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Alenzi M, Schildkraut T, Hartley I, Badiani S, Ding NS, Rao V, Segal JP. The aetiology of pouchitis in patients with inflammatory bowel disease. Therap Adv Gastroenterol 2024; 17:17562848241249449. [PMID: 38812704 PMCID: PMC11135114 DOI: 10.1177/17562848241249449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/08/2024] [Indexed: 05/31/2024] Open
Abstract
Restorative proctocolectomy with ileal pouch-anal anastomosis is a treatment option for patients with refractory ulcerative colitis. Pouchitis is the most common complication, representing a spectrum of diseases ranging from acute antibiotic-responsive type to chronic antibiotic-refractory. Early accurate diagnosis using a combined assessment of symptoms, endoscopy and histology is important for both treatment and prognostication. Most patients respond well to antibiotic therapy; however, management of chronic antibiotic-refractory pouchitis remains a challenge, and treatment options are based on small studies. Pouchitis is thought to be driven by the interaction between genetics, the immune system and the environment but as yet a causal relationship has yet to be identified. Further longitudinal assessment of the pouch integrating new technologies may help us understand the factors driving pouchitis. This review outlines the currently understood risk factors and aetiology of pouchitis.
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Affiliation(s)
- Maram Alenzi
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Tamar Schildkraut
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, VIC, Australia
| | - Imogen Hartley
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, VIC, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Sarit Badiani
- Department of Surgery, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Nik Sheng Ding
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, VIC, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Vikram Rao
- Department of General Medicine, Western Health, Footscray, VIC, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
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Peters DE, Norris LD, Tenora L, Šnajdr I, Ponti AK, Zhu X, Sakamoto S, Veeravalli V, Pradhan M, Alt J, Thomas AG, Majer P, Rais R, McDonald C, Slusher BS. A gut-restricted glutamate carboxypeptidase II inhibitor reduces monocytic inflammation and improves preclinical colitis. Sci Transl Med 2023; 15:eabn7491. [PMID: 37556558 PMCID: PMC10661206 DOI: 10.1126/scitranslmed.abn7491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
There is an urgent need to develop therapeutics for inflammatory bowel disease (IBD) because up to 40% of patients with moderate-to-severe IBD are not adequately controlled with existing drugs. Glutamate carboxypeptidase II (GCPII) has emerged as a promising therapeutic target. This enzyme is minimally expressed in normal ileum and colon, but it is markedly up-regulated in biopsies from patients with IBD and preclinical colitis models. Here, we generated a class of GCPII inhibitors designed to be gut-restricted for oral administration, and we interrogated efficacy and mechanism using in vitro and in vivo models. The lead inhibitor, (S)-IBD3540, was potent (half maximal inhibitory concentration = 4 nanomolar), selective, gut-restricted (AUCcolon/plasma > 50 in mice with colitis), and efficacious in acute and chronic rodent colitis models. In dextran sulfate sodium-induced colitis, oral (S)-IBD3540 inhibited >75% of colon GCPII activity, dose-dependently improved gross and histologic disease, and markedly attenuated monocytic inflammation. In spontaneous colitis in interleukin-10 (IL-10) knockout mice, once-daily oral (S)-IBD3540 initiated after disease onset improved disease, normalized colon histology, and attenuated inflammation as evidenced by reduced fecal lipocalin 2 and colon pro-inflammatory cytokines/chemokines, including tumor necrosis factor-α and IL-17. Using primary human colon epithelial air-liquid interface monolayers to interrogate the mechanism, we further found that (S)-IBD3540 protected against submersion-induced oxidative stress injury by decreasing barrier permeability, normalizing tight junction protein expression, and reducing procaspase-3 activation. Together, this work demonstrated that local inhibition of dysregulated gastrointestinal GCPII using the gut-restricted, orally active, small-molecule (S)-IBD3540 is a promising approach for IBD treatment.
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Affiliation(s)
- Diane E. Peters
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren D. Norris
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lukáš Tenora
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 160 00 Prague, Czechia
| | - Ivan Šnajdr
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 160 00 Prague, Czechia
| | - András K. Ponti
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Xiaolei Zhu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shinji Sakamoto
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vijayabhaskar Veeravalli
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manisha Pradhan
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jesse Alt
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ajit G. Thomas
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 160 00 Prague, Czechia
| | - Rana Rais
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christine McDonald
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Barbara S. Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Gori SS, Thomas AG, Pal A, Wiseman R, Ferraris DV, Gao RD, Wu Y, Alt J, Tsukamoto T, Slusher BS, Rais R. D-DOPA Is a Potent, Orally Bioavailable, Allosteric Inhibitor of Glutamate Carboxypeptidase II. Pharmaceutics 2022; 14:pharmaceutics14102018. [PMID: 36297453 PMCID: PMC9608075 DOI: 10.3390/pharmaceutics14102018] [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: 08/14/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 12/02/2022] Open
Abstract
Glutamate carboxypeptidase-II (GCPII) is a zinc-dependent metalloenzyme implicated in numerous neurological disorders. The pharmacophoric requirements of active-site GCPII inhibitors makes them highly charged, manifesting poor pharmacokinetic (PK) properties. Herein, we describe the discovery and characterization of catechol-based inhibitors including L-DOPA, D-DOPA, and caffeic acid, with sub-micromolar potencies. Of these, D-DOPA emerged as the most promising compound, with good metabolic stability, and excellent PK properties. Orally administered D-DOPA yielded high plasma exposures (AUCplasma = 72.7 nmol·h/mL) and an absolute oral bioavailability of 47.7%. Unfortunately, D-DOPA brain exposures were low with AUCbrain = 2.42 nmol/g and AUCbrain/plasma ratio of 0.03. Given reports of isomeric inversion of D-DOPA to L-DOPA via D-amino acid oxidase (DAAO), we evaluated D-DOPA PK in combination with the DAAO inhibitor sodium benzoate and observed a >200% enhancement in both plasma and brain exposures (AUCplasma = 185 nmol·h/mL; AUCbrain = 5.48 nmol·h/g). Further, we demonstrated GCPII target engagement; orally administered D-DOPA with or without sodium benzoate caused significant inhibition of GCPII activity. Lastly, mode of inhibition studies revealed D-DOPA to be a noncompetitive, allosteric inhibitor of GCPII. To our knowledge, this is the first report of D-DOPA as a distinct scaffold for GCPII inhibition, laying the groundwork for future optimization to obtain clinically viable candidates.
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Affiliation(s)
- Sadakatali S. Gori
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ajit G. Thomas
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Arindom Pal
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Robyn Wiseman
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dana V. Ferraris
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Run-duo Gao
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ying Wu
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jesse Alt
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Takashi Tsukamoto
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Correspondence: (B.S.S.); (R.R.)
| | - Rana Rais
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Correspondence: (B.S.S.); (R.R.)
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Perez K, Ngollo M, Rabinowitz K, Hammoudi N, Seksik P, Xavier RJ, Daly MJ, Dotan I, Le Bourhis L, Allez M. Meta-Analysis of IBD Gut Samples Gene Expression Identifies Specific Markers of Ileal and Colonic Diseases. Inflamm Bowel Dis 2022; 28:775-782. [PMID: 34928348 DOI: 10.1093/ibd/izab311] [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: 08/02/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) are characterized by chronic inflammation and tissue damages in limited segments of the digestive tract. Pathogenesis in the tissue and mucosal inflammation probably differs according to disease location. Our aim was to further analyze transcriptomic profiles in different locations of IBD, differentiating ulcerative colitis (UC), colonic Crohn's disease (CD), ileal CD, and pouchitis, with respect to normal colonic and ileal mucosa. We thus performed a meta-analysis focusing on specific transcriptomic signatures of ileal and colonic diseases. METHODS We identified 5 cohorts with available transcriptomic data in ileal or colonic samples from active IBD and non-IBD control samples. The meta-analysis was performed on 1047 samples. In each cohort separately, we compared gene expression in CD ileitis and normal ileum; in CD colitis, UC, and normal colon; and finally in pouchitis and normal ileum. RESULTS We identified specific markers of ileal (FOLH1, CA2) and colonic (REG3A) inflammation and showed that, with disease, some cells from the ileum start to express colonic markers. We confirmed by immunohistochemistry that these markers were specifically present in ileal or colonic diseases. We highlighted that, overall, colonic CD resembles UC and is distinct from ileal CD, which is in turn closer to pouchitis. CONCLUSIONS We demonstrated that ileal and colonic diseases exhibit specific signatures, independent of their initial clinical classification. This supports molecular, rather than clinical, disease stratification, and may be used to design drugs specifically targeting ileal or colonic diseases.
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Affiliation(s)
- Kevin Perez
- EMily (INSERM U1160), Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Marjolaine Ngollo
- EMily (INSERM U1160), Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Keren Rabinowitz
- Division of Gastroenterology, Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nassim Hammoudi
- EMily (INSERM U1160), Institut de Recherche Saint-Louis, Université de Paris, Paris, France.,Gastroenterology Department, Hôpital Saint-Louis, Asisstance Publique-Hôpitaux de Paris, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Hôpital Saint-Antoine, Université de la Sorbonne, Asisstance Publique-Hôpitaux de Paris, Paris, France
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Finnish Institute for Molecular Medicine, Helsinki, Finland
| | - Iris Dotan
- Division of Gastroenterology, Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lionel Le Bourhis
- EMily (INSERM U1160), Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Matthieu Allez
- EMily (INSERM U1160), Institut de Recherche Saint-Louis, Université de Paris, Paris, France.,Gastroenterology Department, Hôpital Saint-Louis, Asisstance Publique-Hôpitaux de Paris, Paris, France
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5
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Honig G, Larkin PB, Heller C, Hurtado-Lorenzo A. Research-Based Product Innovation to Address Critical Unmet Needs of Patients with Inflammatory Bowel Diseases. Inflamm Bowel Dis 2021; 27:S1-S16. [PMID: 34791292 PMCID: PMC8922161 DOI: 10.1093/ibd/izab230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 12/09/2022]
Abstract
Despite progress in recent decades, patients with inflammatory bowel diseases face many critical unmet needs, demonstrating the limitations of available treatment options. Addressing these unmet needs will require interventions targeting multiple aspects of inflammatory bowel disease pathology, including disease drivers that are not targeted by available therapies. The vast majority of late-stage investigational therapies also focus primarily on a narrow range of fundamental mechanisms. Thus, there is a pressing need to advance to clinical stage differentiated investigational therapies directly targeting a broader range of key mechanistic drivers of inflammatory bowel diseases. In addition, innovations are critically needed to enable treatments to be tailored to the specific underlying abnormal biological pathways of patients; interventions with improved safety profiles; biomarkers to develop prognostic, predictive, and monitoring tests; novel devices for nonpharmacological approaches such as minimally invasive monitoring; and digital health technologies. To address these needs, the Crohn's & Colitis Foundation launched IBD Ventures, a venture philanthropy-funding mechanism, and IBD Innovate®, an innovative, product-focused scientific conference. This special IBD Innovate® supplement is a collection of articles reflecting the diverse and exciting research and development that is currently ongoing in the inflammatory bowel disease field to deliver innovative and differentiated products addressing critical unmet needs of patients. Here, we highlight the pipeline of new product opportunities currently advancing at the preclinical and early clinical development stages. We categorize and describe novel and differentiated potential product opportunities based on their potential to address the following critical unmet patient needs: (1) biomarkers for prognosis of disease course and prediction/monitoring of treatment response; (2) restoration of eubiosis; (3) restoration of barrier function and mucosal healing; (4) more effective and safer anti-inflammatories; (5) neuromodulatory and behavioral therapies; (6) management of disease complications; and (7) targeted drug delivery.
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Wang J, Lv M, He L, Wang X, Lan Y, Chen J, Chen M, Zhang C, Tang R, Zhou D, Deng X, Li J, Guo T, Price M, Yue B, Fan Z. Transcriptomic landscape of persistent diarrhoea in rhesus macaques and comparison with humans and mouse models with inflammatory bowel disease. Gene 2021; 800:145837. [PMID: 34274469 DOI: 10.1016/j.gene.2021.145837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/26/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
Diarrhoea is a widespread disease in captive rhesus macaques (Macaca mulatta) and a small proportion of individuals may experience persistent diarrhoea. Persistent diarrhoea can lead to a compromised immune system, intestinal inflammation and malnutrition. We analyzed the blood transcriptomes of 10 persistent diarrhoeal and 12 healthy rhesus macaques to investigate the gene expression differences between the two groups. We identified 330 DEGs between persistent diarrhoeal and healthy rhesus macaques. The 211 up-regulated DEGs in the diarrhoeal group were mainly enriched in immune-related and interleukin-related categories. Among them, three interleukin (IL) 18 related DEGs (IL18, IL18R1, and IL18BP) played important roles in actively regulating pro-inflammatory responses. Interestingly, the up- and down-regulated DEGs were both enriched in the same immune-related categories. Thus, we applied a new method to examine the distribution of DEGs in all child categories. We found that interleukin and T cell related categories were mainly occupied by up-regulated DEGs, while immunoglobulin production and B cell related categories were enriched by down-regulated DEGs. We also compared rhesus macaque DEGs with the DEGs of inflammatory bowel disease (IBD) humans and IBD mouse models and found that 30-40% of macaque DEGs were shared with IBD humans and mouse models. In conclusion, our results showed that there were significant immune differences between persistent diarrhoeal rhesus macaques and healthy macaques, which was similar to the expression differences in IBD patients and mouse models.
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Affiliation(s)
- Jiao Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Mingyi Lv
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Lewei He
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xinqi Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Jieyun Chen
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Minghui Chen
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Chunhui Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Ruixiang Tang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Dan Zhou
- The First People's Hospital of Neijiang, Neijiang 641000, Sichuan, China
| | - Xiaoyang Deng
- Lasa Sunshine Maternity Hospital, Lasa 850000, Xizang, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Tao Guo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
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Multi-factor mediated functional modules identify novel classification of ulcerative colitis and functional gene panel. Sci Rep 2021; 11:5669. [PMID: 33707495 PMCID: PMC7952401 DOI: 10.1038/s41598-021-85000-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/23/2021] [Indexed: 12/16/2022] Open
Abstract
Ulcerative colitis is a chronic, idiopathic, and inflammatory disease of the rectal and colonic mucosa, the behavior of which is of heterogeneity in individuals. Here, we explored the multifactor-mediated functional modules associated with ulcerative colitis classification in the whole genome. Datasets downloaded from the GEO database were used to identify differentially expressed genes between ulcerative colitis patients and healthy individuals initially, followed by acquisition of the remaining ulcerative colitis -related genes from the OMIM and STRING databases. The results identified 914 ulcerative colitis-related genes, of which 60 were differentially expressed genes obtained from GEO datasets. Through weighted co-expression network analysis of ulcerative colitis-related genes, four modules were obtained, three of which were related to ulcerative colitis. Following interactions between microRNA, long noncoding RNA, transcription factors, and module hub genes were predicted and used to construct ulcerative colitis multifactor networks. Additionally, we performed consensus clustering of the ulcerative colitis samples. The results revealed that ulcerative colitis could be divided into four subtypes, with six hub genes identified as potential biomarkers for classification. These findings offer novel insights into ulcerative colitis and a basis for disease classification of ulcerative colitis.
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Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease. mSystems 2021; 6:6/2/e00984-20. [PMID: 33653942 PMCID: PMC8546988 DOI: 10.1128/msystems.00984-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Crohn's disease (CD), ulcerative colitis (UC), and pouchitis are multifactorial and chronic inflammatory bowel diseases (IBD). Pouchitis develops in former UC patients after proctocolectomy and ileal-pouch-anal anastomosis and is characterized by inflammation of the previously normal small intestine comprising the pouch. The extent to which microbial functional alteration (dysbiosis) in pouchitis resembles that of CD or UC has not been investigated, and the pathogenesis of pouchitis remains unknown. We collected 208 fecal metagenomes from 69 patients with a pouch (normal pouch and pouchitis) and compared them to publicly available metagenomes of patients with CD (n = 88), patients with UC (n = 76), and healthy controls (n = 56). Patients with pouchitis presented the highest alterations in species, metabolic pathways, and enzymes, which was correlated with intestinal inflammation. Ruminococcus gnavus strains encoding mucin-degrading glycoside hydrolases were highly enriched in pouchitis. Butyrate and secondary bile acid biosynthesis pathways were decreased in IBD phenotypes and were especially low in pouchitis. Pathways such as amino acid biosynthesis and degradation of aromatic compounds and sugars, encoded by members of the Enterobacteriaceae, were enriched in pouch and CD but not in UC. We developed microbial feature-based classifiers that can distinguish between patients with a normal pouch and pouchitis and identified species and genes that were predictive of pouchitis. We propose that the noninflamed pouch is already dysbiotic and microbially is similar to CD. Our study reveals microbial functions that outline the pathogenesis of pouchitis and suggests bacterial groups and functions that could be targeted for intervention to attenuate small intestinal inflammation present in pouchitis and CD. IMPORTANCE Crohn's disease (CD), ulcerative colitis (UC), and pouchitis are chronic inflammatory conditions of the bowel. Pouchitis develops in former UC patients after proctocolectomy and ileal-pouch-anal anastomosis and is characterized by inflammation of the previously normal small intestine comprising the pouch. The extent to which microbial dysbiosis in patients with pouchitis resembles that of CD or UC and the pathogenesis of pouchitis remains unclear. We investigated the functions in the gut microbiomes of these patients using metagenomics. We found that the noninflamed pouch is already dysbiotic and microbially is similar to CD. Our study reveals microbial functions with a potential role in pouchitis pathogenesis such as depletion in butyrate and secondary bile acid synthesis and enrichment of amino acid synthesis and degradation of aromatic compounds, encoded by members of the Enterobacteriaceae. We developed microbial feature-based classifiers that can distinguish between patients with a normal pouch and pouchitis and identified species and genes that were predictive of pouchitis. We suggest species and functions that could be targeted for intervention to attenuate small intestinal inflammation present in pouchitis and CD.
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Functional Anatomical Changes in Ulcerative Colitis Patients Determine Their Gut Microbiota Composition and Consequently the Possible Treatment Outcome. Pharmaceuticals (Basel) 2020; 13:ph13110346. [PMID: 33126430 PMCID: PMC7692875 DOI: 10.3390/ph13110346] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Gut microbial composition alters in some special situations, such as in ulcerative colits (UC) after total proctocolectomy and ileal pouch-anal anastomosis (IPAA) surgery. The aim of our study was to determine the composition of the intestinal microbiome in UC patients after IPAA surgery, compared with UC patients, familial adenomatous polyposis (FAP) patients after IPAA surgery and healthy controls. Clinical data of patients, blood and faecal samples were collected. Faecal microbiota structure was determined by sequencing the V4 hypervariable region of the 16S rRNA gene. Overall, 56 patients were enrolled. Compared to the Healthy group, both the Pouch active and UC active groups had higher Enterobacteriaceae, Enterococcaceae and Pasteurellaceae abundance. The Pouch and UC groups showed distinct separation based on their alpha and beta bacterial diversities. The UC group had higher Prevotellaceae, Rikenellaceae, Ruminococcaceae abundance compared to the Pouch active group. Pouch and FAP participants showed similar bacterial community composition. There was no significant difference in the bacterial abundance between the active and inactive subgroups of the Pouch or UC groups. Gut microbiome and anatomical status together construct a functional unit that has influence on diversity, in addition to intestinal inflammation that is a part of the pathomechanism in UC.
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10
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Adherence to the Mediterranean diet is associated with decreased fecal calprotectin in patients with ulcerative colitis after pouch surgery. Eur J Nutr 2019; 59:3183-3190. [PMID: 31813010 DOI: 10.1007/s00394-019-02158-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Mediterranean diet (MED) is associated with health benefits, yet scarce data exist regarding the role of MED in inflammatory bowel diseases (IBD). Herein, we aimed to evaluate the association between MED and inflammatory markers in patients with IBD after pouch surgery. METHODS Consecutive patients after pouch surgery due to ulcerative colitis (UC) were recruited at a comprehensive pouch clinic. Adherence to MED was calculated according to MED score, ranging from 0 (low adherence) to 9 (high adherence), based on food-frequency questionnaires. Pouch behavior was defined as normal pouch (NP) or pouchitis based on Pouchitis Disease Activity Index (PDAI) and disease activity was defined as active or inactive. C-reactive protein (CRP) and fecal calprotectin were assessed. RESULTS Overall 153 patients were enrolled (male gender 47%; mean age 46 ± 14 years; mean pouch age 9.5 ± 7 years). MED scores were higher in patients with normal vs. elevated CRP and calprotectin levels (4.6 ± 1.8 vs. 4.4 ± 1.6, p = 0.28; 4.8 ± 1.8 vs. 4.07 ± 1.7, p < 0.05, respectively). In a multivariate regression, MED score was associated with decreased calprotectin levels (OR = 0.74 [0.56-0.99]). Adherence to MED was associated with dietary fiber and antioxidants intake. Finally, in a subgroup of patients with NP followed up for 8 years, higher adherence to MED trended to be inversely associated with the onset of pouchitis (log rank = 0.17). CONCLUSIONS In patients with UC after pouch surgery, adherence to MED is associated with decreased calprotectin levels. Thus, MED may have a role in modifying intestinal inflammation in IBD.
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11
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Vornov JJ, Peters D, Nedelcovych M, Hollinger K, Rais R, Slusher BS. Looking for Drugs in All the Wrong Places: Use of GCPII Inhibitors Outside the Brain. Neurochem Res 2019; 45:1256-1267. [PMID: 31749072 DOI: 10.1007/s11064-019-02909-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
In tribute to our friend and colleague Michael Robinson, we review his involvement in the identification, characterization and localization of the metallopeptidase glutamate carboxypeptidase II (GCPII), originally called NAALADase. While Mike was characterizing NAALADase in the brain, the protein was independently identified by other laboratories in human prostate where it was termed prostate specific membrane antigen (PSMA) and in the intestines where it was named Folate Hydrolase 1 (FOLH1). It was almost a decade to establish that NAALADase, PSMA, and FOLH1 are encoded by the same gene. The enzyme has emerged as a therapeutic target outside of the brain, with the most notable progress made in the treatment of prostate cancer and inflammatory bowel disease (IBD). PSMA-PET imaging with high affinity ligands is proving useful for the clinical diagnosis and staging of prostate cancer. A molecular radiotherapy based on similar ligands is in trials for metastatic castration-resistant prostate cancer. New PSMA inhibitor prodrugs that preferentially block kidney and salivary gland versus prostate tumor enzyme may improve the clinical safety of this radiotherapy. The wide clinical use of PSMA-PET imaging in prostate cancer has coincidentally led to clinical documentation of GCPII upregulation in a wide variety of tumors and inflammatory diseases, likely associated with angiogenesis. In IBD, expression of the FOLH1 gene that codes for GCPII is strongly upregulated, as is the enzymatic activity in diseased patient biopsies. In animal models of IBD, GCPII inhibitors show substantial efficacy, suggesting potential theranostic use of GCPII ligands for IBD.
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Affiliation(s)
- James J Vornov
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Medpace, Cincinnati, OH, USA
| | - Diane Peters
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Mike Nedelcovych
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kristen Hollinger
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Rana Rais
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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12
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Godny L, Maharshak N, Reshef L, Goren I, Yahav L, Fliss-Isakov N, Gophna U, Tulchinsky H, Dotan I. Fruit Consumption is Associated with Alterations in Microbial Composition and Lower Rates of Pouchitis. J Crohns Colitis 2019; 13:1265-1272. [PMID: 30828722 DOI: 10.1093/ecco-jcc/jjz053] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Patients with ulcerative colitis [UC] who undergo proctocolectomy with an ileal pouch-anal anastomosis commonly develop pouch inflammation [pouchitis]. Pouchitis develops in a previously normal small intestine and may involve environmental factors. We explored whether diet and microbiota alterations contributed to the pathogenesis of pouchitis. METHODS Patients were recruited and prospectively followed at a comprehensive pouch clinic. Pouch behaviour was clinically defined as a normal pouch [NP] or pouchitis. Patients completed Food Frequency Questionnaires [FFQs]. Faecal samples were analysed for microbial composition [16S rRNA gene pyrosequencing]. RESULTS Nutritional evaluation was performed in 172 patients [59% females], and of these, faecal microbial analysis was performed in 75 patients (microbiota cohort: NP [n = 22], pouchitis [n = 53]). Of the entire cohort, a subgroup of 39 [22.6%] patients had NP at recruitment [NP cohort]. Of these, 5 [12.8%] developed pouchitis within a year. Patients at the lowest tertile of fruit consumption [<1.45 servings/day] had higher rates of pouchitis compared with those with higher consumption [30.8% vs 3.8%, log rank, p = 0.03]. Fruit consumption was correlated with microbial diversity [r = 0.35, p = 0.002] and with the abundance of several microbial genera, including Faecalibacterium [r = 0.29, p = 0.01], Lachnospira [r = 0.38, p = 0.001], and a previously uncharacterized genus from the Ruminococcaceae family [r = 0.25, p = 0.05]. Reduction in fruit consumption over time was associated with disease recurrence and with reduced microbial diversity [Δ = -0.8 ± 0.3, p = 0.008]. CONCLUSIONS Fruit consumption is associated with modification of microbial composition, and lower consumption was correlated with the development of pouchitis. Thus, fruit consumption may protect against intestinal inflammation via alteration of microbial composition.
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Affiliation(s)
- L Godny
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - N Maharshak
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Reshef
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - I Goren
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Yahav
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - N Fliss-Isakov
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - U Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - H Tulchinsky
- Colorectal Unit, Department of Surgery, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - I Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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13
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Dash RP, Tichý T, Veeravalli V, Lam J, Alt J, Wu Y, Tenora L, Majer P, Slusher BS, Rais R. Enhanced Oral Bioavailability of 2-(Phosphonomethyl)-pentanedioic Acid (2-PMPA) from its (5-Methyl-2-oxo-1,3-dioxol-4-yl)methyl (ODOL)-Based Prodrugs. Mol Pharm 2019; 16:4292-4301. [PMID: 31503493 DOI: 10.1021/acs.molpharmaceut.9b00637] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
2-(Phosphonomethyl)-pentanedioic acid (2-PMPA) is a potent (IC50 = 300 pM) and selective inhibitor of glutamate carboxypeptidase II (GCPII) with efficacy in multiple neurological and psychiatric disease preclinical models and more recently in models of inflammatory bowel disease (IBD) and cancer. 2-PMPA (1), however, has not been clinically developed due to its poor oral bioavailability (<1%) imparted by its four acidic functionalities (c Log P = -1.14). In an attempt to improve the oral bioavailability of 2-PMPA, we explored a prodrug approach using (5-methyl-2-oxo-1,3-dioxol-4-yl)methyl (ODOL), an FDA-approved promoiety, and systematically masked two (2), three (3), or all four (4) of its acidic groups. The prodrugs were evaluated for in vitro stability and in vivo pharmacokinetics in mice and dog. Prodrugs 2, 3, and 4 were found to be moderately stable at pH 7.4 in phosphate-buffered saline (57, 63, and 54% remaining at 1 h, respectively), but rapidly hydrolyzed in plasma and liver microsomes, across species. In vivo, in a single time-point screening study in mice, 10 mg/kg 2-PMPA equivalent doses of 2, 3, and 4 delivered significantly higher 2-PMPA plasma concentrations (3.65 ± 0.37, 3.56 ± 0.46, and 17.3 ± 5.03 nmol/mL, respectively) versus 2-PMPA (0.25 ± 0.02 nmol/mL). Given that prodrug 4 delivered the highest 2-PMPA levels, we next evaluated it in an extended time-course pharmacokinetic study in mice. 4 demonstrated an 80-fold enhancement in exposure versus oral 2-PMPA (AUC0-t: 52.1 ± 5.9 versus 0.65 ± 0.13 h*nmol/mL) with a calculated absolute oral bioavailability of 50%. In mouse brain, 4 showed similar exposures to that achieved with the IV route (1.2 ± 0.2 versus 1.6 ± 0.2 h*nmol/g). Further, in dogs, relative to orally administered 2-PMPA, 4 delivered a 44-fold enhanced 2-PMPA plasma exposure (AUC0-t for 4: 62.6 h*nmol/mL versus AUC0-t for 2-PMPA: 1.44 h*nmol/mL). These results suggest that ODOL promoieties can serve as a promising strategy for enhancing the oral bioavailability of multiply charged compounds, such as 2-PMPA, and enable its clinical translation.
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Affiliation(s)
| | - Tomáš Tichý
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic v.v.i. , Prague 166 10 , Czech Republic
| | | | | | | | | | - Lukáš Tenora
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic v.v.i. , Prague 166 10 , Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic v.v.i. , Prague 166 10 , Czech Republic
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14
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Verstockt S, De Hertogh G, Van der Goten J, Verstockt B, Vancamelbeke M, Machiels K, Van Lommel L, Schuit F, Van Assche G, Rutgeerts P, Ferrante M, Vermeire S, Arijs I, Cleynen I. Gene and Mirna Regulatory Networks During Different Stages of Crohn's Disease. J Crohns Colitis 2019; 13:916-930. [PMID: 30657881 DOI: 10.1093/ecco-jcc/jjz007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 11/09/2018] [Accepted: 01/11/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Early treatment of Crohn's disease [CD] is required in order to optimize patient outcomes. To this end, we need to gain a better understanding of the molecular changes at the onset of CD. METHODS As a model for the earliest mucosal CD lesions, we study post-operative recurrent CD [Rutgeerts score ≥ i2b]. We are the first to analyse gene and microRNA [miRNA] expression profiles in ileal biopsies from these patients, and compare them with those of newly diagnosed [≤18 months] and late-stage [>10 years after diagnosis] CD patients. RESULTS Except for one gene [WNT5A], there are no differential genes in CD patients without post-operative recurrence [i0], showing that previous disease did not influence gene expression in the neoterminal ileum, and that this model can be used to study early mucosal CD lesions. Gene expression and co-expression network dysregulation is more pronounced in newly diagnosed and late-stage CD than in post-operative recurrent CD, with most important modules associated with [a]granulocyte adhesion/diapedesis, and cholesterol biosynthesis. In contrast, we found a role for snoRNAs/miRNAs in recurrent CD, highlighting the potential importance of regulatory RNAs in early disease stages. Immunohistochemistry confirmed the expression of key dysregulated genes in damaged/regenerating epithelium and immune cells in recurrent CD. CONCLUSIONS Aside from regulatory RNAs, there are no clear gene signatures separating post-operative recurrent, newly diagnosed, and late-stage CD. The relative contribution of dysregulated genes and networks differs, and suggests that surgery may reset the disease at the mucosal site, and therefore post-operative recurrent CD might be a good model a good model to study to study early mucosal CD lesions.
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Affiliation(s)
- Sare Verstockt
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Department of Morphology and Molecular Pathology, University Hospitals, Leuven, Belgium.,Department of Imaging & Pathology, Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
| | - Jan Van der Goten
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals, KU Leuven, Leuven, Belgium
| | - Maaike Vancamelbeke
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium
| | - Kathleen Machiels
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium
| | - Leentje Van Lommel
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frans Schuit
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Gert Van Assche
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals, KU Leuven, Leuven, Belgium
| | - Paul Rutgeerts
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals, KU Leuven, Leuven, Belgium
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals, KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals, KU Leuven, Leuven, Belgium
| | - Ingrid Arijs
- Translational Research Center for Gastrointestinal Disorders [TARGID], Department of Chronic Diseases, Metabolism & Aging [CHROMETA], KU Leuven, Leuven, Belgium.,Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium; Jessa Hospital, Hasselt, Belgium
| | - Isabelle Cleynen
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
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15
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Ben-Shachar S, Finezilber Y, Elad H, Rabinowitz K, Goren I, Isakov O, Yanai H, Dotan I. Genotype-Serotype Interactions Shed Light on Genetic Components of Inflammatory Bowel Diseases. Inflamm Bowel Dis 2019; 25:336-344. [PMID: 30265311 DOI: 10.1093/ibd/izy231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND We evaluated the impact of variations in ATG16L1 and NOD2 and genes on serologic responses in patients with inflammatory bowel disease (IBD). METHODS We recruited 308 IBD patients: 130 with Crohn's disease (CD), 67 with ulcerative colitis (UC), 111 with UC and an ileal pouch (UC-pouch), and 74 healthy controls. NOD2 variants (1007fs, G908R, R702W) and the ATG16L1 A300T variant were analyzed. The antiglycan antibodies anti-Saccharomyces cerevisiae (ASCA), antilaminaribioside (ALCA), antichitobioside (ACCA), and antimannobioside carbohydrate (AMCA) were analyzed by enzyme-linked immunosorbent assay. RESULTS Antichitobioside was positive in 28% of patients with CD carrying the ATG16L1 A300T variant (either heterozygote or homozygote) compared with only 3% in those without the variant (P < 0.001). Anti-Saccharomyces cerevisiae was positive in 86% of patients with CD carrying the NOD2 1007fs variant compared with 36% in those without the variant (P < 0.001). UC-pouch patients with the NOD2 1007fs variant had elevated ASCA and ALCA levels compared with those without the variant (50% vs 7%, P = 0.004, and 50% vs 8%, P = 0.006, respectively). Importantly, ATG16L1 A300T and NOD2 variants were not associated with serologic responses in healthy controls and unoperated UC patients. Multivariate analysis demonstrated that these genetic variants are the main factors associated with specific antiglycan antibody levels in CD and pouch patients. CONCLUSIONS Genetic variants may have disease-specific phenotypic (serotypic) effects. This implies that genetic risk factors may also be disease modifiers.
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Affiliation(s)
| | - Yael Finezilber
- IBD Center, Department of Gastroenterology and Liver Diseases
| | - Hofit Elad
- IBD Center, Department of Gastroenterology and Liver Diseases
| | | | - Idan Goren
- IBD Center, Department of Gastroenterology and Liver Diseases
| | | | - Henit Yanai
- IBD Center, Department of Gastroenterology and Liver Diseases
| | - Iris Dotan
- IBD Center, Department of Gastroenterology and Liver Diseases
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16
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Sherman Horev H, Rabinowitz KM, Elad H, Barkan R, Ben-Shachar S, Pasmanik Chor M, Dotan I. Increase in Processing Factors Is Involved in Skewed MicroRNA Expression in Patients with Ulcerative Colitis Who Develop Small Intestine Inflammation after Pouch Surgery. Inflamm Bowel Dis 2018; 24:1045-1054. [PMID: 29688474 DOI: 10.1093/ibd/izy034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND A large-scale increase in microRNA (miRNA) expression was observed in patients with ulcerative colitis who underwent pouch surgery and developed inflammation of the pouch (pouchitis). In this study, we assessed miRNA expression in these patients and investigated how regulation of its expression changes in the setting of pouchitis. METHODS Autologous samples that included mucosal biopsies, peripheral blood cells, and plasma were collected from the patients. Candidate primary and mature miRNA expressions were analyzed by quantitative polymerase chain reaction. A human intestinal epithelial cell line was used to test DICER activity, and the expression of key miRNA processing factors was analyzed by Western blot. miRNA-424 and its potential target serotonin reuptake transporter (SERT) expressions were examined by quantitative reverse transcription polymerase chain reaction and Western blot in human pouch tissues and in a human intestinal epithelial cell line stimulated with inflammatory cytokines TNF-α, IL-1β, and INF-γ. RESULTS Candidate miRNA expression and protein expression of DICER-1, EXPORTIN-5, and AGO-2 were increased in association with pouch inflammation. Similarly, inflammatory cytokines increased protein expression of DICER-1, EXPORTIN-5, and AGO-2 and DICER activity in the epithelial cell line. The miRNA-424 expression increased whereas SERT expression decreased in the patients' mucosa. Similarly, incubation of the epithelial cell line with inflammatory cytokines resulted in increased miRNA-424 and decreased SERT mRNA and protein expression. CONCLUSIONS The miRNA expression and processing are augmented in the inflamed intestinal mucosa of patients with pouchitis. These alterations are accompanied by increased expression of proteins involved in miRNA processing, suggesting that pouch inflammation contributes to miRNA processing and expression.
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Affiliation(s)
- Hadas Sherman Horev
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Keren M Rabinowitz
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hofit Elad
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Revital Barkan
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Medical Center, Tel Aviv, Israel, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Iris Dotan
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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17
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Yeheskel A, Reiter A, Pasmanik-Chor M, Rubinstein A. Simulation and visualization of multiple KEGG pathways using BioNSi. F1000Res 2017; 6:2120. [PMID: 29946422 PMCID: PMC6008849 DOI: 10.12688/f1000research.13254.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2018] [Indexed: 12/18/2022] Open
Abstract
Motivation: Many biologists are discouraged from using network simulation tools because these require manual, often tedious network construction. This situation calls for building new tools or extending existing ones with the ability to import biological pathways previously deposited in databases and analyze them, in order to produce novel biological insights at the pathway level. Results: We have extended a network simulation tool (BioNSi), which now allows merging of multiple pathways from the KEGG pathway database into a single, coherent network, and visualizing its properties. Furthermore, the enhanced tool enables loading experimental expression data into the network and simulating its dynamics under various biological conditions or perturbations. As a proof of concept, we tested two sets of published experimental data, one related to inflammatory bowel disease condition and the other to breast cancer treatment. We predict some of the major observations obtained following these laboratory experiments, and provide new insights that may shed additional light on these results. Tool requirements: Cytoscape 3.x, JAVA 8 Availability: The tool is freely available at
http://bionsi.wix.com/bionsi, where a complete user guide and a step-by-step manual can also be found.
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Affiliation(s)
- Adva Yeheskel
- Bioinformatics unit, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Adam Reiter
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | | | - Amir Rubinstein
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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18
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Date AA, Rais R, Babu T, Ortiz J, Kanvinde P, Thomas AG, Zimmermann SC, Gadiano AJ, Halpert G, Slusher BS, Ensign LM. Local enema treatment to inhibit FOLH1/GCPII as a novel therapy for inflammatory bowel disease. J Control Release 2017; 263:132-138. [PMID: 28159515 PMCID: PMC5661937 DOI: 10.1016/j.jconrel.2017.01.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/17/2017] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
Abstract
Here we evaluate the potential for local administration of a small molecule FOLH1/GCPII inhibitor 2-phosphonomethyl pentanedioic acid (2-PMPA) as a novel treatment for inflammatory bowel disease (IBD). We found that FOLH1/GCPII enzyme activity was increased in the colorectal tissues of mice with TNBS-induced colitis, and confirmed that 2-PMPA inhibited FOLH1/GCPII enzyme activity ex vivo. In order to maximize local enema delivery of 2-PMPA, we studied the effect of vehicle tonicity on the absorption of 2-PMPA in the colon. Local administration of 2-PMPA in a hypotonic enema vehicle resulted in increased colorectal tissue absorption at 30min compared to 2-PMPA administered in an isotonic enema vehicle. Furthermore, local delivery of 2-PMPA in hypotonic enema vehicle resulted in prolonged drug concentrations for at least 24h with minimal systemic exposure. Finally, daily treatment with the hypotonic 2-PMPA enema ameliorated macroscopic and microscopic symptoms of IBD in the TNBS-induced colitis mouse model, indicating the potential of FOLH1/GCPII inhibitors for the local treatment of IBD.
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Affiliation(s)
- Abhijit A Date
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA; Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N. Broadway, Baltimore, MD 21231, USA
| | - Rana Rais
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taarika Babu
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jairo Ortiz
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA
| | - Pranjali Kanvinde
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA
| | - Ajit G Thomas
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah C Zimmermann
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexandra J Gadiano
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gilad Halpert
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA; Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N. Broadway, Baltimore, MD 21231, USA
| | - Barbara S Slusher
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry and Behavioral Sciences, Medicine, and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Laura M Ensign
- The Center for Nanomedicine, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD 21231, USA; Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 400 N. Broadway, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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Yanai H, Ben-Shachar S, Mlynarsky L, Godny L, Leshno M, Tulchinsky H, Dotan I. The outcome of ulcerative colitis patients undergoing pouch surgery is determined by pre-surgical factors. Aliment Pharmacol Ther 2017; 46:508-515. [PMID: 28664992 DOI: 10.1111/apt.14205] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/09/2017] [Accepted: 06/04/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Pouch surgery, a common intervention for ulcerative colitis (UC) complications, is often associated with the development of pouchitis. AIM To identify predictors of pouch outcome in a cohort of patients with UC. METHODS We conducted a retrospective unmatched case-cohort study in a tertiary IBD referral centre. Adult patients with UC were classified into the worst phenotype throughout follow-up: normal pouch, a form of chronic pouchitis (either chronic pouchitis or Crohn's like disease of pouch [CLDP]), or episodic recurrent acute pouchitis (RAP). Risk factors for pouchitis (chronic forms) were detected using statistical models. RESULTS Two hundred and fifty-three pouch patients were followed up for 13.1±7.3 years. Only 71 patients (28.1%) maintained a favourable outcome of a sustained normal pouch. These patients were older at UC diagnosis (27.8±12.5 vs 23.0±11.4 years), had longer UC duration until surgery (13.4±9.5 vs 8.2±7.9 years), and had higher rates of referral to surgery due to nonrefractory (dysplasia/neoplasia) complications (42.3% vs 16.2%) compared with pouchitis patients. Median survival for sustained normal pouch was 10.8 years (95% CI 8.9-12.7 years), and it was longer in the nonrefractory group (20.3 vs 9.4 years for the refractory group, HR=2.37, 95% CI 1.25-3.52, P=.004). CONCLUSIONS Most patients with UC undergoing pouch surgery will develop pouchitis. Patients operated for nonrefractory indications have a more favourable outcome. These results may contribute to pre- and post-surgical decision-making. The findings imply that the processes determining UC severity may be similar to that causing pouchitis.
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Affiliation(s)
- H Yanai
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - S Ben-Shachar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - L Mlynarsky
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Godny
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Leshno
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Coller School of Management, Tel Aviv University, Tel Aviv, Israel
| | - H Tulchinsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Colorectal Unit, Division of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - I Dotan
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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20
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RNA-seq Reveals Transcriptomic Differences in Inflamed and Noninflamed Intestinal Mucosa of Crohn's Disease Patients Compared with Normal Mucosa of Healthy Controls. Inflamm Bowel Dis 2017; 23:1098-1108. [PMID: 28613228 DOI: 10.1097/mib.0000000000001066] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Aberrant gene expression in the gut mucosa might contribute to the initiation and progression of Crohn's disease (CD). RNA sequencing (RNA-seq) provides precise measurements of expression levels of transcripts and their isoforms. The aim of this study was to use RNA-seq to investigate transcriptomic differences and identify significantly differentially expressed transcripts in inflamed and noninflamed intestinal mucosa of CD patients. METHODS RNA-seq was performed on 13 pairs of inflamed and noninflamed intestinal mucosa from 13 CD patients and on sex-matched normal mucosa of 13 healthy controls. Significantly differentially expressed transcripts were validated by immunohistochemistry, quantitative reverse transcriptase polymerase chain reaction, and enzyme-linked immunosorbent assay. RESULTS RNA-seq revealed genome-wide transcriptomic differences between normal mucosa, noninflamed, and inflamed CD mucosa. Among 950 differentially expressed genes, 19 were up- or downregulated (upregulation: ANGPT2, CHN1, CPXM1, CPZ, CXCL1, FCN3, GJC1, HSD11B1, LZTS1, MEOX1, MMP12, PLA1A, SERPINE1, SGIP1, and TRPC4; downregulation: FAM189A1, PDE6A, SLC38A4, and HMGCS2) with statistical significance (p < 0.01 and q < 0.05). Among them, CXCL1 exhibited the highest fold change between groups. Immunohistochemistry for CXCL1 revealed no expression in normal mucosa, slightly increased expression in noninflamed CD mucosa, and highly increased expression in inflamed CD mucosa. Quantitative reverse transcriptase polymerase chain reaction showed that CXCL1 expression was significantly associated with epithelial damage, increased infiltration of polymorphonuclear leukocytes, and submucosal fibrosis. Serum CXCL1 concentration measured by enzyme-linked immunosorbent assay was better correlated with CD activity index (r = 0.660) than with C-reactive protein (r = 0.204). CONCLUSIONS RNA-seq revealed transcriptomic differences between normal mucosa, noninflamed CD mucosa, and inflamed CD mucosa. Intestinal and serum CXCL1 was substantially increased with CD activity and can be used as a potential biomarker of CD.
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21
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Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis 2017; 23:366-378. [PMID: 28221248 PMCID: PMC5988644 DOI: 10.1097/mib.0000000000001027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Ulcerative colitis (UC) only involves the colonic mucosa. Yet, nearly 50% of patients with UC who undergo total proctocolectomy with ileal pouch anal anastomosis develop UC-like inflammation of the ileal pouch (pouchitis). By contrast, patients with familial adenomatous polyposis (FAP) with ileal pouch anal anastomosis develop pouchitis far less frequently. We hypothesized that pathogenic events associated with the development of UC are recapitulated by colonic-metaplastic transcriptomic reprogramming of the UC pouch. METHODS We prospectively sampled pouch and prepouch ileum mucosal biopsies in patients with UC with ileal pouch anal anastomosis 4, 8, and 12 months after their pouch was in continuity. Mucosal samples were also obtained from patients with FAP. Transcriptional profiles of the UC and FAP pouch and prepouch ileum were investigated via RNA sequencing and compared with data from a previously published microarray study. RESULTS Unlike patients with FAP, subjects with UC exhibited a large set of differentially expressed genes between the pouch and prepouch ileum as early as 4 months after pouch functionalization. Functional pathway analysis of differentially expressed genes in the UC pouch revealed an enhanced state of immune/inflammatory response and extracellular matrix remodeling. Moreover, >70% of differentially expressed genes mapped to published inflammatory bowel diseases microarray data sets displayed directional changes consistent with active UC but not with Crohn's disease. CONCLUSIONS The UC pouch, well before histologic inflammation, already displays a systems-level gain of colon-associated genes and loss of ileum-associated genes. Patients with UC exhibit a unique transcriptomic response to ileal pouch creation that can be observed well before disease and may in part explain their susceptibility to the development of pouchitis.
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22
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Robbins L, Zaghiyan K, Melmed G, Vasiliauskas E, Ahmed S, McGovern D, Rabizadeh S, Singh N, Landers C, Ippoliti A, Shih D, Targan S, Fleshner P. Outcomes with Anti-Tumour Necrosis Factor-Alpha Therapy and Serology in Patients with Denovo Crohn's Disease After Ileal Pouch Anal Anastomosis. J Crohns Colitis 2017; 11:77-83. [PMID: 27466172 DOI: 10.1093/ecco-jcc/jjw134] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS A subset of patients who undergo ileal pouch-anal anastomosis [IPAA] for ulcerative colitis [UC] will later be diagnosed with denovo Crohn's disease [CD]. These patients have a higher risk of pouch failure. In this study we evaluated inflammatory bowel disease [IBD] serology in patients with denovo CD and examined the success of anti-tumour necrosis factor-alpha [anti-TNFα] therapy in preventing ileostomy in denovo CD patients who failed anti-TNFα therapy before IPAA. METHODS A prospectively maintained database of patients undergoing IPAA was reviewed to identify patients who developed denovo CD [defined as small bowel inflammation above the pouch inlet or pouch fistula/perianal disease appearing more than 3 months after stoma closure]. Clinical characteristics and IBD serology were analysed. Treatment failure was defined as pouch failure requiring ileostomy or pouchectomy. RESULTS Of 350 patients included in the study, 92 [26%] patients developed denovo CD. Significantly more denovo CD patients had anti-I2 positivity postoperatively versus preoperatively [p = 0.007]. Anti-TNFα therapy successfully treated denovo CD in 28 out of 38 [74%] patients. Out of 17 patients with denovo CD who had failed to respond to anti-TNFα agents before surgery and were treated with anti-TNFα therapy after surgery, 12 [71%] patients responded to treatment. CONCLUSIONS I2 serology may possibly help identify patients who have developed or are at risk for developing denovo CD. Anti-TNFα therapy for denovo CD after IPAA can help prevent permanent ileostomy in almost 75% of cases, even in patients who previously failed anti-TNFα treatment before surgery.
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Affiliation(s)
- Lori Robbins
- Departments of Medicine, Colon and Rectal Surgery
| | | | | | | | | | | | - Shervin Rabizadeh
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Namita Singh
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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23
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Knecht C, Fretter C, Rosenstiel P, Krawczak M, Hütt MT. Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls. Sci Rep 2016; 6:32584. [PMID: 27585741 PMCID: PMC5009330 DOI: 10.1038/srep32584] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022] Open
Abstract
Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of 'coherence', we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data.
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Affiliation(s)
- Carolin Knecht
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Christoph Fretter
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Center for Molecular Biosciences, Christian-Albrechts University Kiel, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
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24
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Ben-Shachar S, Yanai H, Sherman Horev H, Elad H, Baram L, Issakov O, Tulchinsky H, Pasmanik-Chor M, Shomron N, Dotan I. MicroRNAs Expression in the Ileal Pouch of Patients with Ulcerative Colitis Is Robustly Up-Regulated and Correlates with Disease Phenotypes. PLoS One 2016; 11:e0159956. [PMID: 27536783 PMCID: PMC4990209 DOI: 10.1371/journal.pone.0159956] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Background Gene expression alterations are associated with disease behavior in inflammatory bowel disease (IBD). microRNAs (miRNAs) are dominant in the regulation of gene expression, and may affect IBD phenotype. Our aim was to assess mucosal miRNA expression in IBD and the correlation with intestinal inflammation. Methods We performed a large-scale analysis of ileal mucosal miRNA. Biopsies were retrieved from patients with ileal Crohn’s disease (CD), unoperated ulcerative colitis (UC) patients, UC patients after pouch surgery, and normal controls (NC). Pouch UC patients were classified as having a normal pouch (NP), chronic pouchitis (CP), and Crohn’s-like disease of the pouch (CLDP). miRNA expression was analyzed by parallel massive (next-generation) sequencing (NGS). Bioinformatics tools were applied for clustering and the detection of potential targets. Results Sixty-one subjects were recruited. The ileum of unoperated UC patients was comparable with NC. There were significant miRNA expression alterations (fold change ≥2, corrected P ≤.05) in NP (n = 6), CP (n = 40) and CLDP (n = 139), but only two expression alterations were noted in CD. More than 90% of the altered miRNAs were up-regulated, and many were predicted to be associated with significantly decreased transcripts. miRNAs alterations were generally clustered with disease phenotypes. Conclusions Ileal inflammation causes increased miRNA expression. miRNA alterations correlate with IBD phenotype, apparently by controlling the down-regulation of specific mRNAs.
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Affiliation(s)
- Shay Ben-Shachar
- Genetic Institute, Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Henit Yanai
- IBD Center, Department of Gastroenterology and Liver Diseases Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hadas Sherman Horev
- IBD Center, Department of Gastroenterology and Liver Diseases Tel Aviv Medical Center, Tel Aviv, Israel
| | - Hofit Elad
- IBD Center, Department of Gastroenterology and Liver Diseases Tel Aviv Medical Center, Tel Aviv, Israel
| | - Liran Baram
- IBD Center, Department of Gastroenterology and Liver Diseases Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Issakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Tulchinsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Colorectal Unit, Division of Surgery, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Dotan
- IBD Center, Department of Gastroenterology and Liver Diseases Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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25
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Rais R, Jiang W, Zhai H, Wozniak KM, Stathis M, Hollinger KR, Thomas AG, Rojas C, Vornov JJ, Marohn M, Li X, Slusher BS. FOLH1/GCPII is elevated in IBD patients, and its inhibition ameliorates murine IBD abnormalities. JCI Insight 2016; 1. [PMID: 27536732 DOI: 10.1172/jci.insight.88634] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent gene-profiling analyses showed significant upregulation of the folate hydrolase (FOLH1) gene in the affected intestinal mucosa of patients with inflammatory bowel disease (IBD). The FOLH1 gene encodes a type II transmembrane glycoprotein termed glutamate carboxypeptidase II (GCPII). To establish that the previously reported increased gene expression was functional, we quantified the glutamate carboxypeptidase enzymatic activity in 31 surgical specimens and report a robust 2.8- to 41-fold increase in enzymatic activity in the affected intestinal mucosa of IBD patients compared with an uninvolved area in the same patients or intestinal mucosa from healthy controls. Using a human-to-mouse approach, we next showed a similar enzymatic increase in two well-validated IBD murine models and evaluated the therapeutic effect of the potent FOLH1/ GCPII inhibitor 2-phosphonomethyl pentanedioic acid (2-PMPA) (IC50 = 300 pM). In the dextran sodium sulfate (DSS) colitis model, 2-PMPA inhibited the GCPII activity in the colonic mucosa by over 90% and substantially reduced the disease activity. The significance of the target was confirmed in FOLH1-/- mice who exhibited resistance to DSS treatment. In the murine IL-10-/- model of spontaneous colitis, daily 2-PMPA treatment also significantly reduced both macroscopic and microscopic disease severity. These results provide the first evidence of FOLH1/GCPII enzymatic inhibition as a therapeutic option for IBD.
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Affiliation(s)
- Rana Rais
- Department of Neurology, Baltimore, Maryland, USA; Johns Hopkins Drug Discovery, Baltimore, Maryland, USA
| | - Weiwei Jiang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huihong Zhai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Kristen R Hollinger
- Department of Neurology, Baltimore, Maryland, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ajit G Thomas
- Johns Hopkins Drug Discovery, Baltimore, Maryland, USA
| | - Camilo Rojas
- Johns Hopkins Drug Discovery, Baltimore, Maryland, USA; Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Michael Marohn
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xuhang Li
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Barbara S Slusher
- Department of Neurology, Baltimore, Maryland, USA; Johns Hopkins Drug Discovery, Baltimore, Maryland, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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26
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Nonbloody Diarrhea but Not Significant Weight Loss at Diagnosis Is Associated with the Development of Denovo Crohn's Disease After Ileal Pouch-anal Anastomosis for Ulcerative Colitis. Inflamm Bowel Dis 2016; 22:654-61. [PMID: 26595552 DOI: 10.1097/mib.0000000000000630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Denovo Crohn's disease (CD) develops in 5% to 10% of patients after ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) leading to increased morbidity and rates of pouch failure. Initial nonbloody diarrhea and weight loss at diagnosis are independent risk factors for a change in diagnosis from UC to CD in nonsurgical patients. We investigated whether these features were risk factors for denovo CD in a longitudinal cohort of patients with UC undergoing IPAA. METHODS Prospective profiles of patients with UC undergoing IPAA followed over a 22-year period by 1 surgeon were analyzed. Denovo CD was diagnosed when mucosal inflammation (5 or more ulcers) involved the small bowel mucosa proximal to the ileal pouch any time after surgery and/or when a pouch fistula or other perianal complication developed more than 3 months after ileostomy closure. Patients with inflammatory bowel disease unclassified, acute pouchitis, chronic pouchitis, and those lost to follow-up were excluded from analysis. Cox regression analysis was performed for statistical significance. RESULTS Of the 199 study patients included in the analysis, denovo CD developed in 42 patients (21%). Patients who developed denovo CD had an increased incidence of nonbloody diarrhea (n = 12; 29%) compared with patients who had no evidence of pouch inflammation (n = 25; 16%) (P = 0.03). In contrast, the incidence of weight loss was not significantly increased in patients with denovo CD (n = 7; 17%) compared with patients who never had pouch inflammation (n = 16; 10%) (P = 0.12). CONCLUSIONS Initial nonbloody diarrhea is associated with denovo CD after IPAA. This association warrants close consideration before surgery.
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Serology of Patients with Ulcerative Colitis After Pouch Surgery Is More Comparable with that of Patients with Crohn's Disease. Inflamm Bowel Dis 2015. [PMID: 26197448 DOI: 10.1097/mib.0000000000000487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND The serologic status of patients with ulcerative colitis (UC) who develop postoperative pouchitis was compared with that of patients with Crohn's disease (CD) and unoperated patients with UC. METHODS Pouch patients were stratified into normal pouch, acute/recurrent acute pouchitis, and chronic pouchitis/Crohn's-like disease of the pouch groups. Antibodies against glycans associated with CD (anti-Saccharomyces cerevisiae, anti-laminaribioside, anti-chitobioside, and anti-mannobioside carbohydrate antibodies [ASCA, ALCA, ACCA, and AMCA, respectively]) were detected and correlated with type of inflammatory bowel disease and pouch behavior. RESULTS A total of 501 patients with inflammatory bowel diseases were recruited: 250 (50%) CD, 124 (24.7%) unoperated UC, and 127 (25.3%) UC-pouch. At least 1 positive antibody was detected in 77.6% CD, 52.0% UC-pouch and 33.1% unoperated UC (P < 0.0001 for all). ACCA and AMCA prevalence in CD, UC-pouch and unoperated patients with UC were 33.2%, 24.4%, and 16.9% (P = 0.003 for all) and 35.2%, 26.8%, and 7.3%, respectively (P < 0.0001 for all). ALCA and ASCA were more prevalent in patients with CD than unoperated UC and UC-pouch patients. A longer interval since pouch surgery was associated with inflammatory pouch behavior: 12.45, 11.39, and 8.5 years for acute/recurrent acute pouchitis, chronic pouchitis/Crohn's-like disease of the pouch, and normal pouch, respectively, P = 0.01 for all. CONCLUSIONS The prevalence of the CD-associated anti-glycan antibodies ACCA and AMCA is significantly increased in UC-pouch patients, suggesting that pouch surgery may trigger differential immune responses to glycans. The finding that the serology of UC-pouch patients shares similarities with that of patients with CD supports the notion that those 2 inflammatory bowel diseases share a common pathogenic pathway.
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28
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Reshef L, Kovacs A, Ofer A, Yahav L, Maharshak N, Keren N, Konikoff FM, Tulchinsky H, Gophna U, Dotan I. Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa. Gastroenterology 2015; 149:718-27. [PMID: 26026389 DOI: 10.1053/j.gastro.2015.05.041] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Pouchitis is a common long-term complication in patients with ulcerative colitis (UC) undergoing proctocolectomy with ileal pouch-anal anastomosis. Because the inflammation occurs in a previously normal small bowel, studies of this process might provide information about the development of Crohn's disease. Little is known about the intestinal microbiome of patients with pouchitis. We investigated whether specific bacterial populations correlate with the pouch disease phenotype and inflammatory activity. METHODS We performed a prospective study of patients with UC who underwent pouch surgery (N = 131) from 1981 through 2012 and were followed at Tel Aviv Medical Center. Patients were assigned to groups based on their degree and type of pouch inflammation. Patients with familial adenomatous polyposis after pouch surgery (n = 9), individuals with intact colons undergoing surveillance colonoscopy (n = 10), and patients with UC who did not undergo surgery (n = 9) served as controls. We collected demographic and disease activity data (based on the Pouchitis Disease Activity Index) and measured levels of C-reactive protein. Fecal samples were collected, levels of calprotectin were measured, and microbiota were analyzed by 16S ribosomal RNA gene amplicon pyrosequencing. RESULTS Increased proportions of the Fusobacteriaceae family correlated with increased disease activity and levels of C-reactive protein in patients with UC who underwent pouch surgery. In contrast, proportions of Faecalibacterium were reduced in patients with pouchitis vs controls; there was a negative correlation between proportion of Faecalibacterium and level of C-reactive protein. There was an association between antibiotic treatment, but not biologic or immunomodulatory therapy, with reduced proportions of 11 genera and with increased proportions of Enterococcus and Enterobacteriaceae. CONCLUSIONS Reductions in protective bacteria and increases in inflammatory bacteria are associated with pouch inflammation in patients with UC who underwent pouch surgery. The finding that antibiotics exacerbate dysbiosis indicates that these drugs might not provide long-term benefit for patients with pouchitis. Additional studies of this form of dysbiosis could provide information about the pathogenesis of Crohn's disease.
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Affiliation(s)
- Leah Reshef
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amir Kovacs
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Amos Ofer
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Lior Yahav
- IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Nitsan Maharshak
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Nirit Keren
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Gastroenterology and Hepatology, Meir Medical Center, Kfar Saba, Israel
| | - Fred M Konikoff
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Gastroenterology and Hepatology, Meir Medical Center, Kfar Saba, Israel
| | - Hagit Tulchinsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Colorectal Unit, Department of Surgery, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Iris Dotan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; IBD Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel.
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29
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Yanai H, Ben-Shachar S, Baram L, Elad H, Gitstein G, Brazowski E, Tulchinsky H, Pasmanik-Chor M, Dotan I. Gene expression alterations in ulcerative colitis patients after restorative proctocolectomy extend to the small bowel proximal to the pouch. Gut 2015; 64:756-64. [PMID: 24982202 DOI: 10.1136/gutjnl-2014-307387] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/12/2014] [Indexed: 01/18/2023]
Abstract
OBJECTIVES To evaluate molecular profiles in the small bowel (SB) mucosa proximal to the pouch in ulcerative colitis (UC) patients after pouch surgery. DESIGN Patients were prospectively recruited and stratified according to disease behaviour: normal pouch (NP), chronic pouchitis (CP), and Crohn's-like disease of the pouch (CLDP). Biopsies obtained from the pouch and the normal-appearing proximal SB (40 cm proximal to the anal verge) were compared to ileal biopsies from normal controls (NC). A histopathological score based on the degree of polymorphonuclear and mononuclear infiltrates was used to assess inflammation in the pouch and the proximal SB. Gene expression analysis was performed using microarrays, and validated by real-time PCR. Gene ontology and clustering were evaluated by bioinformatics. RESULTS Thirty-six subjects were recruited (age 18-71 years, 16 males). Histopathology scores demonstrated minimal differences in the normal-appearing proximal SB of all groups. Nonetheless, significant (fold change ≥2, corrected p [FDR] ≤ 0.05) molecular alterations in the proximal SB were detected in all groups (NP n=9; CP n=80; and CLDP n=230) compared with NC. The magnitude of DUOX2 alteration in the proximal SB was highest. An increase of 6.0, 9.8 and 21.7 folds in DUOX2 expression in NP, CP, CLDP, respectively was observed. This was followed by alterations in MMP1, SLC6A14 and PGC. Gene alterations in the proximal SB overlapped with alterations within the pouch (76% and 97% overlap in CP and CLDP, respectively). Gene ontology analysis in the proximal SB and pouch were comparable. CONCLUSIONS Significant gene expression alterations exist in an apparently unaffected proximal SB. Alterations in the pouch and the proximal SB were comparable, suggesting that inflammation may not be limited to the pouch, but that it extends to the proximal SB.
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Affiliation(s)
- Henit Yanai
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv, Israel
| | | | - Liran Baram
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv, Israel
| | - Hofit Elad
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv, Israel
| | - Gilad Gitstein
- Department of Pathology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Eli Brazowski
- Department of Pathology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Hagit Tulchinsky
- Colorectal Unit, Division of Surgery, Tel Aviv Medical Center, Tel Aviv, Israel The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Iris Dotan
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv, Israel
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Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol 2015; 16:67. [PMID: 25887922 PMCID: PMC4414286 DOI: 10.1186/s13059-015-0637-x] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/18/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both host genetics and the microbiota are implicated in its pathogenesis. We use the IPAA model of IBD to associate mucosal host gene expression with mucosal microbiomes and clinical outcomes. We analyze host transcriptomic data and 16S rRNA gene sequencing data from paired biopsies from IPAA patients with UC and familial adenomatous polyposis. To achieve power for a genome-wide microbiome-transcriptome association study, we use principal component analysis for transcript and clade reduction, and identify significant co-variation between clades and transcripts. RESULTS Host transcripts co-vary primarily with biopsy location and inflammation, while microbes co-vary primarily with antibiotic use. Transcript-microbe associations are surprisingly modest, but the most strongly microbially-associated host transcript pattern is enriched for complement cascade genes and for the interleukin-12 pathway. Activation of these host processes is inversely correlated with Sutterella, Akkermansia, Bifidobacteria, and Roseburia abundance, and positively correlated with Escherichia abundance. CONCLUSIONS This study quantifies the effects of inflammation, antibiotic use, and biopsy location upon the microbiome and host transcriptome during pouchitis. Understanding these effects is essential for basic biological insights as well as for well-designed and adequately-powered studies. Additionally, our study provides a method for profiling host-microbe interactions with appropriate statistical power using high-throughput sequencing, and suggests that cross-sectional changes in gut epithelial transcription are not a major component of the host-microbiome regulatory interface during pouchitis.
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Affiliation(s)
- Xochitl C Morgan
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Boyko Kabakchiev
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Levi Waldron
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,City University of New York School of Public Health, Hunter College, 2180 3rd Ave Rm 538, New York, NY, 10035-4003, USA.
| | - Andrea D Tyler
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Timothy L Tickle
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Raquel Milgrom
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Joanne M Stempak
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Dirk Gevers
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Mark S Silverberg
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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31
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Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med 2014; 6:107. [PMID: 25587358 PMCID: PMC4292994 DOI: 10.1186/s13073-014-0107-1] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (IBD), but disease risk cannot be explained fully by either factor individually. Recent findings point to interactions between host genetics and microbial exposures as important contributors to disease risk in IBD. These include evidence of the partial heritability of the gut microbiota and the conferral of gut mucosal inflammation by microbiome transplant even when the dysbiosis was initially genetically derived. Although there have been several tests for association of individual genetic loci with bacterial taxa, there has been no direct comparison of complex genome-microbiome associations in large cohorts of patients with an immunity-related disease. METHODS We obtained 16S ribosomal RNA (rRNA) gene sequences from intestinal biopsies as well as host genotype via Immunochip in three independent cohorts totaling 474 individuals. We tested for correlation between relative abundance of bacterial taxa and number of minor alleles at known IBD risk loci, including fine mapping of multiple risk alleles in the Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene exon. We identified host polymorphisms whose associations with bacterial taxa were conserved across two or more cohorts, and we tested related genes for enrichment of host functional pathways. RESULTS We identified and confirmed in two cohorts a significant association between NOD2 risk allele count and increased relative abundance of Enterobacteriaceae, with directionality of the effect conserved in the third cohort. Forty-eight additional IBD-related SNPs have directionality of their associations with bacterial taxa significantly conserved across two or three cohorts, implicating genes enriched for regulation of innate immune response, the JAK-STAT cascade, and other immunity-related pathways. CONCLUSIONS These results suggest complex interactions between genetically altered host functional pathways and the structure of the microbiome. Our findings demonstrate the ability to uncover novel associations from paired genome-microbiome data, and they suggest a complex link between host genetics and microbial dysbiosis in subjects with IBD across independent cohorts.
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Affiliation(s)
- Dan Knights
- />Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 USA
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Biotechnology Institute, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Mark S Silverberg
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Rinse K Weersma
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Dirk Gevers
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
| | - Gerard Dijkstra
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Hailiang Huang
- />Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114 USA
| | - Andrea D Tyler
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Suzanne van Sommeren
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
- />Department of Genetics, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Floris Imhann
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
- />Department of Genetics, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Joanne M Stempak
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Hu Huang
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Pajau Vangay
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Gabriel A Al-Ghalith
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Caitlin Russell
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
| | - Jenny Sauk
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
| | - Jo Knight
- />Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8 Canada
| | - Mark J Daly
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Department of Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
| | - Curtis Huttenhower
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115 USA
| | - Ramnik J Xavier
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
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