1
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Wang J, Li L, Chen P, He C, Niu X. Exploration and verification a 13-gene diagnostic framework for ulcerative colitis across multiple platforms via machine learning algorithms. Sci Rep 2024; 14:15009. [PMID: 38951638 PMCID: PMC11217275 DOI: 10.1038/s41598-024-65481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with intricate pathogenesis and varied presentation. Accurate diagnostic tools are imperative to detect and manage UC. This study sought to construct a robust diagnostic model using gene expression profiles and to identify key genes that differentiate UC patients from healthy controls. Gene expression profiles from eight cohorts, encompassing a total of 335 UC patients and 129 healthy controls, were analyzed. A total of 7530 gene sets were computed using the GSEA method. Subsequent batch correction, PCA plots, and intersection analysis identified crucial pathways and genes. Machine learning, incorporating 101 algorithm combinations, was employed to develop diagnostic models. Verification was done using four external cohorts, adding depth to the sample repertoire. Evaluation of immune cell infiltration was undertaken through single-sample GSEA. All statistical analyses were conducted using R (Version: 4.2.2), with significance set at a P value below 0.05. Employing the GSEA method, 7530 gene sets were computed. From this, 19 intersecting pathways were discerned to be consistently upregulated across all cohorts, which pertained to cell adhesion, development, metabolism, immune response, and protein regulation. This corresponded to 83 unique genes. Machine learning insights culminated in the LASSO regression model, which outperformed others with an average AUC of 0.942. This model's efficacy was further ratified across four external cohorts, with AUC values ranging from 0.694 to 0.873 and significant Kappa statistics indicating its predictive accuracy. The LASSO logistic regression model highlighted 13 genes, with LCN2, ASS1, and IRAK3 emerging as pivotal. Notably, LCN2 showcased significantly heightened expression in active UC patients compared to both non-active patients and healthy controls (P < 0.05). Investigations into the correlation between these genes and immune cell infiltration in UC highlighted activated dendritic cells, with statistically significant positive correlations noted for LCN2 and IRAK3 across multiple datasets. Through comprehensive gene expression analysis and machine learning, a potent LASSO-based diagnostic model for UC was developed. Genes such as LCN2, ASS1, and IRAK3 hold potential as both diagnostic markers and therapeutic targets, offering a promising direction for future UC research and clinical application.
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Affiliation(s)
- Jing Wang
- Department of Gastroenterology, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China
| | - Lin Li
- Department of Gastroenterology, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China
| | - Pingbo Chen
- Department of Joint-Orthopedics, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China
| | - Chiyi He
- Department of Gastroenterology, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China
| | - Xiaoping Niu
- Department of Gastroenterology, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China.
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2
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Mager LF, Krause T, McCoy KD. Interaction of microbiota, mucosal malignancies, and immunotherapy-Mechanistic insights. Mucosal Immunol 2024; 17:402-415. [PMID: 38521413 DOI: 10.1016/j.mucimm.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The microbiome has emerged as a crucial modulator of host-immune interactions and clearly impacts tumor development and therapy efficacy. The microbiome is a double-edged sword in cancer development and therapy as both pro-tumorigenic and anti-tumorigenic bacterial taxa have been identified. The staggering number of association-based studies in various tumor types has led to an enormous amount of data that makes it difficult to identify bacteria that promote tumor development or modulate therapy efficacy from bystander bacteria. Here we aim to comprehensively summarize the current knowledge of microbiome-host immunity interactions and cancer therapy in various mucosal tissues to find commonalities and thus identify potential functionally relevant bacterial taxa. Moreover, we also review recent studies identifying specific bacteria and mechanisms through which the microbiome modulates cancer development and therapy efficacy.
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Affiliation(s)
- Lukas F Mager
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada; Department of Internal Medicine I, Faculty of Medicine, University of Tübingen, Germany; M3 Research Center for Malignom, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Germany
| | - Tim Krause
- Department of Internal Medicine I, Faculty of Medicine, University of Tübingen, Germany; M3 Research Center for Malignom, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Germany
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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3
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Kosinsky RL, Gonzalez MM, Saul D, Barros LL, Sagstetter MR, Fedyshyn Y, Nair A, Sun Z, Hamdan FH, Gibbons HR, Perez Pachon ME, Druliner BR, Johnsen SA, Faubion WA. The FOXP3 + Pro-Inflammatory T Cell: A Potential Therapeutic Target in Crohn's Disease. Gastroenterology 2024; 166:631-644.e17. [PMID: 38211712 PMCID: PMC10960691 DOI: 10.1053/j.gastro.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND & AIMS The incidence of Crohn's disease (CD) continues to increase worldwide. The contribution of CD4+ cell populations remains to be elucidated. We aimed to provide an in-depth transcriptional assessment of CD4+ T cells driving chronic inflammation in CD. METHODS We performed single-cell RNA-sequencing in CD4+ T cells isolated from ileal biopsies of patients with CD compared with healthy individuals. Cells underwent clustering analysis, followed by analysis of gene signaling networks. We overlapped our differentially expressed genes with publicly available microarray data sets and performed functional in vitro studies, including an in vitro suppression assay and organoid systems, to model gene expression changes observed in CD regulatory T (Treg) cells and to test predicted therapeutics. RESULTS We identified 5 distinct FOXP3+ regulatory Treg subpopulations. Tregs isolated from healthy controls represent the origin of pseudotemporal development into inflammation-associated subtypes. These proinflammatory Tregs displayed a unique responsiveness to tumor necrosis factor-α signaling with impaired suppressive activity in vitro and an elevated cytokine response in an organoid coculture system. As predicted in silico, the histone deacetylase inhibitor vorinostat normalized gene expression patterns, rescuing the suppressive function of FOXP3+ cells in vitro. CONCLUSIONS We identified a novel, proinflammatory FOXP3+ T cell subpopulation in patients with CD and developed a pipeline to specifically target these cells using the US Food and Drug Administration-approved drug vorinostat.
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Affiliation(s)
- Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Michelle M Gonzalez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Dominik Saul
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, Minnesota; Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center, Tübingen, Germany
| | - Luísa Leite Barros
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Gastroenterology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Brooke R Druliner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, Arizona.
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4
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Arosa L, Camba-Gómez M, Golubnitschaja O, Conde-Aranda J. Predictive, preventive and personalised approach as a conceptual and technological innovation in primary and secondary care of inflammatory bowel disease benefiting affected individuals and populations. EPMA J 2024; 15:111-123. [PMID: 38463620 PMCID: PMC10923750 DOI: 10.1007/s13167-024-00351-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 03/12/2024]
Abstract
Inflammatory bowel disease (IBD) is a global health burden which carries lifelong morbidity affecting all age groups in populations with the disease-specific peak of the age groups ranging between 15 and 35 years, which are of great economic importance for the society. An accelerating incidence of IBD is reported for newly industrialised countries, whereas stabilising incidence but increasing prevalence is typical for countries with a Westernised lifestyle, such as the European area and the USA. Although the aetiology of IBD is largely unknown, the interplay between the genetic, environmental, immunological, and microbial components is decisive for the disease manifestation, course, severity and individual outcomes. Contextually, the creation of an individualised patient profile is crucial for the cost-effective disease management in primary and secondary care of IBD. The proposed pathomechanisms include intestinal pathoflora and dysbiosis, chronic inflammation and mitochondrial impairments, amongst others, which collectively may reveal individual molecular signatures defining IBD subtypes and leading to clinical phenotypes, patient stratification and cost-effective protection against health-to-disease transition and treatments tailored to individualised patient profiles-all the pillars of an advanced 3PM approach. The paradigm change from reactive medical services to predictive diagnostics, cost-effective targeted prevention and treatments tailored to individualised patient profiles in overall IBD management holds a promise to meet patient needs in primary and secondary care, to increase the life-quality of affected individuals and to improve health economy in the area of IBD management. This article analyses current achievements and provides the roadmap for future developments in the area in the context of 3P medicine benefiting society at large.
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Affiliation(s)
- Laura Arosa
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
| | - Miguel Camba-Gómez
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
| | - Olga Golubnitschaja
- 3P Medicine Research Unit, University Hospital, Rheinische Friedrich-Wilhelms Universität Bonn, 53127 Bonn, Germany
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
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Makaro A, Świerczyński M, Pokora K, Sarniak B, Kordek R, Fichna J, Salaga M. Empagliflozin attenuates intestinal inflammation through suppression of nitric oxide synthesis and myeloperoxidase activity in in vitro and in vivo models of colitis. Inflammopharmacology 2024; 32:377-392. [PMID: 37086302 PMCID: PMC10907478 DOI: 10.1007/s10787-023-01227-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/07/2023] [Indexed: 04/23/2023]
Abstract
Inflammatory bowel diseases (IBD) are characterized by chronic and relapsing inflammation affecting the gastrointestinal (GI) tract. The incidence and prevalence of IBD are relatively high and still increasing. Additionally, current therapeutic strategies for IBD are not optimal. These facts urge todays' medicine to find a novel way to treat IBD. Here, we focused on the group of anti-diabetic drugs called gliflozins, which inhibit sodium glucose co-transporter type 2 (SGLT-2). Numerous studies demonstrated that gliflozins exhibit pleiotropic effect, including anti-inflammatory properties. In this study, we tested the effect of three gliflozins; empagliflozin (EMPA), dapagliflozin (DAPA), and canagliflozin (CANA) in in vitro and in vivo models of intestinal inflammation. Our in vitro experiments revealed that EMPA and DAPA suppress the production of nitric oxide in LPS-treated murine RAW264.7 macrophages. In in vivo part of our study, we showed that EMPA alleviates acute DSS-induced colitis in mice. Treatment with EMPA reduced macro- and microscopic colonic damage, as well as partially prevented from decrease in tight junction gene expression. Moreover, EMPA attenuated biochemical inflammatory parameters including reduced activity of myeloperoxidase. We showed that SGLT-2 inhibitors act as anti-inflammatory agents independently from their hypoglycemic effects. Our observations suggest that gliflozins alleviate inflammation through their potent effects on innate immune cells.
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Affiliation(s)
- Adam Makaro
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Mikołaj Świerczyński
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Kacper Pokora
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Barbara Sarniak
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Radzisław Kordek
- Department of Pathology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Jakub Fichna
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Maciej Salaga
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland.
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Xie J, Huang Q, Xie H, Liu J, Tian S, Cao R, Yang M, Lin J, Han L, Zhang D. Hyaluronic acid/inulin-based nanocrystals with an optimized ratio of indigo and indirubin for combined ulcerative colitis therapy via immune and intestinal flora regulation. Int J Biol Macromol 2023; 252:126502. [PMID: 37625742 DOI: 10.1016/j.ijbiomac.2023.126502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Indigo (IND) and indirubin (INB) have demonstrated a synergistic effect in treating ulcerative colitis at a ratio of 7.5:1. However, the colon mucus layer, a critical physiological barrier against external threats, is also a biological barrier, limiting the potential for effective drug delivery to the lamina propria for regulating inflammatory cells. Inspired by the potential of Hyaluronic acid (HA), to enhance cellular uptake by inflammatory cells, and Pluronic® F127 (F127), known for overcoming the mucus barrier, this study innovatively developed INB/IND nanosuspensions by co-modifying with F127 and HA. Moreover, inulin serves a dual purpose as a spray protective agent and a regulator of intestinal flora. Therefore, it was incorporated into INB/IND nanosuspensions for subsequent spray drying, resulting in the preparation of INB/IND nanocrystals (INB/IND-NC). The mucus penetration of INB/IND-NC was 24.30 times that of the control group. Besides, INB/IND-NC exhibited enhanced cellular uptake properties proximately twice that of Raw INB/IND. Importantly, INB/IND-NC exhibited improved therapeutic efficacy in DSS-induced mice by regulating the expression of cytokines, regulating immune responses via downregulating the expression of macrophages, neutrophils, and dendritic cells and maintaining intestinal flora homeostasis. Our study provides a new perspective for applying natural products for treating inflammatory diseases.
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Affiliation(s)
- Jin Xie
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qi Huang
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Huijuan Xie
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jun Liu
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shimin Tian
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ruiyi Cao
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ming Yang
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Junzhi Lin
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China.
| | - Li Han
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Dingkun Zhang
- State Key Laboratory of Characteristic Chinese Drug Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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Derakhshan Nazari MH, Shahrokh S, Ghanbari-Maman L, Maleknia S, Ghorbaninejad M, Meyfour A. Prediction of anti-TNF therapy failure in ulcerative colitis patients by ensemble machine learning: A prospective study. Heliyon 2023; 9:e21154. [PMID: 37928018 PMCID: PMC10623293 DOI: 10.1016/j.heliyon.2023.e21154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/05/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Nowadays, anti-TNF therapy remarkably improves the medical management of ulcerative colitis (UC), but approximately 40 % of patients do not respond to this treatment. In this study, we used 79 anti-TNF-naive patients with moderate-to-severe UC from four cohorts to discover alternative therapeutic targets and develop a personalized medicine approach that can diagnose UC non-responders (UCN) prior to receiving anti-TNF therapy. To this end, two microarray data series were integrated to create a discovery cohort with 35 UC samples. A comprehensive gene expression and functional analysis was performed and identified 313 significantly altered genes, among which IL6 and INHBA were highlighted as overexpressed genes in the baseline mucosal biopsies of UCN, whose cooperation may lead to a decrease in the Tregs population. Besides, screening the abundances of immune cell subpopulations showed neutrophils' accumulation increasing the inflammation. Furthermore, the correlation of KRAS signaling activation with unresponsiveness to anti-TNF mAb was observed using network analysis. Using 50x repeated 10-fold cross-validation LASSO feature selection and a stack ensemble machine learning algorithm, a five-mRNA prognostic panel including IL13RA2, HCAR3, CSF3, INHBA, and MMP1 was introduced that could predict the response of UC patients to anti-TNF antibodies with an average accuracy of 95.3 %. The predictive capacity of the introduced biomarker panel was also validated in two independent cohorts (44 UC patients). Moreover, we presented a distinct immune cell landscape and gene signature for UCN to anti-TNF drugs and further studies should be considered to make this predictive biomarker panel and therapeutic targets applicable in the clinical setting.
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Affiliation(s)
- Mohammad Hossein Derakhshan Nazari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Research Center for Gastroenterology and Liver Diseases, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Ghanbari-Maman
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Computer Science, Faculty of Mathematical Sciences, University of Kashan, Kashan, Iran
| | - Samaneh Maleknia
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Ghorbaninejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Chen C, Lan B, Xie G, Liu Z. Analysis and identification of ferroptosis-related genes in ulcerative colitis. Scand J Gastroenterol 2023; 58:1422-1433. [PMID: 37530128 DOI: 10.1080/00365521.2023.2240927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023]
Abstract
BACKGROUND Previous studies have shown that ferroptosis is associated with the pathogenesis of ulcerative colitis (UC). Therefore, this study aimed to identify key ferroptosis-related genes (FRGs) associated with the diagnosis of UC. METHODS UC-related expression datasets were downloaded from the Gene Expression Omnibus (GEO) database. First, Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify UC-related genes (UCRGs). Differentially expressed genes (DEGs) between normal and UC groups were screened in GSE87466, and DEGs were subjected to an intersection analysis with FRGs and UCRGs to obtain ferroptosis-related DEGs (FR DEGs). Then a protein-protein interaction (PPI) network was constructed for FR DEGs. The hub genes were extracted based on the degree, Maximum Neighborhood Component (MNC), closeness, and Maximal Clique Centrality (MCC). Biomarkers with diagnostic values were screened by support vector machine (SVM) and the least absolute shrinkage and selection operator (LASSO) algorithms. Next, the infiltration of immune cells was compared between UC and normal groups, and the correlation between different immune cells and diagnostic genes was analyzed. The biological functions, classical pathways, and intermolecular interaction networks of diagnostic genes were characterized utilizing ingenuity pathway analysis (IPA). Finally, a TF-mRNA network was constructed and potential small-molecule compounds were screened. RESULTS Thirty-six FR DEGs were obtained, and these were enriched in biological processes such as positive regulation of cytokine production, cytokine-mediated signalling pathway, long-chain fatty acid-CoA ligase activity, etc. Among 18 hub genes, five genes (ALOX5, TIMP1, TNFAIP3, SOCS1, DUOX2) were captured with diagnostic values for UC, and they displayed significant differences between UC and normal groups. Sixteen immune cell infiltrates were significantly different between UC and normal groups, such as activated dendritic cells and resting dendritic cells. TNFAIP3 and ALOX5 were positively correlated with neutrophils, and TIMP1, SOCS1, ALOX5, and DUOX2 were negatively correlated with M2 macrophages. IPA showed that diagnostic genes were related to 43 function modules and activated 17 pathways. The constructed TF-mRNA regulatory network comprised three diagnostic genes and 17 differentially expressed TFs. Potential small-molecule compounds including helveticoside and cymarin were identified. CONCLUSION Our findings yielded several promising FRGs for UC, providing a scientific reference for further studies on the pathogenesis of UC.
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Affiliation(s)
- Chen Chen
- Department of Gastroenterology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, P.R. China
| | - Bo Lan
- Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, P.R. China
| | - Guanghong Xie
- Department of Emergency Internal Medicine, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, P.R. China
| | - Zhaoyang Liu
- Department of Emergency Internal Medicine, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, P.R. China
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9
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Martín-Adrados B, Wculek SK, Fernández-Bravo S, Torres-Ruiz R, Valle-Noguera A, Gomez-Sánchez MJ, Hernández-Walias JC, Ferreira FM, Corraliza AM, Sancho D, Esteban V, Rodriguez-Perales S, Cruz-Adalia A, Nakaya HI, Salas A, Bernardo D, Campos-Martín Y, Martínez-Zamorano E, Muñoz-López D, Gómez del Moral M, Cubero FJ, Blumberg RS, Martínez-Naves E. Expression of HMGCS2 in intestinal epithelial cells is downregulated in inflammatory bowel disease associated with endoplasmic reticulum stress. Front Immunol 2023; 14:1185517. [PMID: 37457727 PMCID: PMC10348483 DOI: 10.3389/fimmu.2023.1185517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The Unfolded Protein Response, a mechanism triggered by the cell in response to Endoplasmic reticulum stress, is linked to inflammatory responses. Our aim was to identify novel Unfolded Protein Response-mechanisms that might be involved in triggering or perpetuating the inflammatory response carried out by the Intestinal Epithelial Cells in the context of Inflammatory Bowel Disease. Methods We analyzed the transcriptional profile of human Intestinal Epithelial Cell lines treated with an Endoplasmic Reticulum stress inducer (thapsigargin) and/or proinflammatory stimuli. Several genes were further analyzed in colonic biopsies from Ulcerative Colitis patients and healthy controls. Lastly, we generated Caco-2 cells lacking HMGCS2 by CRISPR Cas-9 and analyzed the functional implications of its absence in Intestinal Epithelial Cells. Results Exposure to a TLR ligand after thapsigargin treatment resulted in a powerful synergistic modulation of gene expression, which led us to identify new genes and pathways that could be involved in inflammatory responses linked to the Unfolded Protein Response. Key differentially expressed genes in the array also exhibited transcriptional alterations in colonic biopsies from active Ulcerative Colitis patients, including NKG2D ligands and the enzyme HMGCS2. Moreover, functional studies showed altered metabolic responses and epithelial barrier integrity in HMGCS2 deficient cell lines. Conclusion We have identified new genes and pathways that are regulated by the Unfolded Protein Response in the context of Inflammatory Bowel Disease including HMGCS2, a gene involved in the metabolism of Short Chain Fatty Acids that may have an important role in intestinal inflammation linked to Endoplasmic Reticulum stress and the resolution of the epithelial damage.
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Affiliation(s)
- Beatriz Martín-Adrados
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - Stefanie K. Wculek
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Sergio Fernández-Bravo
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma of Madrid, Madrid, Spain
| | - Raúl Torres-Ruiz
- Molecular Cytogenetics & Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro, Madrid, Spain
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Advanced Therapies Unit, Hematopoietic Innovative Therapies Division, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ana Valle-Noguera
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - Maria José Gomez-Sánchez
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - José Carlos Hernández-Walias
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | | | - Ana María Corraliza
- Department of Gastroenterology, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Centro de Investigación Biomédica en Red-Enfermedades Hepáticas y Digestivas (CIBER-EHD), Barcelona, Spain
| | - David Sancho
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma of Madrid, Madrid, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics & Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro, Madrid, Spain
| | - Aránzazu Cruz-Adalia
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Azucena Salas
- Department of Gastroenterology, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Centro de Investigación Biomédica en Red-Enfermedades Hepáticas y Digestivas (CIBER-EHD), Barcelona, Spain
| | - David Bernardo
- Gut Immunology Research Group, Instituto de Investigación del Hospital Universitario de la Princesa, Madrid, Spain
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM, Universidad de Valladolid-Consejo Superior de Investigaciones Científicas (CSIC)), Valladolid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Diego Muñoz-López
- Department of Pathology, Hospital Universitario de Toledo, Toledo, Spain
| | - Manuel Gómez del Moral
- Department of Cellular Biology, School of Medicine, Universidad Complutense of Madrid (UCM), Madrid, Spain
| | - Francisco Javier Cubero
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermeddes Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Richard S. Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Eduardo Martínez-Naves
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
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10
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Hu W, Fang T, Zhou M, Chen X. Identification of hub genes and immune infiltration in ulcerative colitis using bioinformatics. Sci Rep 2023; 13:6039. [PMID: 37055495 PMCID: PMC10101977 DOI: 10.1038/s41598-023-33292-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/11/2023] [Indexed: 04/15/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine, whose pathogenesis is not fully understood. Given that immune infiltration plays a key role in UC progression, our study aimed to assess the level of immune cells in UC intestinal mucosal tissues and identify potential immune-related genes. The GSE65114 UC dataset was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between healthy and UC tissues were identified using the "limma" package in R, while their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined with the clusterProfiler package. Protein-protein interaction network analysis and visualization were performed with STRING and Cytoscape. Immune cell infiltration was calculated with CIBERSORT. The relationship between hub genes and immune-infiltrated cells in UC was determined by Pearson correlation. A total of 206 DEGs were identified, of which 174 were upregulated and 32 downregulated. GO and KEGG functional classification indicated DEG enrichment in immune response pathways, including Toll-like receptor signaling, IL-17 signaling, and immune system process and chemokine signaling. 13 hub genes were identified. Infiltration matrix analysis of immune cells showed abundant plasma cells, memory B cells, resting CD4 memory T cells, γδ T cells, M0 and M1 macrophages, and neutrophils in UC intestinal tissues. Correlation analysis revealed 13 hub genes associated with immune-infiltrated cells in UC. 13 hub genes associated with immune-infiltrated cells in UC were identified; they included CXCL13, CXCL10, CXCL9, CXCL8, CCL19, CTLA4, CCR1, CD69, CD163, IL7R, PECAM1, TLR8 and TLR2. These genes could potentially serve as markers for the diagnosis and treatment of UC.
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Affiliation(s)
- Weitao Hu
- Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, 362000, Fujian, People's Republic of China
| | - Taiyong Fang
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, People's Republic of China
| | - Mingxuan Zhou
- Department of General Practice, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, People's Republic of China
| | - Xiaoqing Chen
- Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, 362000, Fujian, People's Republic of China.
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11
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Dan S, Ungar B, Ben-Moshe S, Halpern KB, Yavzori M, Fudim E, Picard O, Abitbol CM, Harnik S, Barshack I, Kopylov U, Ben-Horin S, Itzkovitz S. Distal Fecal Wash Host Transcriptomics Identifies Inflammation Throughout the Colon and Terminal Ileum. Cell Mol Gastroenterol Hepatol 2023; 16:1-15. [PMID: 36791991 DOI: 10.1016/j.jcmgh.2023.02.002] [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: 12/22/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND & AIMS Noninvasive modalities for assessing active endoscopic and histologic inflammation in Crohn's disease and ulcerative colitis patients are critically needed. Fecal wash host shed-cell transcriptomics has been shown to be a robust classifier of endoscopic and histologic inflammation in inflammatory bowel disease patients with distal colitis. Whether such fecal washes can inform on inflammatory processes occurring in more proximal intestinal segments is currently unknown. METHODS Fifty-nine inflammatory bowel disease patients and 50 controls were prospectively enrolled. Biopsy specimens and fecal washes from the distal colon, proximal colon, and terminal ileum were compared. Host transcriptomics were performed on the biopsy specimens and fecal washes obtained during colonoscopy at predefined locations throughout the colon and terminal ileum and results were associated with concurrent clinical, endoscopic, and histologic parameters. RESULTS We found that host transcriptomics of distal fecal washes robustly classify histologic inflammation in ileal and proximal colonic Crohn's disease, even without distal colonic involvement (area under the receiver operating characteristic curve, 0.94 ± 0.09). We further found that fecal washes consist of modules of co-expressed genes of immune, stromal, and epithelial origin that are indicative of endoscopic disease severity. Fecal wash host transcriptomics also capture expression of gene modules previously associated with a lack of response to biological therapies. CONCLUSIONS Our study establishes the accuracy of distal colonic fecal washes for identifying and scoring inflammatory processes throughout the entire ileal-colonic axis.
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Affiliation(s)
- Stav Dan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bella Ungar
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Yavzori
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ella Fudim
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Orit Picard
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Chaya Mushka Abitbol
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Sivan Harnik
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Uri Kopylov
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Shomron Ben-Horin
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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12
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Bauer KM, Nelson MC, Tang WW, Chiaro TR, Brown DG, Ghazaryan A, Lee SH, Weis AM, Hill JH, Klag KA, Tran VB, Thompson JW, Ramstead AG, Monts JK, Marvin JE, Alexander M, Voth WP, Stephens WZ, Ward DM, Petrey AC, Round JL, O'Connell RM. CD11c+ myeloid cell exosomes reduce intestinal inflammation during colitis. JCI Insight 2022; 7:159469. [PMID: 36214220 PMCID: PMC9675566 DOI: 10.1172/jci.insight.159469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/19/2022] [Indexed: 01/25/2023] Open
Abstract
Intercellular communication is critical for homeostasis in mammalian systems, including the gastrointestinal (GI) tract. Exosomes are nanoscale lipid extracellular vesicles that mediate communication between many cell types. Notably, the roles of immune cell exosomes in regulating GI homeostasis and inflammation are largely uncharacterized. By generating mouse strains deficient in cell-specific exosome production, we demonstrate deletion of the small GTPase Rab27A in CD11c+ cells exacerbated murine colitis, which was reversible through administration of DC-derived exosomes. Profiling RNAs within colon exosomes revealed a distinct subset of miRNAs carried by colon- and DC-derived exosomes. Among antiinflammatory exosomal miRNAs, miR-146a was transferred from gut immune cells to myeloid and T cells through a Rab27-dependent mechanism, targeting Traf6, IRAK-1, and NLRP3 in macrophages. Further, we have identified a potentially novel mode of exosome-mediated DC and macrophage crosstalk that is capable of skewing gut macrophages toward an antiinflammatory phenotype. Assessing clinical samples, RAB27A, select miRNAs, and RNA-binding proteins that load exosomal miRNAs were dysregulated in ulcerative colitis patient samples, consistent with our preclinical mouse model findings. Together, our work reveals an exosome-mediated regulatory mechanism underlying gut inflammation and paves the way for potential use of miRNA-containing exosomes as a novel therapeutic for inflammatory bowel disease.
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Affiliation(s)
- Kaylyn M Bauer
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Morgan C Nelson
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - William W Tang
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Tyson R Chiaro
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - D Garrett Brown
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Soh-Hyun Lee
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Allison M Weis
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Jennifer H Hill
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Kendra A Klag
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Van B Tran
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Jacob W Thompson
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Andrew G Ramstead
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Josh K Monts
- University of Utah Flow Cytometry Core, Salt Lake City, Utah, USA
| | - James E Marvin
- University of Utah Flow Cytometry Core, Salt Lake City, Utah, USA
| | - Margaret Alexander
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Warren P Voth
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - W Zac Stephens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Diane M Ward
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Aaron C Petrey
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA.,Department of Internal Medicine, Division of Gastroenterology, and
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA.,Hunstman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ryan M O'Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA.,Hunstman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
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13
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Huang C, Wang Y, Lin X, Chan TF, Lai KP, Li R. Uncovering the functions of plasma proteins in ulcerative colitis and identifying biomarkers for BPA-induced severe ulcerative colitis: A plasma proteome analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113897. [PMID: 35999755 DOI: 10.1016/j.ecoenv.2022.113897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Ulcerative colitis (UC), a long-term inflammation of the colon, is a worldwide disease. Accumulating reports have suggested the contribution of environmental pollutants to UC development. As such, the identification of biomarkers to evaluate pollutant-induced UC could provide a better assessment on the world's pollution problem. In the present study, we applied the plasma proteome to profile the plasma protein changes in three models: dextran sulfate sodium (DSS)-induced colitis, bisphenol A (BPA), and BPA-severe colitis. We aimed to investigate the functional roles of plasma proteins related to colitis development and further understand the synergistic effect of BPA on colitis. In addition, we aimed to identify novel biomarkers for UC non-invasive diagnosis and assessment of BPA-induced colitis. Our results showed a significant dysregulation of plasma proteins in these three models. Bioinformatics analysis, including gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and Ingenuity Pathway Analysis, highlighted the important effects of these dysregulated plasma proteins in immune and inflammatory responses through the regulation of CCR3 signaling in eosinophils, PI3K signaling in B lymphocytes, CD28 signaling in T helper cells, and leukocyte extravasation signaling in DSS-induced colitis model. Furthermore, our data suggested that BPA exposure altered the plasma proteins involved in lipid-related metabolic processes, leukocyte cell-cell adhesion and cytokine response. More importantly, we identified plasma proteins, ALB, APOA4, C3, CFB, DPEP1, HP, LTF, and Retnlg as biomarkers for assessing BPA-induced colitis.
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Affiliation(s)
- Chen Huang
- The Center for Data Science in Health and Medicine, Business School, Qingdao University, Qingdao, Shandong Province 266071, PR China.
| | - Yuqin Wang
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, PR China
| | - Xiao Lin
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Keng Po Lai
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, PR China
| | - Rong Li
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, PR China
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14
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Zhang L, Mao R, Lau CT, Chung WC, Chan JCP, Liang F, Zhao C, Zhang X, Bian Z. Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis based on machine learning methods. Sci Rep 2022; 12:9962. [PMID: 35705632 PMCID: PMC9200771 DOI: 10.1038/s41598-022-14048-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/31/2022] [Indexed: 12/11/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease with an increasing incidence and prevalence worldwide. The diagnosis for UC mainly relies on clinical symptoms and laboratory examinations. As some previous studies have revealed that there is an association between gene expression signature and disease severity, we thereby aim to assess whether genes can help to diagnose UC and predict its correlation with immune regulation. A total of ten eligible microarrays (including 387 UC patients and 139 healthy subjects) were included in this study, specifically with six microarrays (GSE48634, GSE6731, GSE114527, GSE13367, GSE36807, and GSE3629) in the training group and four microarrays (GSE53306, GSE87473, GSE74265, and GSE96665) in the testing group. After the data processing, we found 87 differently expressed genes. Furthermore, a total of six machine learning methods, including support vector machine, least absolute shrinkage and selection operator, random forest, gradient boosting machine, principal component analysis, and neural network were adopted to identify potentially useful genes. The synthetic minority oversampling (SMOTE) was used to adjust the imbalanced sample size for two groups (if any). Consequently, six genes were selected for model establishment. According to the receiver operating characteristic, two genes of OLFM4 and C4BPB were finally identified. The average values of area under curve for these two genes are higher than 0.8, either in the original datasets or SMOTE-adjusted datasets. Besides, these two genes also significantly correlated to six immune cells, namely Macrophages M1, Macrophages M2, Mast cells activated, Mast cells resting, Monocytes, and NK cells activated (P < 0.05). OLFM4 and C4BPB may be conducive to identifying patients with UC. Further verification studies could be conducted.
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Affiliation(s)
- Lin Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Rui Mao
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chung Tai Lau
- Chinese Clinical Trial Registry (Hong Kong), Hong Kong Chinese Medicine Clinical Study Centre, Chinese EQUATOR Centre, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Wai Chak Chung
- Chinese Clinical Trial Registry (Hong Kong), Hong Kong Chinese Medicine Clinical Study Centre, Chinese EQUATOR Centre, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Jacky C P Chan
- Department of Computer Science, HKBU Faculty of Science, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Feng Liang
- Chinese Clinical Trial Registry (Hong Kong), Hong Kong Chinese Medicine Clinical Study Centre, Chinese EQUATOR Centre, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Chenchen Zhao
- Oncology Department, The Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuan Zhang
- Chinese Clinical Trial Registry (Hong Kong), Hong Kong Chinese Medicine Clinical Study Centre, Chinese EQUATOR Centre, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China. .,Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong, SAR, China.
| | - Zhaoxiang Bian
- Chinese Clinical Trial Registry (Hong Kong), Hong Kong Chinese Medicine Clinical Study Centre, Chinese EQUATOR Centre, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China. .,Centre for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Hong Kong, SAR, China.
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15
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Platelet Mass Index and Other Platelet Parameters in the Assessment of Inflammatory Bowel Diseases Activity. CURRENT HEALTH SCIENCES JOURNAL 2021; 47:566-574. [PMID: 35444814 PMCID: PMC8987479 DOI: 10.12865/chsj.47.04.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/18/2021] [Indexed: 11/12/2022]
Abstract
Different qualitative and quantitative changes in platelets are involved in the pathophysiological processes in inflammatory bowel diseases (IBD): ulcerative colitis (UC) and Crohn's disease (CD). The aim of the study was to determine the diagnostic accuracy of Platelet mass Index (PMI) and other platelet parameters in assessment disease activity in patients with UC and CD. A cross-sectional, observational study consisted of 60 IBD patients (30 UC and 30 CD) and 30 healthy subjects (Control group). Patients were grouped according to disease activity into active and inactive (remission). Platelet count (PLC), Plateletcrit (PCT), Mean Platelet Volume (MPV), Platelet Distribution Width (PDW) and PMI were determined for all study participants. Receiver operating characteristic (ROC) curve and their corresponding areas under the curve (AUC) were used to determine diagnostic accuracy. Although PLC had the highest AUC (0.756) compared to PCT (AUC: 0.731), PDW (AUC: 0.722) and PMI (AUC: 0.724), they all had fair diagnostic accuracy in distinguishing active and inactive UC patients. Discriminatory accuracy of PLC was excellent (AUC: 0.909), PCT and PMI good to excellent (AUC: 0.809 and AUC: 0.893, respectively) and PDW fair (AUC: 0.789) in classifying CD patients as active and inactive. Platelet parameters are simple, routinely available biomarkers more useful for assessing disease activity for patients with CD than for patients with UC. Our results indicate, for the first time, that PMI may serve as a novel and simple marker in identifying whether IBD patients are in the active or inactive phase of the disease.
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