Bache-Wiig Mathisen
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway and Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Robert Kruse
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Christine Olbjørn
- Department of Pediatrics and Adolescent Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Svend Andersen
- Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Alexandra J Noble
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Maria Dorn-Rasmussen
- Department of Paediatric and Adolescence Medicine, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Igor Bazov
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Gøri Perminow
- Department of Pediatric Medicine, Oslo University Hospital, Oslo, Norway
| | - Randi Opheim
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway and Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Trond Espen Detlie
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway and Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Charlotte R H Hedin
- Karolinska Institutet, Department of Medicine Solna, Stockholm, Sweden
- Karolinska University Hospital, Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Stockholm, Sweden
| | - Marie Carlson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan D Söderholm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mauro D'Amato
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Gastrointestinal Genetics Lab, CIC bioGUNE - BRTA, Derio, Spain
- Department of Medicine & Surgery, LUM University, Casamassima, Italy
| | - Matej Orešič
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vibeke Wewer
- Department of Paediatric and Adolescence Medicine, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Carl Mårten Lindqvist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Johan Burisch
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Gastrounit, medical division, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Marte Lie Høivik
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway and Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| |
Collapse
|
172
|
Wong C, van Oostrom J, Pittet V, Bossuyt P, Hanzel J, Samaan M, Tripathi M, Czuber-Dochan W, Burisch J, Leone S, Saldaña R, Baert F, Kopylov U, Jaghult S, Adamina M, Gecse K, Arebi N. Baseline Data and Measurement Instruments Reported in Observational Studies in Inflammatory Bowel Disease: Results from a Systematic Review. J Crohns Colitis 2024; 18:875-884. [PMID: 38214470 DOI: 10.1093/ecco-jcc/jjae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Heterogeneity in demographic and outcomes data with corresponding measurement instruments [MIs] creates barriers to data pooling and analysis. Several core outcome sets have been developed in inflammatory bowel disease [IBD] to homogenize outcomes data. A parallel Minimum Data Set [MDS] for baseline characteristics is lacking. We conducted a systematic review to develop the first MDS. METHODS A systematic review was made of observational studies from three databases [2000-2021]. Titles and abstracts were screened, full-text articles were reviewed, and data were extracted by two reviewers. Baseline data were grouped into ten domains: demographics, clinical features, disease behaviour/complications, biomarkers, endoscopy, histology, radiology, healthcare utilization and patient-reported data. Frequency of baseline data and MIs within respective domains are reported. RESULTS From 315 included studies [600 552 subjects], most originated from Europe [196; 62%] and North America [59; 19%], and were published between 2011 and 2021 [251; 80%]. The most frequent domains were demographics [311; 98.7%] and clinical [289; 91.7%]; 224 [71.1%] studies reported on the triad of sex [306; 97.1%], age [289; 91.7%], and disease phenotype [231; 73.3%]. Few included baseline data for radiology [19; 6%], healthcare utilization [19; 6%], and histology [17; 5.4%]. Ethnicity [19; 6%], race [17; 5.4%], and alcohol/drug consumption [6; 1.9%] were the least reported demographics. From 25 MIs for clinical disease activity, the Harvey-Bradshaw Index [n = 53] and Mayo score [n = 37] were most frequently used. CONCLUSIONS Substantial variability exists in baseline population data reporting. These findings will inform a future consensus for MDS in IBD to enhance data harmonization and credibility of real-world evidence.
Collapse
Affiliation(s)
- Charlotte Wong
- Department of Inflammatory Bowel Disease, St Mark's National Bowel Hospital, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Joep van Oostrom
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Valerie Pittet
- Center for Primary Care and Public Health-University of Lausanne, Department of Epidemiology and Health Systems, Lausanne, Switzerland
| | - Peter Bossuyt
- Department of Gastroenterology, Imelda General Hospital and Imelda Clinical Research Centre, Bonheiden, Belgium
| | - Jurij Hanzel
- Faculty of Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Mark Samaan
- Inflammatory Bowel Diseases Unit, Guy's and St Thomas' Hospital, London, UK
| | - Monika Tripathi
- Department of Histopathology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wladyslawa Czuber-Dochan
- Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King's College London, London, UK
| | - Johan Burisch
- Department of Gastroenterology, Medical Division, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Centre for Inflammatory Bowel Disease in Children, Adolescents and Adults, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Salvatore Leone
- European Federation of Crohn's and Colitis Associations [EFCCA], Brussels, Belgium
| | - Roberto Saldaña
- European Federation of Crohn's and Colitis Associations [EFCCA], Brussels, Belgium
- Confederation of Patients with Crohn's Disease and Ulcerative Colitis, Madrid, Spain
| | - Filip Baert
- Department of Gastroenterology, AZ Delta, Roeselare, Belgium
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center, Tel Hashomer, Israel, Israel
| | - Susanna Jaghult
- Department of Clinical Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Michel Adamina
- Department of Surgery, Cantonal Hospital Winterthur, Zurich, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Krisztina Gecse
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Naila Arebi
- Department of Inflammatory Bowel Disease, St Mark's National Bowel Hospital, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| |
Collapse
|
173
|
Yan Ang Q, Plichta D, Kim S, Hyun-A Kim I, Gregory S, Xia Y, Lau H, Xavier R, Ananthakrishnan AN. Differential Impact of Smoking on Methylome and Transcriptome in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis 2024; 30:981-991. [PMID: 38001042 PMCID: PMC11145016 DOI: 10.1093/ibd/izad268] [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: 09/25/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND Smoking is an environmental factor that differentially impacts Crohn's disease (CD) and ulcerative colitis (UC). The mechanism of impact of smoking on disease risk and clinical outcomes remains to be established. METHODS This study used a prospective cohort of patients with CD or UC. Self-reported smoking status was validated using serum cotinine measurement. We profiled methylation changes in peripheral blood using the Illumina Methylation BeadChip. Transcriptomic profiling was performed on ileal and colonic tissue using an Illumina TruSeq platform. We compared the methylation and transcriptional changes in current, former, and never smokers stratified by disease type. RESULTS Our cohort included 200 patients with CD or UC with methylation profiles and 160 with transcriptomic data. The mean serum cotinine level was higher in current compared with former or never smokers. Epigenetic changes common to both CD and UC included hypomethylation at AHRR. Smoking-associated MGAT3 hypomethylation was associated with severe disease course only in UC, while IER3 hypomethylation was associated with worse course only in CD. Smoking downregulated several inflammatory pathways in UC. Current smoking in CD but not in UC was associated with upregulation of several genes mediating Paneth cell function. Genes with opposite direction of effects in CD and UC include HSD3B2 and GSTA1. CONCLUSIONS Our findings suggest both common and differential effects of cigarette smoking on CD and UC. Paneth cell dysfunction may mediate adverse impact of smoking on CD. Bile acid and oxidative stress pathways may be relevant for the differential effect of smoking on CD and UC.
Collapse
Affiliation(s)
| | | | - Sean Kim
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Iris Hyun-A Kim
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Sadie Gregory
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Yan Xia
- Broad Institute, Cambridge, MA, USA
| | - Helena Lau
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| |
Collapse
|
174
|
Di W, Luyao Y, Chengwei Y, Valtonen AM, Juha-Pekka K, Ying G. Exploring the causal link between circulating cytokines and sarcopenia traits: A Mendelian randomization analysis. ENVIRONMENTAL TOXICOLOGY 2024; 39:3434-3447. [PMID: 38450985 DOI: 10.1002/tox.24206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/08/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Previous observational studies have linked circulating cytokines to sarcopenia, but their causal relationship remains unclear. This study employed Mendelian Randomization (MR) to investigate the causal links between circulating cytokines and sarcopenia-related traits using genetic data. METHODS A two-sample bidirectional MR analysis was conducted using data from individuals of European ancestry, utilizing genome-wide association studies (GWAS) statistics. The study selected instrumental single nucleotide polymorphisms (SNPs) significantly associated with circulating cytokines and applied multiple MR methods, including inverse variance weighted (IVW), Weighted Median, MR-Egger, Weighted Mode, Simple Mode, and MR-PRESSO. The traits analyzed were appendicular lean mass (ALM) and grip strength. Heterogeneity, robustness, and consistency of results were assessed using Cochran's Q statistic, MR-Egger regression, and "leave-one-out" sensitivity analyses. RESULTS The IVM-MR analysis showed a casual association between genetically predicted circulating levels of interleukin-16 and both ALM and grip strength (ALM: OR = 0.990, 95% CI: 0.980-1.000, p = .049; grip strength: OR = 0.971, 95% CI: 0.948-0.995, p = .020). Additionally, interferon-gamma-induced protein 10 (IP-10), interleukin-1-beta (IL-1β), and hepatocyte growth factor (HGF) were correlated with ALM and vascular endothelial growth factor (VEGF), interleukin-12 (IL-12), and interleukin-5 (IL-5) with grip strength. Comparable results were confirmed via the MR-Egger, Weighted Median, Weighted Mode, and Simple Mode methods. Sensitivity analysis showed no horizontal pleiotropy to bias the causal estimates. CONCLUSION The results suggest a significant causal effect of inflammatory cytokines on sarcopenia, offering new avenues for therapeutic target development. However, the study's focus on a European ancestry cohort limits its generalizability to other populations. Future research should aim to include diverse ethnic groups to validate and broaden these findings, thereby enhancing our understanding of sarcopenia's mechanisms in a global context.
Collapse
Affiliation(s)
- Wang Di
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| | - Yang Luyao
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| | - Yang Chengwei
- Faculty of Sports and Exercise Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Anu M Valtonen
- School of Rehabilitation and Examination, Metropolia University of Applied Sciences, Finland
| | - Kulmala Juha-Pekka
- Motion Analysis Laboratory, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Gao Ying
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| |
Collapse
|
175
|
Frei O, Hindley G, Shadrin AA, van der Meer D, Akdeniz BC, Hagen E, Cheng W, O'Connell KS, Bahrami S, Parker N, Smeland OB, Holland D, de Leeuw C, Posthuma D, Andreassen OA, Dale AM. Improved functional mapping of complex trait heritability with GSA-MiXeR implicates biologically specific gene sets. Nat Genet 2024; 56:1310-1318. [PMID: 38831010 DOI: 10.1038/s41588-024-01771-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/24/2024] [Indexed: 06/05/2024]
Abstract
While genome-wide association studies are increasingly successful in discovering genomic loci associated with complex human traits and disorders, the biological interpretation of these findings remains challenging. Here we developed the GSA-MiXeR analytical tool for gene set analysis (GSA), which fits a model for the heritability of individual genes, accounting for linkage disequilibrium across variants and allowing the quantification of partitioned heritability and fold enrichment for small gene sets. We validated the method using extensive simulations and sensitivity analyses. When applied to a diverse selection of complex traits and disorders, including schizophrenia, GSA-MiXeR prioritizes gene sets with greater biological specificity compared to standard GSA approaches, implicating voltage-gated calcium channel function and dopaminergic signaling for schizophrenia. Such biologically relevant gene sets, often with fewer than ten genes, are more likely to provide insights into the pathobiology of complex diseases and highlight potential drug targets.
Collapse
Affiliation(s)
- Oleksandr Frei
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.
| | - Guy Hindley
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alexey A Shadrin
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dennis van der Meer
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
| | - Bayram C Akdeniz
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Espen Hagen
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Weiqiu Cheng
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kevin S O'Connell
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Shahram Bahrami
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nadine Parker
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dominic Holland
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| | - Christiaan de Leeuw
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Ole A Andreassen
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders M Dale
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
176
|
Niu Y, Zhang Q, Wei Y. Causal effects of inflammatory bowel disease on risk of type 2 diabetes: a two-sample multivariable Mendelian randomization study. Acta Diabetol 2024; 61:715-724. [PMID: 38427067 DOI: 10.1007/s00592-024-02254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/03/2024] [Indexed: 03/02/2024]
Abstract
AIM This study aimed to explore the causal association between inflammatory bowel disease (IBD) and the risk of type 2 diabetes (T2D) based on a two-sample Mendelian randomization (MR) study. METHODS Summary single nucleotide polymorphism (SNP)-phenotype association data were obtained from published two genome-wide association studies (GWAS) including SNPs related to IBD, UC, or CD in European participants (n = 71,997) and East Asian participants (n = 16,805). Two GWAS including SNPs associated with T2D included 655,666 Europeans and 433,540 East Asians. A series of screening processes were performed to select qualified instrumental SNPs strongly related to exposure. We applied the inverse variance weighted (IVW), the MR-Egger regression, and the weighted median to estimate the causal effects of IBD, ulcerative colitis (UC) or Crohn' disease (CD) on T2D. Cochran's Q test was conducted to evaluate the statistical heterogeneity between SNPs in the IVW method. The leave-one-out analysis was employed to assess whether the results were caused by any single SNP associated with IBD, UC, or CD. Odds ratio (OR) and 95% confidence interval (CI) were calculated. RESULTS The IVW results demonstrated that IBD could increase the risk of T2D in the European population (OR = 1.0230, 95%CI: 1.0073-1.0390). UC was positively associated with the risk of T2D according to the weighted median (OR = 1.0274, 95%CI: 1.0009-1.0546) and IVW (OR = 1.0244, 95%CI: 1.0071-1.0421) results in the European population. The IVW results indicated that the CD was positively associated with the risk of T2D in the European population (OR = 1.0187, 95%CI: 1.0045-1.0330). In the East Asian population, there are no associations between the IBD, UC, or CD and the risk of T2D (all P > 0.05). MVMR results revealed that the causal effect UC on T2D was still statistically significant after including body mass index (BMI) or low-density lipoprotein (LDL). CONCLUSION IBD, UC, or CD had causal effects on the risk of T2D in the European population, which might provide evidence for the prevention of T2D in patients with IBD, UC, or CD.
Collapse
Affiliation(s)
- Yue Niu
- Department of Digestive Internal Medicine, Lianyungang Hospital of Traditional Chinese Medicine, 160# Chaoyang Middle Road, Lianyungang, 222000, Jiangsu, China
| | - Qing Zhang
- Department of Digestive Internal Medicine, Lianyungang Hospital of Traditional Chinese Medicine, 160# Chaoyang Middle Road, Lianyungang, 222000, Jiangsu, China
| | - Yinting Wei
- Department of Digestive Internal Medicine, Lianyungang Hospital of Traditional Chinese Medicine, 160# Chaoyang Middle Road, Lianyungang, 222000, Jiangsu, China.
| |
Collapse
|
177
|
Landorf E, Hammond P, Abu-Assi R, Ellison S, Boyle T, Comerford A, Couper R. Formula modifications to the Crohn's disease exclusion diet do not impact therapy success in paediatric Crohn's disease. J Pediatr Gastroenterol Nutr 2024; 78:1279-1286. [PMID: 38623960 DOI: 10.1002/jpn3.12215] [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: 11/27/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVES The Crohn's disease exclusion diet (CDED) + partial enteral nutrition (PEN) is an emerging diet used to induce clinical remission in children with active Crohn's disease (CD). This study aims to determine the effectiveness of using the CDED+PEN to induce clinical remission in an Australian group of children with active CD using different PEN formulas and incorporating patient dietary requirements. METHODS We retrospectively collected data from children (both newly diagnosed and with existing CD while on therapy) with active CD (Paediatric Crohn's Disease Activity Index [PCDAI] ≥10) and biochemical evidence of active disease (elevated C-reactive protein [CRP], erythrocyte sedimentation rate [ESR] or faecal calprotectin [FC]) who completed at least phase 1 (6 weeks) of the CDED+PEN to induce clinical remission. Data were collected at baseline, Week 6 and Week 12. The primary endpoint was clinical remission at Week 6 defined as PCDAI < 10. RESULTS Twenty-four children were included in phase 1 analysis (mean age 13.8 ± 3.2 years). Clinical remission at Week 6 was achieved in 17/24 (70.8%) patients. Mean PCDAI, CRP, ESR and FC decreased significantly after 6 weeks (p < 0.05). Formula type (cow's milk based, rice based, soy based) did not affect treatment efficacy. A greater than 50% decrease in FC was achieved in 14/21 (66.7%) patients who completed phase 1 and 12/14 (85.7%) patients who completed phase 2 of the CDED+PEN. CONCLUSIONS Formula modifications to the CDED+PEN do not impact the expected treatment efficacy in Australian children with active luminal CD.
Collapse
Affiliation(s)
- Emma Landorf
- Department of Nutrition, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Paul Hammond
- Department of Gastroenterology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Rammy Abu-Assi
- Department of Gastroenterology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Samuel Ellison
- Department of Gastroenterology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Terry Boyle
- Allied Health and Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Annabel Comerford
- Department of Nutrition, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Richard Couper
- Department of Gastroenterology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| |
Collapse
|
178
|
Eibauer M, Weber MS, Kronenberg-Tenga R, Beales CT, Boujemaa-Paterski R, Turgay Y, Sivagurunathan S, Kraxner J, Köster S, Goldman RD, Medalia O. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol 2024; 31:939-949. [PMID: 38632361 PMCID: PMC11189308 DOI: 10.1038/s41594-024-01261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
Collapse
Affiliation(s)
- Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Charlie T Beales
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Yagmur Turgay
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- MDC Berlin-Buch, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
179
|
Jia W, Li N, Wang J, Gong X, Ouedraogo SY, Wang Y, Zhao J, Grech G, Chen L, Zhan X. Immune-related gene methylation prognostic instrument for stratification and targeted treatment of ovarian cancer patients toward advanced 3PM approach. EPMA J 2024; 15:375-404. [PMID: 38841623 PMCID: PMC11148001 DOI: 10.1007/s13167-024-00359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/07/2024] [Indexed: 06/07/2024]
Abstract
Background DNA methylation is an important mechanism in epigenetics, which can change the transcription ability of genes and is closely related to the pathogenesis of ovarian cancer (OC). We hypothesize that DNA methylation is significantly different in OCs compared to controls. Specific DNA methylation status can be used as a biomarker of OC, and targeted drugs targeting these methylation patterns and DNA methyltransferase may have better therapeutic effects. Studying the key DNA methylation sites of immune-related genes (IRGs) in OC patients and studying the effects of these methylation sites on the immune microenvironment may provide a new method for further exploring the pathogenesis of OC, realizing early detection and effective monitoring of OC, identifying effective biomarkers of DNA methylation subtypes and drug targets, improving the efficacy of targeted drugs or overcoming drug resistance, and better applying it to predictive diagnosis, prevention, and personalized medicine (PPPM; 3PM) of OC. Method Hypermethylated subtypes (cluster 1) and hypomethylated subtypes (cluster 2) were established in OCs based on the abundance of different methylation sites in IRGs. The differences in immune score, immune checkpoints, immune cells, and overall survival were analyzed between different methylation subtypes in OC samples. The significant pathways, gene ontology (GO), and protein-protein interaction (PPI) network of the identified methylation sites in IRGs were enriched. In addition, the immune-related methylation signature was constructed with multiple regression analysis. A methylation site model based on IRGs was constructed and verified. Results A total of 120 IRGs with 142 differentially methylated sites (DMSs) were identified. The DMSs were clustered into a high-level methylation group (cluster 1) and a low-level methylation group (cluster 2). The significant pathways and GO analysis showed many immune-related and cancer-associated enrichments. A methylation site signature based on IRGs was constructed, including RORC|cg25112191, S100A13|cg14467840, TNF|cg04425624, RLN2|cg03679581, and IL1RL2|cg22797169. The methylation sites of all five genes showed hypomethylation in OC, and there were statistically significant differences among RORC|cg25112191, S100A13|cg14467840, and TNF|cg04425624 (p < 0.05). This prognostic model based on low-level methylation and high-level methylation groups was significantly linked to the immune microenvironment as well as overall survival in OC. Conclusions This study provided different methylation subtypes for OC patients according to the methylation sites of IRGs. In addition, it helps establish a relationship between methylation and the immune microenvironment, which showed specific differences in biological signaling pathways, genomic changes, and immune mechanisms within the two subgroups. These data provide ones to deeply understand the mechanism of immune-related methylation genes on the occurrence and development of OC. The methylation-site signature is also to establish new possibilities for OC therapy. These data are a precious resource for stratification and targeted treatment of OC patients toward an advanced 3PM approach. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00359-3.
Collapse
Affiliation(s)
- Wenshuang Jia
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Jingjing Wang
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xiaoxia Gong
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Yan Wang
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
- Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117 People’s Republic of China
| | - Junkai Zhao
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Godfrey Grech
- Department of Pathology, University of Malta, Msida, Malta
| | - Liang Chen
- Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117 People’s Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| |
Collapse
|
180
|
Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [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: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
Collapse
Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| |
Collapse
|
181
|
Vekara L, Kantanen S, Kolho KL, Räsänen K, Lakka T, Huhtala H, Piippo-Savolainen E, Arikoski P, Hiltunen P. Psychological well-being of children and adolescents with inflammatory bowel disease. J Pediatr Gastroenterol Nutr 2024; 78:1287-1296. [PMID: 38629478 DOI: 10.1002/jpn3.12220] [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: 12/18/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 06/10/2024]
Abstract
OBJECTIVES Prior studies on the psychological well-being in pediatric inflammatory bowel disease (PIBD) have reported controversial results. Our aim was to compare the psychological well-being and lifestyle factors in patients with PIBD and their controls and to assess the role of contributing disease characteristics. METHODS This cross-sectional study included 60 PIBD patients aged 6-17 years (26 with Crohn's disease [CD], 34 with ulcerative colitis [UC] or unclassified colitis [IBD-U]) from two university hospitals in Finland, and their age- and sex-matched healthy controls. Psychological well-being was assessed with three measures: a questionnaire on overall psychological well-being (PSWB) and for adolescents also Beck Depression Inventory (BDI Ia) and Perceived Stress Scale (PSS). In addition to disease characteristics and pain, we assessed physical activity, sleep, screen time, and social well-being. RESULTS Controls were more likely of stressing more (odds ratio [OR] = 3.67, 95% confidence interval [95% CI] 95% CI = 1.02-13.14), but other measures of psychological well-being did not differ statistically significantly between patients and controls. In CD, a clinically more active disease associated with inferior psychological well-being in adolescents (BDI [ρ = 0.63, p = 0.021], PSS [ρ = 0.70, p = 0.008], PSWB [ρ = 0.56, p = 0.049]). Longer time from diagnosis correlated with better psychological well-being on BDI (ρ = -0.39, p = 0.024) and PSS (ρ = -0.38, p = 0.034). Lifestyle was more sedentary in PIBD (less physical activity in children OR = 0.82, 95% CI = 0.68-0.99 and more screen time in adolescents OR = 1.18, 95% CI = 1.00-1.40). CONCLUSION Although the clinical features of PIBD are potentially a burden for psychological well-being, many young patients cope well with their disease. Individual variation in well-being is remarkable, making supportive measures challenging.
Collapse
Affiliation(s)
- Laura Vekara
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saija Kantanen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Kaija-Leena Kolho
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Faculty of Medicine, University of Helsinki and Department of Pediatric Gastroenterology, Helsinki University Hospital HUS, Helsinki, Finland
| | - Kati Räsänen
- Kuopio Pediatric Research Unit, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Heini Huhtala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Eija Piippo-Savolainen
- Kuopio Pediatric Research Unit, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Pekka Arikoski
- Kuopio Pediatric Research Unit, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Pauliina Hiltunen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| |
Collapse
|
182
|
Abstract
Diet plays an important role in human health and disease. Of all human diseases, diarrheal illnesses bring diet into sharp focus as it has a direct causal and therapeutic relationship. With the advent and widespread use of next generation sequencing, significant advances have been made in unraveling the etiologies of congenital diarrheas and enteropathies, some of which are eminently treatable with dietary modification. Early institution of appropriate dietary therapy is lifesaving in congenital osmotic diarrheas. Chronic diarrhea in older children and adolescents often have an underlying dietary basis, depending on the etiology. Identification and exclusion of the offending food in the diet results in dramatic improvement in symptoms. It is equally important to be prudent and cautious in the use of exclusion diets in management of chronic diarrhea as it is associated with micronutrient deficiencies, needless escalation of cost and enable maladaptive food intake behaviors. In this review, authors discuss etiology specific dietary management of diarrhea in children with emphasis on congenital diarrheas and enteropathies.
Collapse
Affiliation(s)
- Sahana Shankar
- Division of Pediatric Gastroenterology, Department of Pediatrics, Mazumdar Shaw Medical Center, Narayana Health, Bangalore, India.
| | - Emmany Durairaj
- Department of Clinical Nutrition and Dietetics, Mazumdar Shaw Medical Center, Narayana Health, Bangalore, India
| |
Collapse
|
183
|
Stankey CT, Bourges C, Haag LM, Turner-Stokes T, Piedade AP, Palmer-Jones C, Papa I, Silva Dos Santos M, Zhang Q, Cameron AJ, Legrini A, Zhang T, Wood CS, New FN, Randzavola LO, Speidel L, Brown AC, Hall A, Saffioti F, Parkes EC, Edwards W, Direskeneli H, Grayson PC, Jiang L, Merkel PA, Saruhan-Direskeneli G, Sawalha AH, Tombetti E, Quaglia A, Thorburn D, Knight JC, Rochford AP, Murray CD, Divakar P, Green M, Nye E, MacRae JI, Jamieson NB, Skoglund P, Cader MZ, Wallace C, Thomas DC, Lee JC. A disease-associated gene desert directs macrophage inflammation through ETS2. Nature 2024; 630:447-456. [PMID: 38839969 PMCID: PMC11168933 DOI: 10.1038/s41586-024-07501-1] [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: 04/17/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22-which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu's arteritis3-6-we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures7, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.
Collapse
Affiliation(s)
- C T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Washington University School of Medicine, St Louis, MO, USA
| | - C Bourges
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - L M Haag
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - T Turner-Stokes
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - A P Piedade
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - C Palmer-Jones
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - I Papa
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | | | - Q Zhang
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
| | - A J Cameron
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - A Legrini
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - T Zhang
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - C S Wood
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - F N New
- NanoString Technologies, Seattle, WA, USA
| | - L O Randzavola
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - L Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Genetics Institute, University College London, London, UK
| | - A C Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Hall
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
- Department of Cellular Pathology, Royal Free Hospital, London, UK
| | - F Saffioti
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
| | - E C Parkes
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - W Edwards
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - H Direskeneli
- Department of Internal Medicine, Division of Rheumatology, Marmara University, Istanbul, Turkey
| | - P C Grayson
- Systemic Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, MD, USA
| | - L Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - P A Merkel
- Division of Rheumatology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - G Saruhan-Direskeneli
- Department of Physiology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Lupus Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - E Tombetti
- Department of Biomedical and Clinical Sciences, Milan University, Milan, Italy
- Internal Medicine and Rheumatology, ASST FBF-Sacco, Milan, Italy
| | - A Quaglia
- Department of Cellular Pathology, Royal Free Hospital, London, UK
- UCL Cancer Institute, London, UK
| | - D Thorburn
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
| | - J C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - A P Rochford
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - C D Murray
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - P Divakar
- NanoString Technologies, Seattle, WA, USA
| | - M Green
- Experimental Histopathology STP, The Francis Crick Institute, London, UK
| | - E Nye
- Experimental Histopathology STP, The Francis Crick Institute, London, UK
| | - J I MacRae
- Metabolomics STP, The Francis Crick Institute, London, UK
| | - N B Jamieson
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - P Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - M Z Cader
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C Wallace
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
| | - D C Thomas
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - J C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK.
- Department of Gastroenterology, Royal Free Hospital, London, UK.
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK.
| |
Collapse
|
184
|
Deas J, Shah ND, Konijeti GG, Lundin A, Lanser O, Magavi P, Ali S. Dietary therapies for adult and pediatric inflammatory bowel disease. Nutr Clin Pract 2024; 39:530-545. [PMID: 38505875 DOI: 10.1002/ncp.11146] [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: 12/25/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
Diet is an environmental exposure implicated in the development of inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC). Dietary therapy is also a tool for management of these conditions. Nutrition therapy for IBD has been shown to reduce intestinal inflammation, promote healing, and alleviate symptoms, as well as improve patients' nutrition status. Although the mechanisms of action of most nutrition therapies for IBD are not well understood, the diets are theorized to eliminate triggers for gut dysbiosis and mucosal immune dysfunction associated with the typical Western diet. Exclusive enteral nutrition and the Crohn's disease exclusion diet are increasingly being used as the primary treatment modality for the induction of remission and/or maintenance therapy in children, and in some adults, with CD. Several other diets, such as the Mediterranean diet, anti-inflammatory diet for IBD, and diets excluding gluten, FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols), lactose, or other compounds, may be helpful in symptom management in both CD and UC, though evidence for biochemical efficacy is limited. In this review, we discuss the role of diet components in IBD pathogenesis and examine diets currently used in the management of children and adults with IBD. We also address practical, psychosocial, and cultural considerations for dietary therapy across diverse populations.
Collapse
Affiliation(s)
- Jessica Deas
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Neha D Shah
- Colitis and Crohn's Disease Center, University of California San Francisco, San Francisco, California, USA
| | - Gauree G Konijeti
- Division of Gastroenterology & Hepatology, Scripps Clinic, La Jolla, California, USA
| | - Abigail Lundin
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Benioff Children Hospitals, University of California San Francisco, San Francisco, California, USA
| | - Olivia Lanser
- Division of Gastroenterology & Hepatology, Scripps Clinic, La Jolla, California, USA
| | - Pooja Magavi
- Division of Gastroenterology & Hepatology, Scripps Clinic, La Jolla, California, USA
| | - Sabina Ali
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Benioff Children Hospitals, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
185
|
Hudson AS, Huynh HQ. Pediatric inflammatory bowel disease: What's new and what has changed? Paediatr Child Health 2024; 29:144-149. [PMID: 38827368 PMCID: PMC11141611 DOI: 10.1093/pch/pxae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/19/2024] [Indexed: 06/04/2024] Open
Abstract
The incidence and prevalence of inflammatory bowel disease (IBD) is on the rise in North America and worldwide, with young children being the fastest growing patient population. It is therefore essential for pediatricians and pediatric sub-specialists to be able to recognize signs and symptoms suspicious for a new diagnosis of IBD, as well as potential complications associated with IBD or its treatment. This article reviews the most recent literature regarding clinical presentation, helpful diagnostic clues, newer monitoring tools being used by pediatric gastroenterologists, and emerging new biologic and small molecule treatments.
Collapse
Affiliation(s)
- Alexandra S Hudson
- Division of Pediatric Gastroenterology and Nutrition, Department of Pediatrics, Edmonton Pediatric IBD Clinic (EPIC), University of Alberta, Edmonton, Alberta, Canada
| | - Hien Q Huynh
- Division of Pediatric Gastroenterology and Nutrition, Department of Pediatrics, Edmonton Pediatric IBD Clinic (EPIC), University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
186
|
Laskar RS, Qu C, Huyghe JR, Harrison T, Hayes RB, Cao Y, Campbell PT, Steinfelder R, Talukdar FR, Brenner H, Ogino S, Brendt S, Bishop DT, Buchanan DD, Chan AT, Cotterchio M, Gruber SB, Gsur A, van Guelpen B, Jenkins MA, Keku TO, Lynch BM, Le Marchand L, Martin RM, McCarthy K, Moreno V, Pearlman R, Song M, Tsilidis KK, Vodička P, Woods MO, Wu K, Hsu L, Gunter MJ, Peters U, Murphy N. Genome-wide association studies and Mendelian randomization analyses provide insights into the causes of early-onset colorectal cancer. Ann Oncol 2024; 35:523-536. [PMID: 38408508 PMCID: PMC11213623 DOI: 10.1016/j.annonc.2024.02.008] [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: 07/31/2023] [Revised: 01/30/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The incidence of early-onset colorectal cancer (EOCRC; diagnosed <50 years of age) is rising globally; however, the causes underlying this trend are largely unknown. CRC has strong genetic and environmental determinants, yet common genetic variants and causal modifiable risk factors underlying EOCRC are unknown. We conducted the first EOCRC-specific genome-wide association study (GWAS) and Mendelian randomization (MR) analyses to explore germline genetic and causal modifiable risk factors associated with EOCRC. PATIENTS AND METHODS We conducted a GWAS meta-analysis of 6176 EOCRC cases and 65 829 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colorectal Transdisciplinary Study (CORECT), the Colon Cancer Family Registry (CCFR), and the UK Biobank. We then used the EOCRC GWAS to investigate 28 modifiable risk factors using two-sample MR. RESULTS We found two novel risk loci for EOCRC at 1p34.1 and 4p15.33, which were not previously associated with CRC risk. We identified a deleterious coding variant (rs36053993, G396D) at polyposis-associated DNA repair gene MUTYH (odds ratio 1.80, 95% confidence interval 1.47-2.22) but show that most of the common genetic susceptibility was from noncoding signals enriched in epigenetic markers present in gastrointestinal tract cells. We identified new EOCRC-susceptibility genes, and in addition to pathways such as transforming growth factor (TGF) β, suppressor of Mothers Against Decapentaplegic (SMAD), bone morphogenetic protein (BMP) and phosphatidylinositol kinase (PI3K) signaling, our study highlights a role for insulin signaling and immune/infection-related pathways in EOCRC. In our MR analyses, we found novel evidence of probable causal associations for higher levels of body size and metabolic factors-such as body fat percentage, waist circumference, waist-to-hip ratio, basal metabolic rate, and fasting insulin-higher alcohol drinking, and lower education attainment with increased EOCRC risk. CONCLUSIONS Our novel findings indicate inherited susceptibility to EOCRC and suggest modifiable lifestyle and metabolic targets that could also be used to risk-stratify individuals for personalized screening strategies or other interventions.
Collapse
Affiliation(s)
- R S Laskar
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France; Early Cancer Institute, Department of Oncology, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
| | - C Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle
| | - J R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle
| | - T Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle
| | - R B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York
| | - Y Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis; Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis; Alvin J. Siteman Cancer Center, St Louis
| | - P T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, USA
| | - R Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle
| | - F R Talukdar
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - H Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston; Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston
| | - S Brendt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - D T Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - D D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia
| | - A T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - M Cotterchio
- Ontario Health (Cancer Care Ontario), Toronto; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - S B Gruber
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, USA
| | - A Gsur
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - B van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - M A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - T O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, USA
| | - B M Lynch
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne; Physical Activity Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | | | - R M Martin
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol; National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol
| | - K McCarthy
- Department of Colorectal Surgery, North Bristol NHS Trust, Bristol, UK
| | - V Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - R Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus
| | - M Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, USA
| | - K K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - P Vodička
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - M O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Canada
| | - K Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, USA
| | - L Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle
| | - M J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - U Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle; Department of Epidemiology, University of Washington, Seattle, USA
| | - N Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France.
| |
Collapse
|
187
|
Klomberg RCW, Hellendoorn AE, Kemos P, Rizopoulos D, Ruemmele FM, Croft NM, de Ridder L. Rare and severe adverse events in children with inflammatory bowel disease: analysis of data from the PIBD-SETQuality Safety Registry. THE LANCET. CHILD & ADOLESCENT HEALTH 2024; 8:422-432. [PMID: 38697175 DOI: 10.1016/s2352-4642(24)00078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND Rare and severe adverse events can occur in children with inflammatory bowel disease (IBD), and the relationship with disease or drug treatment is often uncertain. We aimed to establish a method of reporting adverse events of interest in children with IBD, allowing for estimates of incidence rates with comparison between different regions, and, if possible, to compare with published data on rates of adverse events in children overall. METHODS For this analysis, we used data from the Paediatric Inflammatory Bowel Disease Network for Safety, Efficacy and Treatment and Quality improvement of care (PIBD-SETQuality) Safety Registry, which collects data on multiple rare and severe adverse events in children younger than 19 years with IBD. Overall, the registry collected data on ten prespecified rare and severe adverse events in children with IBD, as established by a panel of paediatric IBD experts, via reports from paediatric gastroenterologists at participating hospitals between Nov 1, 2016, and March 31, 2023. Reporting physicians, who could only be paediatric gastroenterologists or IBD nurses reporting on behalf of paediatric gastroenterologists, were recruited through invitations sent to both national and international IBD networks and at conferences. Once per month, participating paediatric gastroenterologists received an email with an anonymous and unique link to an online survey asking them to report whether any of ten rare and severe adverse events had occurred in a patient in their paediatric-IBD population in the previous month. Prevalent or retrospective rare and severe adverse events were excluded, as were events occurring in children with an unconfirmed diagnosis of IBD or for whom inflammatory colitis was part of a monogenic immunodeficiency disorder. Duplicates and events that did not meet the definitions and criteria were excluded. Physicians could also report other, non-categorised adverse events if they considered them rare and severe. In case of no response, up to two reminders were sent for each per-month survey. Annual denominator data surveys were sent to obtain the total number of person-years for the estimation of incidence rates, which were calculated via Poisson regression models. FINDINGS Responses were gathered from 220 paediatric gastroenterologists from 167 centres. 121 centres were in Europe, 23 centres were in North America, 17 centres were in Asia, and six centres were in Oceania. Combined, the total population with paediatric IBD consisted of an estimated 30 193 children with 114 528 person-years of follow-up. 451 adverse events were initially reported. After excluding and reorganising adverse events, 402 were eligible; 261 (65%) were categorised and 141 (35%) were non-categorised. The most frequently reported adverse events were venous-thromboembolic events (n=66), renal failure (n=43), opportunistic infections (n=42), and cancer (n=33). Haemophagocytic lymphohistiocytosis (n=4) and liver failure (n=3) were the least frequently reported adverse events. Incidence rates per 10 000 person-years were 5·50 (95% CI 4·25-6·97) for venous-thromboembolic events, 3·75 (2·74-4·99) for renal failure, 3·67 (2·67-4·89) for opportunistic infection, and 2·88 (2·01-3·98) for cancer. Of 66 venous-thromboembolic events, 31 (47%) involved cerebral venous sinus thrombosis at an incidence rate of 2·71 (95% CI 1·86-3·77). INTERPRETATION The PIBD-SETQuality Safety Registry enabled us to identify incidence rates of rare and severe adverse events in children with IBD. Our findings can guide physicians and enhance awareness of the incidence of adverse events in children with IBD that are considered to be rare. FUNDING EU Horizon 2020 Research and Innovation Programme.
Collapse
Affiliation(s)
- Renz C W Klomberg
- Department of Pediatric Gastroenterology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Astrid E Hellendoorn
- Department of Pediatric Gastroenterology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Polychronis Kemos
- Paediatric Gastroenterology, Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Dimitris Rizopoulos
- Department of Epidemiology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank M Ruemmele
- Department of Pediatric Gastroenterology, Université Paris Descartes, Sorbonne Paris Cité, Assistance Publique Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Nicholas M Croft
- Paediatric Gastroenterology, Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Lissy de Ridder
- Department of Pediatric Gastroenterology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands.
| |
Collapse
|
188
|
Radford SJ, Abdul-Aema B, Tench C, Leighton P, Coad J, Moran GW. Substantial cost savings of ultrasound-based management over magnetic resonance imaging-based management in an inflammatory bowel disease service. Scand J Gastroenterol 2024; 59:683-689. [PMID: 38501494 DOI: 10.1080/00365521.2024.2330588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Imaging is used to monitor disease activity in small bowel Crohn's disease (CD). Magnetic Resonance Enterography is often employed as a first modality in the United Kingdom for assessment and monitoring; however, waiting times, cost, patient burden and limited access are significant. It is as yet uncertain if small bowel intestinal ultrasound (IUS) may be a quicker, more acceptable, and cheaper alternative for monitoring patients with CD. METHODS A clinical service evaluation of imaging pathways was undertaken at a single NHS site in England, United Kingdom. Data were collected about patients who were referred and underwent an imaging analysis for their IBD. Only patients who underwent a therapy change were included in the analysis. Data were collected from care episodes between 01 January 2021-30 March 2022. RESULTS A combined total of 193 patient care episodes were reviewed, 107 from the IUS pathway and 86 from the MRE pathway. Estimated costs per patient in the IUS pathway was £78.86, and £375.35 per patient in the MRE pathway. The MRE pathway had an average time from referral to treatment initiation of 91 days (SD= ±61) with patients in the IUS pathway waiting an average of 46 days (SD= ±17). CONCLUSIONS Findings from this work indicate that IUS is a potential cost-saving option when compared to MRE when used in the management of CD. This is in addition to the cost difference of the radiological modalities. A large, multicentre, prospective study is needed to validate these initial findings.
Collapse
Affiliation(s)
- Shellie J Radford
- Nottingham NIHR Biomedical Research Centre, Nottingham University Hospitals NHS trust and the University of Nottingham, United Kingdom of Great Britain and Northern Ireland
- University of Nottingham, Translational Medical Sciences, School of Medicine, Faculty of Medicine and Health Sciences, United Kingdom of Great Britain and Northern Ireland
| | - Buraq Abdul-Aema
- Nottingham NIHR Biomedical Research Centre, Nottingham University Hospitals NHS trust and the University of Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Chris Tench
- University of Nottingham, Translational Medical Sciences, School of Medicine, Faculty of Medicine and Health Sciences, United Kingdom of Great Britain and Northern Ireland
| | - Paul Leighton
- University of Nottingham, Translational Medical Sciences, School of Medicine, Faculty of Medicine and Health Sciences, United Kingdom of Great Britain and Northern Ireland
| | - Jane Coad
- University of Nottingham, School of Health Sciences, Faculty of Medicine and Health Sciences, United Kingdom of Great Britain and Northern Ireland
| | - Gordon W Moran
- Nottingham NIHR Biomedical Research Centre, Nottingham University Hospitals NHS trust and the University of Nottingham, United Kingdom of Great Britain and Northern Ireland
- University of Nottingham, Translational Medical Sciences, School of Medicine, Faculty of Medicine and Health Sciences, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
189
|
Lee RB, Gasparetto M. Novel pharmacological developments in the management of paediatric inflammatory bowel disease: Time for guideline update - A narrative review. J Paediatr Child Health 2024; 60:168-175. [PMID: 37953693 DOI: 10.1111/jpc.16519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023]
Abstract
AIM The incidence of paediatric inflammatory bowel disease (IBD) continues to increase in both adults and children across the globe, with more than one third of the patients not responding to anti-tumour necrosis factor biologics and immune modulators. This narrative review provides an overview of novel pharmacological developments in the management of paediatric IBD, including new biological therapies. METHODS A PubMed Medline search was performed to include randomised controlled trials, retrospective and prospective observational studies, and relevant case reports of children with IBD published between 2018 and January 2023. Guidelines and protocols from relevant paediatric and adult gastroenterology societies, such as the European Society for Paediatric Gastroenterology, Hepatology and Nutrition and the European Crohn's and Colitis Organisation, were also included. Non-pharmacological treatments including therapeutic diets and faecal microbiota transplantation were outside the scope of this work. RESULTS Early real-world evidence suggests that newer biologics and small molecules, such as anti-integrins, interleukin-12 and/or interleukin-23 inhibitors, Janus kinase and signal transducer and activator of transcription proteins inhibitors, are safe and effective in adult patients with IBD, with promising growing evidence for paediatric IBD. CONCLUSION While many developments have been achieved with novel pharmacological treatments to manage IBD, ongoing research is required to confirm their effectiveness and safety in the paediatric age. Extending the licence of novel treatments to children will be crucial to tackle the increasing loss of response to conventional treatments. International guidelines will require timely updating to incorporate novel treatments within the existing protocols.
Collapse
Affiliation(s)
- Rachel By Lee
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Marco Gasparetto
- Paediatric Gastroenterology, Norfolk and Norwich University Hospital, Jenny Lind Children's Hospital, Norwich, United Kingdom
- Faculty of Medicine and Health Science, University of East Anglia, Norwich Medical School, Norwich, United Kingdom
| |
Collapse
|
190
|
Henderson P. Editorial: Mortality in immune-mediated inflammatory diseases during early adulthood. Aliment Pharmacol Ther 2024; 59:1624-1625. [PMID: 38643504 DOI: 10.1111/apt.18012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
LINKED CONTENTThis article is linked to Malham et al papers. To view these articles, visit https://doi.org/10.1111/apt.17994 and https://doi.org/10.1111/apt.18026.
Collapse
Affiliation(s)
- Paul Henderson
- Child Life and Health, Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh, UK
- Department of Paediatric Gastroenterology and Nutrition, Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
191
|
Alsoud D, Moes DJAR, Wang Z, Soenen R, Layegh Z, Barclay M, Mizuno T, Minichmayr IK, Keizer RJ, Wicha SG, Wolbink G, Lambert J, Vermeire S, de Vries A, Papamichael K, Padullés-Zamora N, Dreesen E. Best Practice for Therapeutic Drug Monitoring of Infliximab: Position Statement from the International Association of Therapeutic Drug Monitoring and Clinical Toxicology. Ther Drug Monit 2024; 46:291-308. [PMID: 38648666 DOI: 10.1097/ftd.0000000000001204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Infliximab, an anti-tumor necrosis factor monoclonal antibody, has revolutionized the pharmacological management of immune-mediated inflammatory diseases (IMIDs). This position statement critically reviews and examines existing data on therapeutic drug monitoring (TDM) of infliximab in patients with IMIDs. It provides a practical guide on implementing TDM in current clinical practices and outlines priority areas for future research. METHODS The endorsing TDM of Biologics and Pharmacometrics Committees of the International Association of TDM and Clinical Toxicology collaborated to create this position statement. RESULTS Accumulating data support the evidence for TDM of infliximab in the treatment of inflammatory bowel diseases, with limited investigation in other IMIDs. A universal approach to TDM may not fully realize the benefits of improving therapeutic outcomes. Patients at risk for increased infliximab clearance, particularly with a proactive strategy, stand to gain the most from TDM. Personalized exposure targets based on therapeutic goals, patient phenotype, and infliximab administration route are recommended. Rapid assays and home sampling strategies offer flexibility for point-of-care TDM. Ongoing studies on model-informed precision dosing in inflammatory bowel disease will help assess the additional value of precision dosing software tools. Patient education and empowerment, and electronic health record-integrated TDM solutions will facilitate routine TDM implementation. Although optimization of therapeutic effectiveness is a primary focus, the cost-reducing potential of TDM also merits consideration. CONCLUSIONS Successful implementation of TDM for infliximab necessitates interdisciplinary collaboration among clinicians, hospital pharmacists, and (quantitative) clinical pharmacologists to ensure an efficient research trajectory.
Collapse
Affiliation(s)
- Dahham Alsoud
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Dirk Jan A R Moes
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Zhigang Wang
- Clinical Pharmacology and Pharmacotherapy Unit, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Rani Soenen
- Dermatology Research Unit, Ghent University, Ghent, Belgium
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Zohra Layegh
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Murray Barclay
- Departments of Gastroenterology and Clinical Pharmacology, Christchurch Hospital, Te Whatu Ora Waitaha and University of Otago, Christchurch, New Zealand
| | - Tomoyuki Mizuno
- Division of Translational and Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Iris K Minichmayr
- Department of Clinical Pharmacology, Medical University Vienna, Vienna, Austria
| | | | - Sebastian G Wicha
- Department of Clinical Pharmacy, Institute of Pharmacy, University of Hamburg, Hamburg, Germany
| | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center Location Reade, Amsterdam, Netherlands
- Sanquin Research and Landsteiner Laboratory, Department of Immunopathology, Amsterdam UMC, Amsterdam, Netherlands
| | - Jo Lambert
- Dermatology Research Unit, Ghent University, Ghent, Belgium
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Séverine Vermeire
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Annick de Vries
- Sanquin Diagnostic Services, Pharma & Biotech Services, Amsterdam, the Netherlands
| | - Konstantinos Papamichael
- Center for Inflammatory Bowel Diseases, Division of Gastroenterology, Beth-Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Núria Padullés-Zamora
- Department of Pharmacy, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain; and
- School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Erwin Dreesen
- Clinical Pharmacology and Pharmacotherapy Unit, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
192
|
Li L, Cheng R, Wu Y, Lin H, Gan H, Zhang H. Diagnosis and management of inflammatory bowel disease. J Evid Based Med 2024; 17:409-433. [PMID: 38934234 DOI: 10.1111/jebm.12626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic and relapsing immune-mediated disease of the gastrointestinal tract with a gradually increasing global incidence and prevalence. A prolonged course of IBD leads to a decline in patient quality of life and the creation of a substantial economic burden on society. Owing to the lack of specific diagnostic markers, the diagnosis of IBD still needs a gold standard based on a combination of clinical manifestations, imaging, laboratory, and endoscopic results. Accordingly, the current goals of IBD treatment are to alleviate clinical symptoms and reduce recurrence rates. Therefore, it is imperative to develop a standard set of procedures to diagnose and treat IBD. In this review, we summarize prominent and emerging studies, outline classical and contemporary approaches to diagnosing and managing IBD, and integrate multiple guidelines. Furthermore, we propose the possibility of establishing an early and comprehensive diagnostic workflow and personalized management strategy in the future. We aim to enhance the quality and standardization of diagnostic and treatment procedures for IBD.
Collapse
Affiliation(s)
- Lili Li
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Rui Cheng
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yushan Wu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Lin
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Huatian Gan
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- The Center of Gerontology and Geriatrics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Hu Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
193
|
Mansour M, Doumet G, Kadan A, Bajour D, Madania M, Alsarraj MA, Alhamwi A, Antakli K, Almohammad A, Saiouf Y, Mahmod J. Early diagnosis and treatment of perianal Crohn's disease in a 1-year-old infant: Case report and review of literature. Clin Case Rep 2024; 12:e8963. [PMID: 38803326 PMCID: PMC11128492 DOI: 10.1002/ccr3.8963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
Inflammatory bowel disease is rare in infants and it includes perianal Crohn's disease, which is inflammation at or near the anus. An early diagnosis is essential to prevent the complications that may affect the development and growth of the child.
Collapse
Affiliation(s)
- Marah Mansour
- Faculty of MedicineTartous UniversityTartousSyria
- Division of Colon and Rectal Surgery, Department of SurgeryMayo ClinicRochesterMinnesotaUSA
| | | | - Ahmad Kadan
- Faculty of MedicineUniversity of AleppoAleppoSyria
| | - Dina Bajour
- Faculty of MedicineDamascus UniversityDamascusSyria
| | | | | | | | | | | | - Yaman Saiouf
- Faculty of MedicineDamascus UniversityDamascusSyria
| | - Jaber Mahmod
- Department of GastroenterologyPediatric University HospitalDamascusSyria
| |
Collapse
|
194
|
Herauf M, Coward S, Peña-Sánchez JN, Bernstein CN, Benchimol EI, Kaplan GG. Commentary on the Epidemiology of Inflammatory Bowel Disease in Compounding Prevalence Nations: Toward Sustaining Healthcare Delivery. Gastroenterology 2024; 166:949-956. [PMID: 38378092 DOI: 10.1053/j.gastro.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/24/2024] [Accepted: 02/13/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Michelle Herauf
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Stephanie Coward
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Juan-Nicolás Peña-Sánchez
- Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Charles N Bernstein
- Department of Medicine, University of Manitoba IBD Clinical and Research Centre, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Eric I Benchimol
- SickKids Inflammatory Bowel Disease Centre, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children (SickKids), Toronto, Ontario, Canada; Department of Paediatrics, Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Child Health Evaluative Sciences, SickKids Research Institute, Toronto, Ontario, Canada; ICES, Toronto, Ontario, Canada
| | - Gilaad G Kaplan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
195
|
Grover Z, Day AS. Novel pharmacological developments in the management of paediatric inflammatory bowel disease. J Paediatr Child Health 2024; 60:162-163. [PMID: 38923605 DOI: 10.1111/jpc.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Zubin Grover
- Perth Children's Hospital, Perth, Western Australia, Australia
| | - Andrew S Day
- Cure Kids Chair of Paediatric Research, Department of Paediatrics, University of Otago Christchurch, Christchurch, New Zealand
- Discipline of Paediatrics and Child Health, School of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
196
|
Vuijk SA, Jongsma MME, Hoeven BM, Cozijnsen MA, van Pieterson M, de Meij TGJ, Norbruis OF, Groeneweg M, Wolters VM, van Wering H, Hummel T, Stapelbroek J, van der Feen C, van Rheenen PF, van Wijk MP, Teklenburg S, Rizopoulos D, Poley MJ, Escher JC, de Ridder L. Randomised clinical trial: First-line infliximab biosimilar is cost-effective compared to conventional treatment in paediatric Crohn's disease. Aliment Pharmacol Ther 2024; 59:1510-1520. [PMID: 38644588 DOI: 10.1111/apt.18000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/10/2023] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Data on cost-effectiveness of first-line infliximab in paediatric patients with Crohn's disease are limited. Since biologics are increasingly prescribed and accompanied by high costs, this knowledge gap needs to be addressed. AIM To investigate the cost-effectiveness of first-line infliximab compared to conventional treatment in children with moderate-to-severe Crohn's disease. METHODS We included patients from the Top-down Infliximab Study in Kids with Crohn's disease randomised controlled trial. Children with newly diagnosed moderate-to-severe Crohn's disease were treated with azathioprine maintenance and either five induction infliximab (biosimilar) infusions or conventional induction treatment (exclusive enteral nutrition or corticosteroids). Direct healthcare consumption and costs were obtained per patient until week 104. This included data on outpatient hospital visits, hospital admissions, drug costs, endoscopies and surgeries. The primary health outcome was the odds ratio of being in clinical remission (weighted paediatric Crohn's disease activity index<12.5) during 104 weeks. RESULTS We included 89 patients (44 in the first-line infliximab group and 45 in the conventional treatment group). Mean direct healthcare costs per patient were €36,784 for first-line infliximab treatment and €36,874 for conventional treatment over 2 years (p = 0.981). The odds ratio of first-line infliximab versus conventional treatment to be in clinical remission over 104 weeks was 1.56 (95%CI 1.03-2.35, p = 0.036). CONCLUSIONS First-line infliximab treatment resulted in higher odds of being in clinical remission without being more expensive, making it the dominant strategy over conventional treatment in the first 2 years after diagnosis in children with moderate-to-severe Crohn's disease. TRIAL REGISTRATION NUMBER NCT02517684.
Collapse
Affiliation(s)
- Stephanie A Vuijk
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Maria M E Jongsma
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Britt M Hoeven
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Maarten A Cozijnsen
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Merel van Pieterson
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Tim G J de Meij
- Department of Paediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Obbe F Norbruis
- Department of Paediatric Gastroenterology, Isala Hospital, Zwolle, The Netherlands
| | - Michael Groeneweg
- Department of Paediatric Gastroenterology, Maasstad Hospital, Rotterdam, The Netherlands
| | - Victorien M Wolters
- Department of Paediatric Gastroenterology, UMC Utrecht/Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Herbert van Wering
- Department of Paediatric Gastroenterology, Amphia Hospital, Breda, The Netherlands
| | - Thalia Hummel
- Department of Paediatric Gastroenterology, Medical Spectrum Twente, Enschede, The Netherlands
| | - Janneke Stapelbroek
- Department of Paediatric Gastroenterology, Catharina Hospital, Eindhoven, The Netherlands
| | - Cathelijne van der Feen
- Department of Paediatric Gastroenterology, Jeroen Bosch Hospital, 's Hertogenbosch, The Netherlands
| | - Patrick F van Rheenen
- Department of Paediatric Gastroenterology, University Medical Center, University of Groningen, Groningen, The Netherlands
| | - Michiel P van Wijk
- Department of Paediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Sarah Teklenburg
- Department of Paediatric Gastroenterology, Isala Hospital, Zwolle, The Netherlands
| | - Dimitris Rizopoulos
- Department of Biostatistics, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Marten J Poley
- Institute for Medical Technology Assessment and Erasmus School of Health Policy & Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
- Department of Pediatric Surgery and Intensive Care, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Johanna C Escher
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| |
Collapse
|
197
|
Weigl E, Schwerd T, Lurz E, Häberle B, Koletzko S, Hubertus J. Children with Localized Crohn's Disease Benefit from Early Ileocecal Resection and Perioperative Anti-Tumor Necrosis Factor Therapy. Eur J Pediatr Surg 2024; 34:236-244. [PMID: 36929126 DOI: 10.1055/s-0043-1764320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
INTRODUCTION In pediatric Crohn's disease ileocecal resection is performed reluctantly as postoperative recurrence is frequent. Anti-tumor necrosis factor (TNF) therapy reduces postoperative recurrence rates but increases the risk for infections. MATERIALS AND METHODS We retrospectively reviewed pediatric Crohn's disease patients who underwent ileocecal resection in our center. We compared disease activity and z-scores for height, weight, and body mass index of patients, who continuously received perioperative anti-TNF therapy (TNF + ), with those who did not (TNF-). RESULTS Of 29 patients (48% females), 13 and 16 were grouped to TNF+ and TNF-, respectively. Patients' characteristics did not differ between groups, except a longer follow-up time in TNF-. We saw significant postoperative improvement but no normalization in z-scores for weight (1.78 vs. 0.77, p < 0.001), body mass index (1.08 vs. 0.22, p < 0.001), and height (0.88 vs. 0.66, p < 0.001). Disease activity improved significantly more in patients receiving anti-TNF therapy (moderate improvement in 83% vs. 31%, p = 0.02). Endoscopic recurrence was more frequent in patients without anti-TNF therapy (80% vs. 20%; p = 0.023), but endoscopic follow-up was incomplete. There was no increase of infections under perioperative anti-TNF therapy (1 patient each; p = 1.000). CONCLUSION In patients with localized Crohn's disease an ileocecal resection leads to short-term postoperative improvement of disease activity, body mass index, weight, and growth. For relevant catch-up growth an earlier intervention is necessary. Continuous perioperative anti-TNF therapy had no increased risk of perioperative infections.
Collapse
Affiliation(s)
- Elena Weigl
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Bayern, Germany
| | - Tobias Schwerd
- Department of Pediatric Gastroenterology, Dr. von Hauner Children's Hospital, University Hospital Munich, LMU Munich, Bayern, Germany
| | - Eberhard Lurz
- Department of Pediatric Gastroenterology, Dr. von Hauner Children's Hospital, University Hospital Munich, LMU Munich, Bayern, Germany
| | - Beate Häberle
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Bayern, Germany
| | - Sibylle Koletzko
- Department of Pediatric Gastroenterology, Dr. von Hauner Children's Hospital, University Hospital Munich, LMU Munich, Bayern, Germany
- Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Jochen Hubertus
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Bayern, Germany
| |
Collapse
|
198
|
Papadimitriou N, Kim A, Kawaguchi ES, Morrison J, Diez-Obrero V, Albanes D, Berndt SI, Bézieau S, Bien SA, Bishop DT, Bouras E, Brenner H, Buchanan DD, Campbell PT, Carreras-Torres R, Chan AT, Chang-Claude J, Conti DV, Devall MA, Dimou N, Drew DA, Gruber SB, Harrison TA, Hoffmeister M, Huyghe JR, Joshi AD, Keku TO, Kundaje A, Küry S, Le Marchand L, Lewinger JP, Li L, Lynch BM, Moreno V, Newton CC, Obón-Santacana M, Ose J, Pellatt AJ, Peoples AR, Platz EA, Qu C, Rennert G, Ruiz-Narvaez E, Shcherbina A, Stern MC, Su YR, Thomas DC, Thomas CE, Tian Y, Tsilidis KK, Ulrich CM, Um CY, Visvanathan K, Wang J, White E, Woods MO, Schmit SL, Macrae F, Potter JD, Hopper JL, Peters U, Murphy N, Hsu L, Gunter MJ, Gauderman WJ. Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer. EBioMedicine 2024; 104:105146. [PMID: 38749303 PMCID: PMC11112268 DOI: 10.1016/j.ebiom.2024.105146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Consumption of fibre, fruits and vegetables have been linked with lower colorectal cancer (CRC) risk. A genome-wide gene-environment (G × E) analysis was performed to test whether genetic variants modify these associations. METHODS A pooled sample of 45 studies including up to 69,734 participants (cases: 29,896; controls: 39,838) of European ancestry were included. To identify G × E interactions, we used the traditional 1--degree-of-freedom (DF) G × E test and to improve power a 2-step procedure and a 3DF joint test that investigates the association between a genetic variant and dietary exposure, CRC risk and G × E interaction simultaneously. FINDINGS The 3-DF joint test revealed two significant loci with p-value <5 × 10-8. Rs4730274 close to the SLC26A3 gene showed an association with fibre (p-value: 2.4 × 10-3) and G × fibre interaction with CRC (OR per quartile of fibre increase = 0.87, 0.80, and 0.75 for CC, TC, and TT genotype, respectively; G × E p-value: 1.8 × 10-7). Rs1620977 in the NEGR1 gene showed an association with fruit intake (p-value: 1.0 × 10-8) and G × fruit interaction with CRC (OR per quartile of fruit increase = 0.75, 0.65, and 0.56 for AA, AG, and GG genotype, respectively; G × E -p-value: 0.029). INTERPRETATION We identified 2 loci associated with fibre and fruit intake that also modify the association of these dietary factors with CRC risk. Potential mechanisms include chronic inflammatory intestinal disorders, and gut function. However, further studies are needed for mechanistic validation and replication of findings. FUNDING National Institutes of Health, National Cancer Institute. Full funding details for the individual consortia are provided in acknowledgments.
Collapse
Affiliation(s)
- Nikos Papadimitriou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Andre Kim
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eric S Kawaguchi
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John Morrison
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Virginia Diez-Obrero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, 08908, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, 08908, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Barcelona, 08908, Spain; Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Emmanouil Bouras
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumour Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Australia; University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert Carreras-Torres
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, 08908, Spain; Digestive Diseases and Microbiota Group, Girona Biomedical Research Institute (IDIBGI), 17190 Salt, Girona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - David V Conti
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew A Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, Center for Public Health Genomics, Charlottesville, VA, USA
| | - Niki Dimou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen B Gruber
- Department of Medical Oncology & Therapeutics Research and Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Amit D Joshi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | | | - Juan Pablo Lewinger
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA, USA
| | - Brigid M Lynch
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, 08908, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, 08908, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Barcelona, 08908, Spain; Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Christina C Newton
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, 08908, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, 08908, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Barcelona, 08908, Spain
| | - Jennifer Ose
- Huntsman Cancer Institute, Salt Lake City, UT, USA; Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Andrew J Pellatt
- Department of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anita R Peoples
- Huntsman Cancer Institute, Salt Lake City, UT, USA; Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel; Clalit National Cancer Control Center, Haifa, Israel
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mariana C Stern
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Duncan C Thomas
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Claire E Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yu Tian
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; School of Public Health, Capital Medical University, Beijing, China
| | - Konstantinos K Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece; Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK
| | - Cornelia M Ulrich
- Huntsman Cancer Institute, Salt Lake City, UT, USA; Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Caroline Y Um
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jun Wang
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Canada
| | - Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA; Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Finlay Macrae
- The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia; Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA.
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France; Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, London, UK.
| | - W James Gauderman
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
199
|
Jang CS, Kim H, Kim D, Han B. MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data. Genes Genomics 2024; 46:701-712. [PMID: 38700829 PMCID: PMC11102407 DOI: 10.1007/s13258-024-01514-w] [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: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND The importance of the human microbiome in the analysis of various diseases is emerging. The two main methods used to profile the human microbiome are 16S rRNA gene sequencing (16S sequencing) and whole-genome shotgun sequencing (WGS). Owing to the full coverage of the genome in sequencing, WGS has multiple advantages over 16S sequencing, including higher taxonomic profiling resolution at the species-level and functional profiling analysis. However, 16S sequencing remains widely used because of its relatively low cost. Although WGS is the standard method for obtaining accurate species-level data, we found that 16S sequencing data contained rich information to predict high-resolution species-level abundances with reasonable accuracy. OBJECTIVE In this study, we proposed MicroPredict, a method for accurately predicting WGS-comparable species-level abundance data using 16S taxonomic profile data. METHODS We employed a mixed model using two key strategies: (1) modeling both sample- and species-specific information for predicting WGS abundances, and (2) accounting for the possible correlations among different species. RESULTS We found that MicroPredict outperformed the other machine learning methods. CONCLUSION We expect that our approach will help researchers accurately approximate the species-level abundances of microbiome profiles in datasets for which only cost-effective 16S sequencing has been applied.
Collapse
Affiliation(s)
- Chloe Soohyun Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hakin Kim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea
| | - Donghyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea.
| |
Collapse
|
200
|
Sigvardsson I, Ludvigsson J, Andersson B, Størdal K, Mårild K. Tobacco Smoke Exposure in Early Childhood and Later Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study. J Crohns Colitis 2024; 18:661-670. [PMID: 38329478 PMCID: PMC11140631 DOI: 10.1093/ecco-jcc/jjae020] [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: 09/26/2023] [Indexed: 02/09/2024]
Abstract
OBJECTIVES To examine the association between early-life smoking exposure and later risk of inflammatory bowel disease [IBD]. METHODS We followed 115663 participants from the Norwegian Mother, Father and Child [MoBa] and All Babies in Southeast Sweden [ABIS] cohorts from birth [1997-2009] through 2021. IBD was identified through national patient registers. Validated questionnaire data defined maternal smoking during pregnancy, maternal environmental tobacco smoke [ETS] exposure during pregnancy, and child ETS exposure by ages 12 and 36 months. Cox regression was used to estimate adjusted hazard ratios [aHRs] for sex, maternal age, education level, parental IBD, and origin. Cohort-specific estimates were pooled using a random-effects model. RESULTS During 1 987 430 person-years of follow-up, 444 participants developed IBD [ABIS, 112; MoBa, 332]. Any vs no maternal smoking during pregnancy yielded a pooled aHR of 1.30 [95% CI = 0.97-1.74] for offspring IBD. Higher level of maternal smoking during pregnancy (compared with no smoking, average ≥6 cigarettes/day: pooled aHR = 1.60 [95% CI = 1.08-2.38]) was associated with offspring IBD, whereas a lower smoking level was not (average 1-5 cigarettes/day: pooled aHR = 1.09 [95% CI = 0.73-1.64]). Child ETS exposure in the first year of life was associated with later IBD (any vs no ETS, pooled aHR = 1.32 [95% CI = 1.03-1.69]). Estimates observed for child ETS exposure by 36 months were similar but not statistically significant. CONCLUSIONS In this prospective Scandinavian cohort study, children exposed to higher levels of maternal smoking during pregnancy or ETS during the first year of life were at increased risk of later IBD.
Collapse
Affiliation(s)
- Ida Sigvardsson
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg, Sweden
| | - Johnny Ludvigsson
- Crown Princess Victoria Children’s Hospital, Region Östergötland, Linköping, Sweden
- Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Björn Andersson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ketil Størdal
- Department of Pediatric Research, Faculty of Medicine, University of Oslo, Oslo, Norway
- Children’s Center, Oslo University Hospital, Oslo, Norway
| | - Karl Mårild
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Pediatrics, Queen Silvia Children’s Hospital, Gothenburg, Sweden
| |
Collapse
|