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Sokouti B. The identification of biomarkers for Alzheimer's disease using a systems biology approach based on lncRNA-circRNA-miRNA-mRNA ceRNA networks. Comput Biol Med 2024; 179:108860. [PMID: 38996555 DOI: 10.1016/j.compbiomed.2024.108860] [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: 03/13/2024] [Revised: 06/16/2024] [Accepted: 07/06/2024] [Indexed: 07/14/2024]
Abstract
In addition to being the most prevalent form of neurodegeneration among the elderly, AD is a devastating multifactorial disease. Currently, treatments address only its symptoms. Several clinical studies have shown that the disease begins to manifest decades before the first symptoms appear, indicating that studying early changes is crucial to improving early diagnosis and discovering novel treatments. Our study used bioinformatics and systems biology to identify biomarkers in AD that could be used for diagnosis and prognosis. The procedure was performed on data from the GEO database, and GO and KEGG enrichment analysis were performed. Then, we set up a network of interactions between proteins. Several miRNA prediction tools including miRDB, miRWalk, and TargetScan were used. The ceRNA network led to the identification of eight mRNAs, four circRNAs, seven miRNAs, and seven lncRNAs. Multiple mechanisms, including the cell cycle and DNA replication, have been linked to the promotion of AD development by the ceRNA network. By using the ceRNA network, it should be possible to extract prospective biomarkers and therapeutic targets for the treatment of AD. It is possible that the processes involved in DNA cell cycle and the replication of DNA contribute to the development of Alzheimer's disease.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Feng J, Wang H, Luo X, Zhang L, Zhou P. Identification and molecular mechanism of the anti-inflammatory effect of sea cucumber peptides: Network pharmacology, molecular docking and animal experiments. Int J Biol Macromol 2024; 279:134958. [PMID: 39222781 DOI: 10.1016/j.ijbiomac.2024.134958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease for which there is currently no efficacious therapeutic drug with fewer side effects. Therefore, the development of approaches for the prevention of UC from natural food sources is urgently needed. In this study, mice were pre-fed with sea cucumber peptides prior to dextran sodium sulfate (DSS) induction. Results showed that sea cucumber peptides decreased pro-inflammatory cytokine (IL-4 and IL-10) levels and remissions of main clinic symptoms in a dose-dependent manner. The composition of peptides was identified, and the anti-inflammatory molecular mechanism was evaluated by silico prediction. The molecular weight of the peptides was 243-1800 Da and composed of 3-18 amino acid residues. Online activity assessment and molecular docking prediction revealed that tripeptides of FGI, FLI, FLL, GFL, GFM, IGF and LDF exhibited strong anti-inflammatory activity. Particularly, LDF showed the highest potency, with a binding energy of -5.37 kJ/mol. Network pharmacology analysis of UC related diseases indicated that active peptides interact with colitis disease targets, primarily proto-oncogene tyrosine-protein kinase Src (SRC), E3 ubiquitin-protein ligase XIAP (XIAP) and angiotensin-converting enzyme (ACE). The results suggest that sea cucumber peptides have potential as a novel nutraceutical option for colitis relief.
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Affiliation(s)
- Jianhui Feng
- Center for Mitochondria and Healthy Aging, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Haojie Wang
- Center for Mitochondria and Healthy Aging, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Xinyue Luo
- Center for Mitochondria and Healthy Aging, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Lina Zhang
- State Key Laboratory of Food Science & Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
| | - Peng Zhou
- State Key Laboratory of Food Science & Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
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Chen W, Xu Z, Jiang J, Chen H, Shi R. Identification of LPCAT1 as a key biomarker for Crohn's disease based on bioinformatics and machine learnings and experimental verification. Gene 2024; 920:148519. [PMID: 38703867 DOI: 10.1016/j.gene.2024.148519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Epithelial-mesenchymal transition (EMT) plays a crucial role in regulating inflammatory responses and fibrosis formation. This study aims to explore the molecular mechanisms of EMT-related genes in Crohn's disease (CD) through bioinformatics methods and identify potential key biomarkers. In our research, we identified differentially expressed genes (DEGs) related to EMT based on the GSE52746 dataset and the gene set in the GeneCards database. Key genes were identified through Lasso-cox and Random Forest and validated using the external dataset GSE10616. Immune infiltration analysis showed that Lysophosphatidylcholine acyltransferase 1 (LPCAT1) was positively correlated with Neutrophils and Macrophages M1. The Gene Set Enrichment Analysis (GSEA) results for LPCAT1 showed associations with celladhesionmolecules and ECM receptor interaction. Additionally, a lncRNA-miRNA-mRNA ceRNA network was constructed. Finally, we validated that knocking down LPCAT1 could inhibit the release of inflammatory factors, EMT, and the elevation of fibrosis indices as well as the activation of NF-κB signaling pathway in LPS-induced HT-29 cells. LPCAT1 plays an important role in the occurrence and development of CD and may become a new biomarker.
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Affiliation(s)
- Wei Chen
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Zeyan Xu
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Jingjing Jiang
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Hong Chen
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
| | - Ruihua Shi
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
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Ye C, Zhu S, Yuan J, Yuan X. FPR1, as a Potential Biomarker of Diagnosis and Infliximab Therapy Responses for Crohn's Disease, is Related to Disease Activity, Inflammation and Macrophage Polarization. J Inflamm Res 2024; 17:3949-3966. [PMID: 38911989 PMCID: PMC11193993 DOI: 10.2147/jir.s459819] [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: 01/16/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024] Open
Abstract
Purpose Crohn's disease (CD) represents a multifaceted inflammatory gastrointestinal condition, with a profound significance placed on unraveling its molecular pathways to enhance both diagnostic capabilities and therapeutic interventions. This study focused on identifying a robust macrophage-related signatures (MacroSig) for diagnosing CD, emphasizing the role of FPR1 in macrophage polarization and its implications in CD. Patients and Methods Expression profiles from intestinal biopsies and macrophages of 1804 CD patients were retrieved from the Gene Expression Omnibus (GEO). Utilizing CIBERSORTx, differential expression analysis, and weighted correlation network analysis to to identify macrophage-related genes (MRGs). By unsupervised clustering, distinct clusters of CD were identified. Potential biomarkers were identified via using four machine learning algorithms, leading to the establishment of MacroSig which combines insights from 12 machine learning algorithms. Furthermore, the expression of FPR1 was verified in intestinal biopsies of CD patients and two murine experimental colitis models. Finally, we further explored the role of FPR1 in macrophage polarization through single-cell analysis as well as through the study of RAW264.7 cells and peritoneal macrophages. Results Two distinct clusters with differential levels of macrophage infiltration and inflammation were identified. The MacroSig, which included FPR1 and LILRB2, exhibited high diagnostic accuracy and outperformed existing biomarkers and signatures. Clinical analysis demonstrated a strong correlation of FPR1 with disease activity, endoscopic inflammation status, and response to infliximab treatment. The expression levels of FPR1 were validated in our CD cohort by immunohistochemistry and confirmed in two colitis mouse models. Single-cell analysis indicated that FPR1 is predominantly expressed in macrophages and monocytes. In vitro studies demonstrated that FPR1 was upregulated in M1 macrophages, and its activation promoted M1 polarization. Conclusion We developed a promising diagnostic signature for CD, and targeting FPR1 to modulate macrophage polarization may represent a novel therapeutic strategy.
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Affiliation(s)
- Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Sizhe Zhu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, People’s Republic of China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Xiuxue Yuan
- Medical College of Wuhan University of Science and Technology, Wuhan, Hubei, People’s Republic of China
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Ortiz-Cerda T, Argüelles-Arias F, Macías-García L, Vázquez-Román V, Tapia G, Xie K, García-García MD, Merinero M, García-Montes JM, Alcudia A, Witting PK, De-Miguel M. Effects of polyphenolic maqui ( Aristotelia chilensis) extract on the inhibition of NLRP3 inflammasome and activation of mast cells in a mouse model of Crohn's disease-like colitis. Front Immunol 2024; 14:1229767. [PMID: 38283356 PMCID: PMC10811055 DOI: 10.3389/fimmu.2023.1229767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction Crohn's disease (CD) involves activation of mast cells (MC) and NF-кB in parallel with the PPAR-α/NLRP3 inflammasome/IL-1β pathway in the inflamed colon. Whether polyphenols from maqui (Aristotelia chilensis) represent a natural alternative treatment for CD is unclear. Therefore, we used an animal model of 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced CD-like colitis to investigate protective effects of maqui extract through monitoring NLRP3 inflammasome and MC activation in colon tissue. Methods Maqui extract was administered via orogastric route to mice after (post-Treatment group) or prior (pre-Treatment group) to TNBS-induction. Colon pathology was characterized by histoarchitectural imaging, disease activity index (DAI), and assessing NF-кB, p-NF-кB, PPAR-α/NLRP3 expression and IL-1β levels. Results Compared to mice treated with TNBS alone administration of anthocyanin-rich maqui extract improved the DAI, colon histoarchitecture and reduced both colon wet-weight and transmural inflammation. Induction with TNBS significantly increased colonic NLPR3 inflammasome activation, while co-treatment with maqui extract (either post- or pre-Treatment) significantly downregulated NLRP3, ASC and caspase-1 levels, which manifested as reduced colonic IL-1β levels. Supplemented maqui extract marginally diminished NF-кB activity in epithelial cells but reached statistical significance in immune cells (as judged by decreased NF-кB phosphorylation). PPAR-α signaling was largely unaffected by Maqui whereas MC infiltration into the colon mucosa and submucosa decreased and their level of degranulation was suppressed. Conclusion These outcomes show the post- and pre- Treatment effect of a polyphenolic extract rich in anthocyanins from maqui the acute phase of TNBS- induced CD-like colitis is linked to suppression of the NLRP3 inflammasome and reduced MC responses. These data indicate that maqui extract represents a potential nutraceutical for the treatment of inflammatory bowel disease (IBD).
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Affiliation(s)
- Tamara Ortiz-Cerda
- Departamento de Citología e Histología Normal y Patológica, Facultad de medicina, Universidad de Sevilla, Seville, Spain
- Redox Biology Group, The Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Federico Argüelles-Arias
- Departamento de Medicina, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Department of Gastroenterology, University Hospital Virgen Macarena, Seville, Spain
| | - Laura Macías-García
- Departamento de Citología e Histología Normal y Patológica, Facultad de medicina, Universidad de Sevilla, Seville, Spain
| | - Victoria Vázquez-Román
- Departamento de Citología e Histología Normal y Patológica, Facultad de medicina, Universidad de Sevilla, Seville, Spain
| | - Gladys Tapia
- Molecular and Clinical Pharmacology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Kangzhe Xie
- Redox Biology Group, The Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | | | - Manuel Merinero
- Departamento de Citología e Histología Normal y Patológica, Facultad de medicina, Universidad de Sevilla, Seville, Spain
- Departamento de Química Orgánica y Farmacéutica, Universidad de Sevilla, Seville, Spain
| | | | - Ana Alcudia
- Departamento de Química Orgánica y Farmacéutica, Universidad de Sevilla, Seville, Spain
| | - Paul K. Witting
- Redox Biology Group, The Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Manuel De-Miguel
- Departamento de Citología e Histología Normal y Patológica, Facultad de medicina, Universidad de Sevilla, Seville, Spain
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Ye C, Zhu S, Gao Y, Huang Y. Landscape of sialylation patterns identify biomarkers for diagnosis and prediction of response to anti-TNF therapy in crohn's disease. Front Genet 2022; 13:1065297. [PMID: 36452157 PMCID: PMC9702336 DOI: 10.3389/fgene.2022.1065297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 10/21/2022] [Indexed: 07/22/2023] Open
Abstract
Crohn's disease (CD), a subtype of inflammatory bowel disease (IBD), causes chronic gastrointestinal tract inflammation. Thirty percent of patients do not respond to anti-tumor necrosis factor (TNF) therapy. Sialylation is involved in the pathogenesis of IBD. We aimed to identify potential biomarkers for diagnosing CD and predicting anti-TNF medication outcomes in CD. Three potential biomarkers (SERPINB2, TFPI2, and SLC9B2) were screened using bioinformatics analysis and machine learning based on sialylation-related genes. Moreover, the combined model of SERPINB2, TFPI2, and SLC9B2 showed excellent diagnostic value in both the training and validation cohorts. Importantly, a Sial-score was constructed based on the expression of SERPINB2, TFPI2, and SLC9B2. The Sial-low group showed a lower level of immune infiltration than the Sial-high group. Anti-TNF therapy was effective for 94.4% of patients in the Sial-low group but only 15.8% in the Sial-high group. The Sial-score had an outstanding ability to predict and distinguish between responders and non-responders. Our comprehensive analysis indicates that SERPINB2, TFPI2, and SLC9B2 play essential roles in pathogenesis and anti-TNF therapy resistance in CD. Furthermore, it may provide novel concepts for customizing treatment for individual patients with CD.
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Affiliation(s)
- Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sizhe Zhu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Gao
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yabing Huang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
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Wen Z, Wu L, Wang L, Ou Q, Ma H, Wu Q, Zhang S, Song Y. Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers. Front Genet 2022; 13:832739. [PMID: 35345666 PMCID: PMC8957076 DOI: 10.3389/fgene.2022.832739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/10/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose: The purpose of this study is to use the data in the GEO database to analyze, screen biomarkers that can diagnose tuberculosis, and verification of candidate biomarkers. Materials and methods: GSE158767 dataset were used to process WGCNA analysis, differential gene analysis, Gene ontology and KEGG analysis, protein-protein network analysis and hub genes analysis. Based on our previous study, the intersect between WGCNA and differential gene analysis could be used as candidate biomarkers. Then, the enzyme-linked immunosorbent assay was used to validate candidate biomarkers, and receiver operating characteristic was used to assess diagnose ability of candidate biomarkers. Results: A total of 412 differential genes were screened. And we obtained 105 overlapping genes between DEGs and WGCNA. GO and KEGG analysis showed that most of the differential genes were significantly enriched in innate immunity. A total of 15 hub genes were screened, and four of them were verified by Enzyme-linked immunosorbent assay. CCL5 performed well in distinguishing the healthy group from the TB group (AUC = 0.723). And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811). Conclusion: CCL19, C1Qb, CCL5 and HLA-DMB may play important role in tuberculosis, which indicated four genes may become effective biomarkers and could be conveniently used to facilitate the individual tuberculosis diagnosis in Chinese people.
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Affiliation(s)
- Zilu Wen
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liwei Wu
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lin Wang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qinfang Ou
- Department of TB, The fifth people's hospital of Wuxi, Wuxi, China
| | - Hui Ma
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qihang Wu
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shulin Zhang
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yanzheng Song
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,TB Center, Shanghai Emerging and Re-emerging Infectious Diseases Institute, Shanghai, China
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