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Han M, Liang J, Hou M, Liu Y, Li H, Gao Z. Bifidobacterium bifidum Ameliorates DSS-Induced Colitis in Mice by Regulating Microbial Metabolome and Targeting Gut Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38838169 DOI: 10.1021/acs.jafc.4c00365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Inflammatory bowel disease (IBD) is a recurrent inflammatory condition affecting the gastrointestinal tract, and its clinical treatment remains suboptimal. Probiotics have shown effectiveness in alleviating dextran sulfate sodium salt (DSS)-induced colitis, exhibiting strain-specific anti-inflammatory properties. In this study, we compared the therapeutic effects of five strains of Bifidobacterium bifidum isolated from healthy adult feces on DSS-induced colitis in mice. Additionally, we investigated the underlying mechanisms by examining gut microbiota composition and microbial metabolome. Our findings highlighted the superior efficacy of B. bifidum M1-3 compared to other strains. It significantly improved colitis symptoms, mitigated gut barrier disruption, and reduced colonic inflammation in DSS-treated mice. Moreover, gut microbiota composition analysis revealed that B. bifidum M1-3 treatment increased the abundance and diversity of gut microbiota. Specifically, it significantly increased the abundance of Muribaculaceae, Lactobacillus, Bacteroides, and Enterorhabdus, while decreasing the abundance of Escherichia-Shigella. Furthermore, our nontargeted metabolomics analysis illustrated that B. bifidum M1-3 treatment had a regulatory effect on various metabolic pathways, including tyrosine metabolism, lysine degradation, and tryptophan metabolism. Importantly, we confirmed that the therapeutic efficiency of B. bifidum M1-3 was dependent on the gut microbiota. These results are conducive to the development of probiotic products for alleviating colitis.
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Affiliation(s)
- Mengzhen Han
- College of Food Science and Engineering, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Jingjing Liang
- College of Food Science and Engineering, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Mengxin Hou
- College of Food Science and Engineering, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Yuanye Liu
- College of Food Science and Engineering, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Hongcai Li
- College of Food Science and Engineering, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Zhenpeng Gao
- College of Food Science and Engineering, Northwest A&F University, 712100 Yangling, Shaanxi, China
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de Jesus LCL, Freitas ADS, Dutra JDCF, Campos GM, Américo MF, Laguna JG, Dornelas EG, Carvalho RDDO, Vital KD, Fernandes SOA, Cardoso VN, de Oliveira JS, de Oliveira MFA, Faria AMC, Ferreira E, Souza RDO, Martins FS, Barroso FAL, Azevedo V. Lactobacillus delbrueckii CIDCA 133 fermented milk modulates inflammation and gut microbiota to alleviate acute colitis. Food Res Int 2024; 186:114322. [PMID: 38729712 DOI: 10.1016/j.foodres.2024.114322] [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: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
Lactobacillus delbrueckii subsp. lactis CIDCA 133 is a health-promoting bacterium that can alleviate gut inflammation and improve the epithelial barrier in a mouse model of mucositis. Despite these beneficial effects, the protective potential of this strain in other inflammation models, such as inflammatory bowel disease, remains unexplored. Herein, we examined for the first time the efficacy of Lactobacillus delbrueckii CIDCA 133 incorporated into a fermented milk formulation in the recovery of inflammation, epithelial damage, and restoration of gut microbiota in mice with dextran sulfate sodium-induced colitis. Oral administration of Lactobacillus delbrueckii CIDCA 133 fermented milk relieved colitis by decreasing levels of inflammatory factors (myeloperoxidase, N-acetyl-β-D-glucosaminidase, toll-like receptor 2, nuclear factor-κB, interleukins 10 and 6, and tumor necrosis factor), secretory immunoglobulin A levels, and intestinal paracellular permeability. This immunobiotic also modulated the expression of tight junction proteins (zonulin and occludin) and the activation of short-chain fatty acids-related receptors (G-protein coupled receptors 43 and 109A). Colonic protection was effectively associated with acetate production and restoration of gut microbiota composition. Treatment with Lactobacillus delbrueckii CIDCA 133 fermented milk increased the abundance of Firmicutes members (Lactobacillus genus) while decreasing the abundance of Proteobacteria (Helicobacter genus) and Bacteroidetes members (Bacteroides genus). These promising outcomes influenced the mice's mucosal healing, colon length, body weight, and disease activity index, demonstrating that this immunobiotic could be explored as an alternative approach for managing inflammatory bowel disease.
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Affiliation(s)
- Luís Cláudio Lima de Jesus
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Andria Dos Santos Freitas
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Joyce da Cruz Ferraz Dutra
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriela Munis Campos
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Monique Ferrary Américo
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Guimarães Laguna
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | - Evandro Gonçalves Dornelas
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil
| | | | - Kátia Duarte Vital
- Federal University of Minas Gerais, Department of Clinical and Toxicological Analysis, Belo Horizonte, Minas Gerais, Brazil
| | | | - Valbert Nascimento Cardoso
- Federal University of Minas Gerais, Department of Clinical and Toxicological Analysis, Belo Horizonte, Minas Gerais, Brazil
| | - Jamil Silvano de Oliveira
- Federal University of Minas Gerais, Department of Biochemistry and Immunology, Belo Horizonte, Minas Gerais, Brazil
| | | | - Ana Maria Caetano Faria
- Federal University of Minas Gerais, Department of Biochemistry and Immunology, Belo Horizonte, Minas Gerais, Brazil
| | - Enio Ferreira
- Federal University of Minas Gerais, Department of General Pathology, Belo Horizonte, Minas Gerais, Brazil
| | - Ramon de Oliveira Souza
- Federal University of Minas Gerais, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil; Ezequiel Dias Foundation, Research and Development Board, Belo Horizonte, Minas Gerais, Brazil
| | - Flaviano Santos Martins
- Federal University of Minas Gerais, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | | | - Vasco Azevedo
- Federal University of Minas Gerais, Department of Genetics, Ecology, and Evolution, Belo Horizonte, Minas Gerais, Brazil.
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Zeng J, Gao X, Ge W, Huai M, Yang Z, Luo T, Gao L, Pan X. Development of a scoring system for predicting the severity of ulcerative colitis. Arab J Gastroenterol 2023; 24:211-217. [PMID: 37532662 DOI: 10.1016/j.ajg.2023.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND AND STUDY AIMS Monitoring disease activity in ulcerative colitis (UC) is critical in preventing long-term complications. This study aims to develop a scoring system using non-invasive indicators to predict endoscopic activities for ulcerative colitis (UC) patients. PATIENTS AND METHODS All enrolled patients with UC admitted to Shanghai Xinhua Hospital between June 2017 and January 2021 were enrolled, and their clinical data were retrospectively collected and a number of serological biomarkers concentrations were analyzed. Patients were categorized into mild and moderate-to-severe disease groups. Univariate and multivariate logistic regression was used to predict moderate-to-severe endoscopic activities, which were then incorporated into a nomogram to establish a prediction scoring model. RESULT Overall, 231 patients were divided into a mild group (n = 111, 48.0%) and a moderate-to-severe group (n = 120, 52.0%). The following variables were independently associated with the disease severity and were subsequently included into the prediction model: Proteinase 3 antineutrophil cytoplasmic antibody (PR3-ANCA), C-reactive protein (CRP), hemoglobin(Hb), IL-10, stool frequency ≥ 5 times/day and hematochezia. Incorporating these 6 factors, the nomogram showed good discrimination with C-index of 0.819 and reliable calibration. A scoring model was established with the area under the curve 0.818. Moreover, PR3-ANCA and CRP correlated with the duration of hospital stay. CONCLUSION We developed a predictive model for endoscopic disease activities by using noninvasive factors based on PR3-ANCA, CRP, Hb, IL-10, stool frequency and hematochezia. This prediction model might assist clinicians in managing patients with UC.
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Affiliation(s)
- Junxiang Zeng
- Department of Clinical Laboratory, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiupan Gao
- Department of Clinical Laboratory, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wensong Ge
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Manxiu Huai
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhigang Yang
- Department of Gastroenterology Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Luo
- Department of Clinical Laboratory, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Limei Gao
- Department of Clinical Laboratory, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiujun Pan
- Department of Clinical Laboratory, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Carlini V, Noonan DM, Abdalalem E, Goletti D, Sansone C, Calabrone L, Albini A. The multifaceted nature of IL-10: regulation, role in immunological homeostasis and its relevance to cancer, COVID-19 and post-COVID conditions. Front Immunol 2023; 14:1161067. [PMID: 37359549 PMCID: PMC10287165 DOI: 10.3389/fimmu.2023.1161067] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Interleukin-10 (IL-10) is a pleiotropic cytokine that has a fundamental role in modulating inflammation and in maintaining cell homeostasis. It primarily acts as an anti-inflammatory cytokine, protecting the body from an uncontrolled immune response, mostly through the Jak1/Tyk2 and STAT3 signaling pathway. On the other hand, IL-10 can also have immunostimulating functions under certain conditions. Given the pivotal role of IL-10 in immune modulation, this cytokine could have relevant implications in pathologies characterized by hyperinflammatory state, such as cancer, or infectious diseases as in the case of COVID-19 and Post-COVID-19 syndrome. Recent evidence proposed IL-10 as a predictor of severity and mortality for patients with acute or post-acute SARS-CoV-2 infection. In this context, IL-10 can act as an endogenous danger signal, released by tissues undergoing damage in an attempt to protect the organism from harmful hyperinflammation. Pharmacological strategies aimed to potentiate or restore IL-10 immunomodulatory action may represent novel promising avenues to counteract cytokine storm arising from hyperinflammation and effectively mitigate severe complications. Natural bioactive compounds, derived from terrestrial or marine photosynthetic organisms and able to increase IL-10 expression, could represent a useful prevention strategy to curb inflammation through IL-10 elevation and will be discussed here. However, the multifaceted nature of IL-10 has to be taken into account in the attempts to modulate its levels.
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Affiliation(s)
- Valentina Carlini
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), MultiMedica, Milan, Italy
| | - Douglas M. Noonan
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), MultiMedica, Milan, Italy
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Eslam Abdalalem
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), MultiMedica, Milan, Italy
| | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Clementina Sansone
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Napoli, Italy
| | - Luana Calabrone
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), MultiMedica, Milan, Italy
| | - Adriana Albini
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) European Institute of Oncology IEO-, Milan, Italy
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Li Y, Ye Z, He H, Hu Y, Wu M, Li L, Chen L, Qian H, Shi Q, Zhang C, Yu H, Zhao Q, Liu X, Qin K, Ye Q. The application of Tong-fu therapeutic method on ulcerative colitis: A systematic review and meta-analysis for efficacy and safety of rhubarb-based therapy. Front Pharmacol 2022; 13:1036593. [DOI: 10.3389/fphar.2022.1036593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Tong-fu therapeutic method (TFTM) is a traditional Chinese medicine treatment method for ulcerative colitis, which is a novel treatment strategies and have purgative effect. As the most representative medicinal of TFTM, Rhubarb has been reported to have a therapeutic impact on ulcerative colitis by regulating intestinal flora, anti-inflammation, and improving intestinal microcirculation. Although rhubarb has been widely used in Chinese medicine for the treatment of ulcerative colitis, the appropriate protocol is still demanded to its rational use in clinic, which promoted to evaluate the efficacy and safety for rhubarb-based therapy on ulcerative colitis.Method: Clinical trials were searched through PubMed, Cochrane Library, Web of Science, Excerpta Medica Database, Chinese National Knowledge Infrastructure, WAN FANG Database, Chinese Scientific Journal Database, and Chinese Biomedical Literature Database. The subgroup analyses were performed with three groups: medication, course of treatment, and route of administration. The statistical analyses were performed on Review Manager software (version 5.4.1).Results: A total of 2, 475 patients in 30 original studies were analyzed in this article. It was found that rhubarb-based therapy could increase clinical efficacy and reduce the recurrence rate. Subgroup analyses showed that rhubarb-based therapy was more effective than 5-aminosalicylic acid or sulfasalazine alone. In addition, the hypercoagulable state of ulcerative colitis could be ameliorated by decreasing platelet (PLT) and fibrinogen (FIB), and increasing prothrombin time (PT) significantly. Moreover, C-reaction protein (CRP), tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL-8, and IL-1β expression were significantly reduced, while IL-10 production was increased, which mediated the alleviation of intestinal inflammation stress.Conclusion: Rhubarb-based therapy could effectively improve ulcerative colitis. Of note, the rhubarb-based medicinal formulas combined with 5-ASA or SASP are more effective than the 5-ASA or SASP alone. In addition, although rhubarb has side effect, the results of our analysis showed that rhubarb-based therapy did not exhibit significant side effects. This means it has a high safety profile in clinical use. Moreover, the use of rhubarb-based therapy is recommend to use within 1–13 weeks or 3 months via administered orally or by enema, which is contributes to ensure the curative effect and avoid its toxic and side effects. As an important case of TFTM, rhubarb-based therapy provides evidence for the practical application of TFTM.
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Shi G, Jiang H, Feng J, Zheng X, Zhang D, Jiang C, Zhang J. Aloe vera mitigates dextran sulfate sodium-induced rat ulcerative colitis by potentiating colon mucus barrier. JOURNAL OF ETHNOPHARMACOLOGY 2021; 279:114108. [PMID: 33839199 DOI: 10.1016/j.jep.2021.114108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Aloe vera (L.) Burm. f. (Aloe vera) is a medicinal herb that used in Traditional Chinese Medicine (TCM) practice for the treatment of gastrointestinal diseases such as constipation and colitis. Recent studies also reported its beneficial effect in mitigating ulcerative colitis (UC). Nevertheless, the underlying mechanisms of Aloe vera against UC remain largely unknown. AIM OF THE STUDY This study aimed to explore a relation between the therapeutical effects of Aloe vera in UC and colonic mucus secretion, and further investigate the underlying pathways through which Aloe vera regulates colon mucus as well as preliminarily studied the main active constitute of Aloe vera to alleviate UC. MATERIALS AND METHODS UPLC-MS/MS were employed to analyze the Aloe vera extract. The rat models of UC were induced by free subjected to fresh 3% dextran sulfate sodium (DSS) solution for 8 days and then accessed to tap water for 2 days. Aloe vera extract (18 mg/kg and 72 mg/kg) or 5-ASA (400 mg/kg) was administered orally from day 1-10. At the end of experiment, rats were sacrificed and the colon tissues were harvested for analysis. UC symptoms was evaluated by disease activity index (DAI), colon length and H&E staining. The Alcian blue stain were determined colon mucus layer. Myeloperoxidase (MPO) activity, mucin and inflammatory cytokines in colon tissues were determined by ELISA. The expression of related proteins on PI3K/AKT and PKC/ERK signaling pathway was analyzed by Western blot. We then evaluated the effects of three main components of Aloe vera (Aloe-emodin, aloin A and B) on mucin secretion and cytokine expression in vitro by ELISA. RESULTS Oral supplement with Aloe vera extract resulted in a significantly decreased DSS-induced UC symptoms, including decreased DAI, prevention of the colon length shortening, and alleviation of the pathological changes occurring in colon. The expression of colonic pro-inflammatory mediators, including IL-6, IL-1β and TNF-α were suppressed, yet the expression of IL-10 was up-regulated by Aloe vera treatment. Moreover, Aloe vera significantly up-regulated the expressions of mucin proteins (e.g., MUC2 and MUC5AC) and increased the thickness of mucus layer in the colon. Further, we revealed that Aloe vera significantly upregulated p-PKC and p-ERK expression and downregulated p-PI3K and p-AKT expression. Finally, we discovered that treat with aloin A markedly decreased IL-6 levels and increased MUC2 expression in LPS-stimulated LS174T cell. CONCLUSION These results support that Aloe vera improved UC by enhancing colon mucus barrier functions in addition to reducing inflammation. Moreover, aloin A might be a main active components of Aloe vera to ameliorate UC.
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Affiliation(s)
- Gaofeng Shi
- School of Third Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, PR China
| | - Hui Jiang
- Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, PR China; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jianrong Feng
- Department of colorectal surgery, Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, 211200, PR China
| | - Xian Zheng
- Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, PR China; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Dongjian Zhang
- Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, PR China
| | - Cuihua Jiang
- Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, PR China
| | - Jian Zhang
- School of Third Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, PR China.
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Calatayud M, Verstrepen L, Ghyselinck J, Van den Abbeele P, Marzorati M, Modica S, Ranjanoro T, Maquet V. Chitin Glucan Shifts Luminal and Mucosal Microbial Communities, Improve Epithelial Barrier and Modulates Cytokine Production In Vitro. Nutrients 2021; 13:nu13093249. [PMID: 34579126 PMCID: PMC8467507 DOI: 10.3390/nu13093249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 12/15/2022] Open
Abstract
The human gut microbiota has been linked to the health status of the host. Modulation of human gut microbiota through pro- and prebiotic interventions has yielded promising results; however, the effect of novel prebiotics, such as chitin-glucan, on gut microbiota-host interplay is still not fully characterized. We assessed the effect of chitin-glucan (CG) and chitin-glucan plus Bifidobacterium breve (CGB) on human gut microbiota from the luminal and mucosal environments in vitro. Further, we tested the effect of filter-sterilized fecal supernatants from CG and CGB fermentation for protective effects on inflammation-induced barrier disruption and cytokine production using a co-culture of enterocytes and macrophage-like cells. Overall, CG and CGB promote health-beneficial short-chain fatty acid production and shift human gut microbiota composition, with a consistent effect increasing Roseburia spp. and butyrate producing-bacteria. In two of three donors, CG and CGB also stimulated Faecalibacterium prausniitzi. Specific colonization of B. breve was observed in the lumen and mucosal compartment; however, no synergy was detected for different endpoints when comparing CGB and CG. Both treatments included a significant improvement of inflammation-disrupted epithelial barrier and shifts on cytokine production, especially by consistent increase in the immunomodulatory cytokines IL10 and IL6.
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Affiliation(s)
- Marta Calatayud
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium; (L.V.); (J.G.); (P.V.d.A.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9052 Ghent, Belgium
- Correspondence: (M.C.); or (M.M.)
| | - Lynn Verstrepen
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium; (L.V.); (J.G.); (P.V.d.A.)
| | - Jonas Ghyselinck
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium; (L.V.); (J.G.); (P.V.d.A.)
| | | | - Massimo Marzorati
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium; (L.V.); (J.G.); (P.V.d.A.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9052 Ghent, Belgium
- Correspondence: (M.C.); or (M.M.)
| | - Salvatore Modica
- KitoZyme SA., Parc Industriel des Hauts Sarts, 4040 Herstal, Belgium; (S.M.); (T.R.); (V.M.)
| | - Thibaut Ranjanoro
- KitoZyme SA., Parc Industriel des Hauts Sarts, 4040 Herstal, Belgium; (S.M.); (T.R.); (V.M.)
| | - Véronique Maquet
- KitoZyme SA., Parc Industriel des Hauts Sarts, 4040 Herstal, Belgium; (S.M.); (T.R.); (V.M.)
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Maden SF, Acuner SE. Mapping Transcriptome Data to Protein-Protein Interaction Networks of Inflammatory Bowel Diseases Reveals Disease-Specific Subnetworks. Front Genet 2021; 12:688447. [PMID: 34484291 PMCID: PMC8416454 DOI: 10.3389/fgene.2021.688447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/19/2021] [Indexed: 12/31/2022] Open
Abstract
Inflammatory bowel disease (IBD) is the common name for chronic disorders associated with the inflammation of the gastrointestinal tract. IBD is triggered by environmental factors in genetically susceptible individuals and has a significant number of incidences worldwide. Crohn’s disease (CD) and ulcerative colitis (UC) are the two distinct types of IBD. While involvement in ulcerative colitis is limited to the colon, Crohn’s disease may involve the whole gastrointestinal tract. Although these two disorders differ in macroscopic inflammation patterns, they share various molecular pathogenesis, yet the diagnosis can remain unclear, and it is important to reveal their molecular signatures in the network level. Improved molecular understanding may reveal disease type-specific and even individual-specific targets. To this aim, we determine the subnetworks specific to UC and CD by mapping transcriptome data to protein–protein interaction (PPI) networks using two different approaches [KeyPathwayMiner (KPM) and stringApp] and perform the functional enrichment analysis of the resulting disease type-specific subnetworks. TP63 was identified as the hub gene in the UC-specific subnet and p63 tumor protein, being in the same family as p53 and p73, has been studied in literature for the risk associated with colorectal cancer and IBD. APP was identified as the hub gene in the CD-specific subnet, and it has an important role in the pathogenesis of Alzheimer’s disease (AD). This relation suggests that some similar genetic factors may be effective in both AD and CD. Last, in order to understand the biological meaning of these disease-specific subnets, they were functionally enriched. It is important to note that chemokines—special types of cytokines—and antibacterial response are important in UC-specific subnets, whereas cytokines and antimicrobial responses as well as cancer-related pathways are important in CD-specific subnets. Overall, these findings reveal the differences between IBD subtypes at the molecular level and can facilitate diagnosis for UC and CD as well as provide potential molecular targets that are specific to disease subtypes.
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Affiliation(s)
- Sefika Feyza Maden
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
| | - Saliha Ece Acuner
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
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