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Minea H, Singeap AM, Minea M, Juncu S, Muzica C, Sfarti CV, Girleanu I, Chiriac S, Miftode ID, Stanciu C, Trifan A. The Contribution of Genetic and Epigenetic Factors: An Emerging Concept in the Assessment and Prognosis of Inflammatory Bowel Diseases. Int J Mol Sci 2024; 25:8420. [PMID: 39125988 PMCID: PMC11313574 DOI: 10.3390/ijms25158420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) represents heterogeneous and relapsing intestinal conditions with a severe impact on the quality of life of individuals and a continuously increasing prevalence. In recent years, the development of sequencing technology has provided new means of exploring the complex pathogenesis of IBD. An ideal solution is represented by the approach of precision medicine that investigates multiple cellular and molecular interactions, which are tools that perform a holistic, systematic, and impartial analysis of the genomic, transcriptomic, proteomic, metabolomic, and microbiomics sets. Hence, it has led to the orientation of current research towards the identification of new biomarkers that could be successfully used in the management of IBD patients. Multi-omics explores the dimension of variation in the characteristics of these diseases, offering the advantage of understanding the cellular and molecular mechanisms that affect intestinal homeostasis for a much better prediction of disease development and choice of treatment. This review focuses on the progress made in the field of prognostic and predictive biomarkers, highlighting the limitations, challenges, and also the opportunities associated with the application of genomics and epigenomics technologies in clinical practice.
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Affiliation(s)
- Horia Minea
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Ana-Maria Singeap
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Manuela Minea
- Department of Microbiology, The National Institute of Public Health, 700464 Iasi, Romania;
| | - Simona Juncu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Cristina Muzica
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Catalin Victor Sfarti
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Irina Girleanu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Stefan Chiriac
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Ioana Diandra Miftode
- Department of Radiology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Department of Radiology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Carol Stanciu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Anca Trifan
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
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Hu Y, Lu Y, Fang Y, Zhang Q, Zheng Z, Zheng X, Ye X, Chen Y, Ding J, Yang J. Role of long non-coding RNA in inflammatory bowel disease. Front Immunol 2024; 15:1406538. [PMID: 38895124 PMCID: PMC11183289 DOI: 10.3389/fimmu.2024.1406538] [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: 03/25/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a group of recurrent chronic inflammatory diseases, including Crohn's disease (CD) and ulcerative colitis (UC). Although IBD has been extensively studied for decades, its cause and pathogenesis remain unclear. Existing research suggests that IBD may be the result of an interaction between genetic factors, environmental factors and the gut microbiome. IBD is closely related to non-coding RNAs (ncRNAs). NcRNAs are composed of microRNA(miRNA), long non-coding RNA(lnc RNA) and circular RNA(circ RNA). Compared with miRNA, the role of lnc RNA in IBD has been little studied. Lnc RNA is an RNA molecule that regulates gene expression and regulates a variety of molecular pathways involved in the pathbiology of IBD. Targeting IBD-associated lnc RNAs may promote personalized treatment of IBD and have therapeutic value for IBD patients. Therefore, this review summarized the effects of lnc RNA on the intestinal epithelial barrier, inflammatory response and immune homeostasis in IBD, and summarized the potential of lnc RNA as a biomarker of IBD and as a predictor of therapeutic response to IBD in the future.
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Affiliation(s)
- Yufei Hu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yifan Lu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yi Fang
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Qizhe Zhang
- Department of Geriatrics, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Zhuoqun Zheng
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Xiaojuan Zheng
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Xiaohua Ye
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yanping Chen
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Jin Ding
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Jianfeng Yang
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
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McDonald GB, Landsverk OJ, McGovern DP, Aasebø A, Paulsen V, Haritunians T, Reims HM, McLaughlin BM, Zisman T, Li D, Elholm ET, Jahnsen FL, Georges GE, Gedde-Dahl T. Allogeneic bone marrow transplantation for patients with treatment-refractory Crohn's Disease. Heliyon 2024; 10:e24026. [PMID: 38283244 PMCID: PMC10818189 DOI: 10.1016/j.heliyon.2024.e24026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
Background & aims Durable remissions of Crohn's Disease (CD) have followed myeloablative conditioning therapy and allogeneic marrow transplantation. For patients with treatment-refractory disease, we used reduced-intensity conditioning to minimize toxicity, marrow from donors with low Polygenic Risk Scores for CD as cell sources, and protracted immune suppression to lower the risk of graft-versus-host disease (GVHD). Our aim was to achieve durable CD remissions while minimizing transplant-related complications. Methods DNA from patients and their HLA-matched unrelated donors was genotyped and Polygenic Risk Scores calculated. Donor marrow was infused following non-myeloablative conditioning. Patient symptoms and endoscopic findings were documented at intervals after transplant. Results We screened 807 patients, 143 of whom met eligibility criteria; 2 patients received allografts. Patient 1 had multiple complications and died at day 332 from respiratory failure. Patient 2 had resolution of CD symptoms until day 178 when CD recurred, associated with persistent host chimerism in both peripheral blood and intestinal mucosa. Withdrawal of immune suppression was followed by dominant donor immune chimerism in peripheral blood and resolution of CD findings. Over time, mucosal T-cells became donor-dominant. At 5 years after allografting, Patient 2 remained off all medications but had mild symptoms related to a jejunal stricture that required stricturoplasty at 6 years. At 8 years, she remains stable off medications. Conclusions The kinetics of immunologic chimerism after allogeneic marrow transplantation for CD patients depends on the intensity of the conditioning regimen and the magnitude of immune suppression. One patient achieved durable improvement of her previously refractory CD only after establishing donor immunologic chimerism in intestinal mucosa. Her course provides proof-of-principal for allografting as a potential treatment for refractory CD, but an immunoablative conditioning regimen should be considered for future studies.(ClinicalTrials.gov, NCT01570348).
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Affiliation(s)
- George B. McDonald
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anders Aasebø
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Vemund Paulsen
- Department of Transplantation Medicine, Section of Gastroenterology, Oslo University Hospital Rikshospitalet, Norway
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Henrik M. Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Timothy Zisman
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elisabeth T.M.M. Elholm
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Hematology, Oslo University Hospital, Norway and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Frode L. Jahnsen
- Department of Pathology, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Norway
| | - George E. Georges
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Tobias Gedde-Dahl
- Department of Hematology, Oslo University Hospital, Norway and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Shin MJ, Kim HS, Lee P, Yang NG, Kim JY, Eun YS, Lee W, Kim D, Lee Y, Jung KE, Hong D, Shin JM, Lee SH, Lee SY, Kim CD, Kim JE. Mechanistic Investigation of WWOX Function in NF-kB-Induced Skin Inflammation in Psoriasis. Int J Mol Sci 2023; 25:167. [PMID: 38203337 PMCID: PMC10779412 DOI: 10.3390/ijms25010167] [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: 11/28/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by epidermal hyperproliferation, aberrant differentiation of keratinocytes, and dysregulated immune responses. WW domain-containing oxidoreductase (WWOX) is a non-classical tumor suppressor gene that regulates multiple cellular processes, including proliferation, apoptosis, and migration. This study aimed to explore the possible role of WWOX in the pathogenesis of psoriasis. Immunohistochemical analysis showed that the expression of WWOX was increased in epidermal keratinocytes of both human psoriatic lesions and imiquimod-induced mice psoriatic model. Immortalized human epidermal keratinocytes were transduced with a recombinant adenovirus expressing microRNA specific for WWOX to downregulate its expression. Inflammatory responses were detected using Western blotting, real-time quantitative reverse transcription polymerase chain reaction (PCR), and enzyme-linked immunosorbent assay. In human epidermal keratinocytes, WWOX knockdown reduced nuclear factor-kappa B signaling and levels of proinflammatory cytokines induced by polyinosinic: polycytidylic acid [(poly(I:C)] in vitro. Furthermore, calcium chelator and protein kinase C (PKC) inhibitors significantly reduced poly(I:C)-induced inflammatory reactions. WWOX plays a role in the inflammatory reaction of epidermal keratinocytes by regulating calcium and PKC signaling. Targeting WWOX could be a novel therapeutic approach for psoriasis in the future.
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Affiliation(s)
- Min-Jeong Shin
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
| | - Hyun-Sun Kim
- Department of Dermatology, Soonchunhyang University Graduate School of Medicine, Asan 31538, Republic of Korea (P.L.)
| | - Pyeongan Lee
- Department of Dermatology, Soonchunhyang University Graduate School of Medicine, Asan 31538, Republic of Korea (P.L.)
| | - Na-Gyeong Yang
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
| | - Jae-Yun Kim
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
| | - Yun-Su Eun
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
| | - Whiin Lee
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
| | - Doyeon Kim
- Department of Dermatology, School of Medicine, Chungnam National University Hospital, Daejeon 35015, Republic of Korea (Y.L.)
| | - Young Lee
- Department of Dermatology, School of Medicine, Chungnam National University Hospital, Daejeon 35015, Republic of Korea (Y.L.)
| | - Kyung-Eun Jung
- Department of Dermatology, School of Medicine, Chungnam National University Hospital, Daejeon 35015, Republic of Korea (Y.L.)
| | - Dongkyun Hong
- Department of Dermatology, School of Medicine, Chungnam National University Hospital, Daejeon 35015, Republic of Korea (Y.L.)
| | - Jung-Min Shin
- Department of Dermatology, School of Medicine, Chungnam National University Hospital, Daejeon 35015, Republic of Korea (Y.L.)
| | - Sul-Hee Lee
- Department of Dermatology, College of Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Republic of Korea
| | - Sung-Yul Lee
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
| | - Chang-Deok Kim
- Department of Dermatology, School of Medicine, Chungnam National University Hospital, Daejeon 35015, Republic of Korea (Y.L.)
- Department of Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jung-Eun Kim
- Department of Dermatology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea (N.-G.Y.)
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Battaglia L, Scorrano G, Spiaggia R, Basile A, Palmucci S, Foti PV, Spatola C, Iacomino M, Marinangeli F, Francia E, Comisi F, Corsello A, Salpietro V, Vittori A, David E. Neuroimaging features of WOREE syndrome: a mini-review of the literature. Front Pediatr 2023; 11:1301166. [PMID: 38161429 PMCID: PMC10757851 DOI: 10.3389/fped.2023.1301166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
The WWOX gene encodes a 414-amino-acid protein composed of two N-terminal WW domains and a C-terminal short-chain dehydrogenase/reductase (SDR) domain. WWOX protein is highly conserved among species and mainly expressed in the cerebellum, cerebral cortex, brain stem, thyroid, hypophysis, and reproductive organs. It plays a crucial role in the biology of the central nervous system, and it is involved in neuronal development, migration, and proliferation. Biallelic pathogenic variants in WWOX have been associated with an early infantile epileptic encephalopathy known as WOREE syndrome. Both missense and null variants have been described in affected patients, leading to a reduction in protein function and stability. The most severe WOREE phenotypes have been related to biallelic null/null variants, associated with the complete loss of function of the protein. All affected patients showed brain anomalies on magnetic resonance imaging (MRI), suggesting the pivotal role of WWOX protein in brain homeostasis and developmental processes. We provided a literature review, exploring both the clinical and radiological spectrum related to WWOX pathogenic variants, described to date. We focused on neuroradiological findings to better delineate the WOREE phenotype with diagnostic and prognostic implications.
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Affiliation(s)
- Laura Battaglia
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
| | - Giovanna Scorrano
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Rossana Spiaggia
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
| | - Antonio Basile
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
| | - Stefano Palmucci
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
| | - Pietro Valerio Foti
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
| | - Corrado Spatola
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
| | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Instituto Giannina Gaslini, Genoa, Italy
| | - Franco Marinangeli
- Department of Anesthesia, Critical Care and Pain Therapy, University of L’aquila, L’aquila, Italy
| | - Elisa Francia
- Department of Anesthesia and Critical Care, ARCO ROMA, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | | | | | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Alessandro Vittori
- Department of Anesthesia and Critical Care, ARCO ROMA, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Emanuele David
- Department of Medical Surgical Sciences and Advanced Technologies “GF Ingrassia”, University Hospital Policlinic “G. Rodolico-San Marco”, Catania, Italy
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Kim SW, Lee JY, Lee HC, Ahn JB, Kim JH, Park IS, Cheon JH, Kim DH. Downregulation of Heat Shock Protein 72 Contributes to Fibrostenosis in Crohn's Disease. Gut Liver 2023; 17:905-915. [PMID: 36814356 PMCID: PMC10651382 DOI: 10.5009/gnl220308] [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: 07/18/2022] [Revised: 10/21/2022] [Accepted: 11/29/2022] [Indexed: 02/24/2023] Open
Abstract
Background/Aims Crohn's disease (CD) with recurrent inflammation can cause intestinal fibrostenosis due to dysregulated deposition of extracellular matrix. However, little is known about the pathogenesis of fibrostenosis. Here, we performed a differential proteomic analysis between normal, inflamed, and fibrostenotic specimens of patients with CD and investigated the roles of the candidate proteins in myofibroblast activation and fibrosis. Methods We performed two-dimensional difference gel electrophoresis and identified candidate proteins using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and orbitrap liquid chromatography-mass spectrometry. We also verified the levels of candidate proteins in clinical specimens and examined their effects on 18Co myofibroblasts and Caco-2 intestinal epithelial cells. Results We identified five of 30 proteins (HSP72, HSPA5, KRT8, PEPCK-M, and FABP6) differentially expressed in fibrostenotic CD. Among these proteins, the knockdown of heat shock protein 72 (HSP72) promoted the activation and wound healing of myofibroblasts. Moreover, knockdown of HSP72 induced the epithelial-mesenchymal transition of intestinal epithelial cells by reducing E-cadherin and inducing fibronectin and α-smooth muscle actin, which contribute to fibrosis. Conclusions HSP72 is an important mediator that regulates myofibroblasts and epithelial-mesenchymal transition in fibrosis of CD, suggesting that HSP72 can serve as a target for antifibrotic therapy.
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Affiliation(s)
- Seung Won Kim
- Department of Internal Medicine and Institute of Gastroenterology, Graduate School of Medical Science, Brain Korea 21 Project, Seoul, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Young Lee
- Department of Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Han Cheol Lee
- Department of Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Bum Ahn
- Department of Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Hyung Kim
- Department of Internal Medicine and Institute of Gastroenterology, Graduate School of Medical Science, Brain Korea 21 Project, Seoul, Korea
| | - I Seul Park
- Department of Internal Medicine and Institute of Gastroenterology, Graduate School of Medical Science, Brain Korea 21 Project, Seoul, Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Graduate School of Medical Science, Brain Korea 21 Project, Seoul, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Duk Hwan Kim
- Digestive Disease Center, CHA Bundang Medical Center, CHA University, Seongnam, Korea
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Hussain T, Sanchez K, Crayton J, Saha D, Jeter C, Lu Y, Abba M, Seo R, Noebels JL, Fonken L, Aldaz CM. WWOX P47T partial loss-of-function mutation induces epilepsy, progressive neuroinflammation, and cerebellar degeneration in mice phenocopying human SCAR12. Prog Neurobiol 2023; 223:102425. [PMID: 36828035 PMCID: PMC10835625 DOI: 10.1016/j.pneurobio.2023.102425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/11/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
WWOX gene loss-of-function (LoF) has been associated with neuropathologies resulting in developmental, epileptic, and ataxic phenotypes of varying severity based on the level of WWOX dysfunction. WWOX gene biallelic germline variant p.Pro47Thr (P47T) has been causally associated with a new form of autosomal recessive cerebellar ataxia with epilepsy and intellectual disability (SCAR12, MIM:614322). This mutation affecting the WW1 protein binding domain of WWOX, impairs its interaction with canonical proline-proline-X-tyrosine motifs in partner proteins. We generated a mutant knock-in mouse model of Wwox P47T mutation that phenocopies human SCAR12. WwoxP47T/P47T mice displayed epilepsy, profound social behavior and cognition deficits, and poor motor coordination, and unlike KO models that survive only for 1 month, live beyond 1 year of age. These deficits progressed with age and mice became practically immobile, suggesting severe cerebellar dysfunction. WwoxP47T/P47T mice brains revealed signs of progressive neuroinflammation with elevated astro-microgliosis that increased with age. Cerebellar cortex displayed significantly reduced molecular and granular layer thickness and a strikingly reduced number of Purkinje cells with degenerated dendrites. Transcriptome profiling from various brain regions of WW domain LoF mice highlighted widespread changes in neuronal and glial pathways, enrichment of bioprocesses related to neuroinflammation, and severe cerebellar dysfunction. Our results show significant pathobiological effects and potential mechanisms through which WWOX partial LoF leads to epilepsy, cerebellar neurodegeneration, neuroinflammation, and ataxia. Additionally, the mouse model described here will be a useful tool to understand the role of WWOX in common neurodegenerative conditions in which this gene has been identified as a novel risk factor.
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Affiliation(s)
- Tabish Hussain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kevin Sanchez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer Crayton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Collene Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Martin Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, School of Medicine, Universidad de La Plata, La Plata 1900, Argentina
| | - Ryan Seo
- Developmental Neurogenetics Laboratory, Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey L Noebels
- Developmental Neurogenetics Laboratory, Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura Fonken
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - C Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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Steiner CA, Berinstein JA, Louissaint J, Higgins PDR, Spence JR, Shannon C, Lu C, Stidham RW, Fletcher JG, Bruining DH, Feagan BG, Jairath V, Baker ME, Bettenworth D, Rieder F. Biomarkers for the Prediction and Diagnosis of Fibrostenosing Crohn's Disease: A Systematic Review. Clin Gastroenterol Hepatol 2022; 20:817-846.e10. [PMID: 34089850 PMCID: PMC8636551 DOI: 10.1016/j.cgh.2021.05.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Intestinal strictures are a common complication of Crohn's disease (CD). Biomarkers of intestinal strictures would assist in their prediction, diagnosis, and monitoring. Herein we provide a comprehensive systematic review of studies assessing biomarkers that may predict or diagnose CD-associated strictures. METHODS We performed a systematic review of PubMed, EMBASE, ISI Web of Science, Cochrane Library, and Scopus to identify citations pertaining to biomarkers of intestinal fibrosis through July 6, 2020, that used a reference standard of full-thickness histopathology or cross-sectional imaging or endoscopy. Studies were categorized based on the type of biomarker they evaluated (serum, genetic, histopathologic, or fecal). RESULTS Thirty-five distinct biomarkers from 3 major groups were identified: serum (20 markers), genetic (9 markers), and histopathology (6 markers). Promising markers include cartilage oligomeric matrix protein, hepatocyte growth factor activator, and lower levels of microRNA-19-3p (area under the curves were 0.805, 0.738, and 0.67, respectively), and multiple anti-flagellin antibodies (A4-Fla2 [odds ratio, 3.41], anti Fla-X [odds ratio, 2.95], and anti-CBir1 [multiple]). Substantial heterogeneity was observed and none of the markers had undergone formal validation. Specific limitations to acceptance of these markers included failure to use a standardized definition of stricturing disease, lack of specificity, and insufficient relevance to the pathogenesis of intestinal strictures or incomplete knowledge regarding their operating properties. CONCLUSIONS There is a lack of well-defined studies on biomarkers of intestinal stricture. Development of reliable and accurate biomarkers of stricture is a research priority. Biomarkers can support the clinical management of CD patients and aid in the stratification and monitoring of patients during clinical trials of future antifibrotic drug candidates.
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Affiliation(s)
- Calen A Steiner
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
| | - Jeffrey A Berinstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jeremy Louissaint
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Peter D R Higgins
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Carol Shannon
- Taubman Health Sciences Library, University of Michigan, Ann Arbor, Michigan
| | - Cathy Lu
- Division of Gastroenterology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ryan W Stidham
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | | | - David H Bruining
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brian G Feagan
- Alimentiv Inc, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada; Department of Biostatistics and Epidemiology, Western University, London, Ontario, Canada
| | - Vipul Jairath
- Alimentiv Inc, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada; Department of Biostatistics and Epidemiology, Western University, London, Ontario, Canada
| | - Mark E Baker
- Section of Abdominal Imaging, Imaging Institute, Digestive Diseases and Surgery Institute and Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Dominik Bettenworth
- Department of Medicine B, Gastroenterology and Hepatology, University of Münster, Münster, Germany
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio; Department of Gastroenterology, Hepatology, and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio
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9
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Sudhakar P, Alsoud D, Wellens J, Verstockt S, Arnauts K, Verstockt B, Vermeire S. Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All. J Crohns Colitis 2022; 16:1306-1320. [PMID: 35150242 PMCID: PMC9426669 DOI: 10.1093/ecco-jcc/jjac027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease [IBD] has a multifactorial origin and originates from a complex interplay of environmental factors with the innate immune system at the intestinal epithelial interface in a genetically susceptible individual. All these factors make its aetiology intricate and largely unknown. Multi-omic datasets obtained from IBD patients are required to gain further insights into IBD biology. We here review the landscape of multi-omic data availability in IBD and identify barriers and gaps for future research. We also outline the various technical and non-technical factors that influence the utility and interpretability of multi-omic datasets and thereby the study design of any research project generating such datasets. Coordinated generation of multi-omic datasets and their systemic integration with clinical phenotypes and environmental exposures will not only enhance understanding of the fundamental mechanisms of IBD but also improve therapeutic strategies. Finally, we provide recommendations to enable and facilitate generation of multi-omic datasets.
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Affiliation(s)
- Padhmanand Sudhakar
- Corresponding author: Padhmanand Sudhakar, Translational Research in Gastrointestinal Disorders [TARGID], ON I, Herestraat 49, box 701, 3000 Leuven, Belgium. Tel.: 0032 [0]16 19 49 40;
| | - Dahham Alsoud
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Judith Wellens
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Kaline Arnauts
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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10
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Aldaz CM, Hussain T. WWOX Loss of Function in Neurodevelopmental and Neurodegenerative Disorders. Int J Mol Sci 2020; 21:E8922. [PMID: 33255508 PMCID: PMC7727818 DOI: 10.3390/ijms21238922] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 01/13/2023] Open
Abstract
The WWOX gene was initially discovered as a putative tumor suppressor. More recently, its association with multiple central nervous system (CNS) pathologies has been recognized. WWOX biallelic germline pathogenic variants have been implicated in spinocerebellar ataxia type 12 (SCAR12; MIM:614322) and in early infantile epileptic encephalopathy (EIEE28; MIM:616211). WWOX germline copy number variants have also been associated with autism spectrum disorder (ASD). All identified germline genomic variants lead to partial or complete loss of WWOX function. Importantly, large-scale genome-wide association studies have also identified WWOX as a risk gene for common neurodegenerative conditions such as Alzheimer's disease (AD) and multiple sclerosis (MS). Thus, the spectrum of CNS disorders associated with WWOX is broad and heterogeneous, and there is little understanding of potential mechanisms at play. Exploration of gene expression databases indicates that WWOX expression is comparatively higher in the human cerebellar cortex than in other CNS structures. However, RNA in-situ hybridization data from the Allen Mouse Brain Atlas show that specific regions of the basolateral amygdala (BLA), the medial entorhinal cortex (EC), and deep layers of the isocortex can be singled out as brain regions with specific higher levels of Wwox expression. These observations are in close agreement with single-cell RNA-seq data which indicate that neurons from the medial entorhinal cortex, Layer 5 from the frontal cortex as well as GABAergic basket cells and granule cells from cerebellar cortex are the specific neuronal subtypes that display the highest Wwox expression levels. Importantly, the brain regions and cell types in which WWOX is most abundantly expressed, such as the EC and BLA, are intimately linked to pathologies and syndromic conditions in turn associated with this gene, such as epilepsy, intellectual disability, ASD, and AD. Higher Wwox expression in interneurons and granule cells from cerebellum points to a direct link to the described cerebellar ataxia in cases of WWOX loss of function. We now know that total or partial impairment of WWOX function results in a wide and heterogeneous variety of neurodegenerative conditions for which the specific molecular mechanisms remain to be deciphered. Nevertheless, these observations indicate an important functional role for WWOX in normal development and function of the CNS. Evidence also indicates that disruption of WWOX expression at the gene or protein level in CNS has significant deleterious consequences.
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Affiliation(s)
- C. Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA;
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11
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Longhi MS, Kokkotou E. Lnc-ing RNA Expression with Disease Pathogenesis: MALAT1 and ANRIL in Ulcerative Colitis. Dig Dis Sci 2020; 65:3061-3063. [PMID: 32232616 PMCID: PMC7529722 DOI: 10.1007/s10620-020-06216-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Maria Serena Longhi
- Department of Anesthesia, Critical Care and Pain Medicine, Harvard Medical School, Boston, MA, USA
| | - Efi Kokkotou
- Department of Medicine, Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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12
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Which long noncoding RNAs and circular RNAs contribute to inflammatory bowel disease? Cell Death Dis 2020; 11:456. [PMID: 32541691 PMCID: PMC7295799 DOI: 10.1038/s41419-020-2657-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD), a chronic relapsing gastrointestinal inflammatory disease, mainly comprises ulcerative colitis (UC) and Crohn’s disease (CD). Although the mechanisms and pathways of IBD have been widely examined in recent decades, its exact pathogenesis remains unclear. Studies have focused on the discovery of new therapeutic targets and application of precision medicine. Recently, a strong connection between IBD and noncoding RNAs (ncRNAs) has been reported. ncRNAs include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). The contributions of lncRNAs and circRNAs in IBD are less well-studied compared with those of miRNAs. However, lncRNAs and circRNAs are likely to drive personalized therapy for IBD. They will enable accurate diagnosis, prognosis, and prediction of therapeutic responses and promote IBD therapy. Herein, we briefly describe the molecular functions of lncRNAs and circRNAs and provide an overview of the current knowledge of the altered expression profiles of lncRNAs and circRNAs in patients with IBD. Further, we discuss how these RNAs are involved in the nosogenesis of IBD and are emerging as biomarkers.
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13
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Annese V. Genetics and epigenetics of IBD. Pharmacol Res 2020; 159:104892. [PMID: 32464322 DOI: 10.1016/j.phrs.2020.104892] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel diseases (IBD) are chronic intermittent inflammatory disorders of the gastrointestinal tract of unknown etiology but a clear genetic predisposition. Prompted by the first investigations on IBD families and twins, the genetic and epigenetic studies have produced an unprecedented amount of information in comparison with other immune-mediated or complex diseases. New inflammatory pathways and possible mechanisms of action have been disclosed, potentially leading to new-targeted therapy. However, the identification of genetic markers due to the great disease heterogeneity and the overwhelming contribution of environmental risk factors has not modified yet the disease management. The possibility for the future of a better prediction of disease course, response to therapy and therapy-related adverse events may allow a more efficient and personalized strategy. This review will focus on more recent discoveries that may potentially be of relevance in daily clinical practice.
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Affiliation(s)
- Vito Annese
- Head of Gastroenterology and Medical Director, Valiant Clinic, Dubai, United Arab Emirates; CBP American Hospital, Dubai, United Arab Emirates; Aggregate Professor United Arabian Emirates University, College of Medicine & Health Science, Al Ain, United Arab Emirates.
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14
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Levels of Intestinal Inflammation and Fibrosis in Resection Specimens after Preoperative Anti-Tumor Necrosis Factor Alpha Treatment in Patients with Crohn's Disease: A Comparative Pilot Study. Surg Res Pract 2020; 2020:6085678. [PMID: 32149183 PMCID: PMC7054778 DOI: 10.1155/2020/6085678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/13/2020] [Accepted: 02/04/2020] [Indexed: 11/23/2022] Open
Abstract
Background Strictures are a common complication in Crohn's disease (CD), found in more than 50% of patients. They are characterized by the excessive deposition of extracellular proteins in the tissue as a result of the chronic inflammatory process. The effect of anti-tumor necrosis factor alpha (TNF-α) therapy on the development of fibrosis is not yet fully understood. Aim To investigate whether the degree of intestinal inflammation and fibrosis is correlated with preoperative anti-TNF-α) therapy on the development of fibrosis is not yet fully understood. Methods This unblinded, prospective, single tertiary center, pilot cohort study included all adult patients with CD who underwent elective, laparoscopic, or open intestinal resection. Preoperative investigations included measurement of blood TNF-α) therapy on the development of fibrosis is not yet fully understood. Results Histopathological specimens from 10 patients with CD who underwent ileocecal or ileocolic resections were retrieved. Four of those patients were on anti-TNF-α) therapy on the development of fibrosis is not yet fully understood. α) therapy on the development of fibrosis is not yet fully understood. α) therapy on the development of fibrosis is not yet fully understood. p=0.01). Anti-TNF-α) therapy on the development of fibrosis is not yet fully understood. α) therapy on the development of fibrosis is not yet fully understood. α) therapy on the development of fibrosis is not yet fully understood. Conclusions Patients who underwent preoperative anti-TNF-α treatment had a higher fibrosis score than controls.α) therapy on the development of fibrosis is not yet fully understood.
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15
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Lee HS, Cleynen I. Molecular Profiling of Inflammatory Bowel Disease: Is It Ready for Use in Clinical Decision-Making? Cells 2019; 8:E535. [PMID: 31167397 PMCID: PMC6627070 DOI: 10.3390/cells8060535] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a heterogeneous disorder in terms of age at onset, clinical phenotypes, severity, disease course, and response to therapy. This underlines the need for predictive and precision medicine that can optimize diagnosis and disease management, provide more cost-effective strategies, and minimize the risk of adverse events. Ideally, we can leverage molecular profiling to predict the risk to develop IBD and disease progression. Despite substantial successes of genome-wide association studies in the identification of genetic variants affecting IBD susceptibility, molecular profiling of disease onset and progression as well as of treatment responses has lagged behind. Still, thanks to technological advances and good study designs, predicting phenotypes using genomics and transcriptomics in IBD has been rapidly evolving. In this review, we summarize the current status of prediction of disease risk, clinical course, and response to therapy based on clinical case presentations. We also discuss the potential and limitations of the currently used approaches.
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Affiliation(s)
- Ho-Su Lee
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, Herestraat 49 - box 610, 3000 Leuven, Belgium.
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Isabelle Cleynen
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, Herestraat 49 - box 610, 3000 Leuven, Belgium.
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16
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Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vich Vila A, Collij V, Spekhorst LM, der Sloot KWJ V, Peters V, Van Dullemen HM, Visschedijk MC, EAM F, Swertz MA, Dijkstra G, Weersma RK. The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. BMC Gastroenterol 2019; 19:5. [PMID: 30621600 PMCID: PMC6325838 DOI: 10.1186/s12876-018-0917-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients. CONSTRUCTION AND CONTENT We initiated the 1000IBD project ( https://1000ibd.org ) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing. UTILITY AND DISCUSSION All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive ( https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models. CONCLUSIONS We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.
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Affiliation(s)
- Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - K. J. Van der Velde
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. D. Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - A. Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - V. Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - L. M. Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Van der Sloot KWJ
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - V. Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - H. M. Van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - M. C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - Festen EAM
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. A. Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - G. Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - R. K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
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