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Yang Y, Hua Y, Zheng H, Jia R, Ye Z, Su G, Gu Y, Zhan K, Tang K, Qi S, Wu H, Qin S, Huang S. Biomarkers prediction and immune landscape in ulcerative colitis: Findings based on bioinformatics and machine learning. Comput Biol Med 2024; 168:107778. [PMID: 38070204 DOI: 10.1016/j.compbiomed.2023.107778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/02/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Ulcerative colitis (UC) presents diagnostic and therapeutic difficulties. The primary objective of this study is to identify efficacious biomarkers for diagnosis and treatment, as well as acquire a deeper understanding of the immuneological characteristics associated with the disease. METHODS Datasets relating to UC were obtained from GEO database. Among these, three datasets were merged to create a metadata for bioinformatics analysis and machine learning. Additionally, one dataset specifically utilized for external validation. Least absolute shrinkage and selection operator (LASSO) and random forest (RF) were employed to screen signature genes. The artificial neural network (ANN) model and receiver operating characteristic (ROC) curve were used to assess the diagnostic performance of signature genes. The single sample gene set enrichment analysis (ssGSEA) was applied to reveal the immune landscape. Finally, the relationship between the signature genes, immune infiltration, and clinical characteristics was investigated through correlation analysis. RESULT By intersecting the result of LASSO, RF and WGCNA, 8 signature genes were identified, including S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14. The biological progress of this gene mostly encompasses acute inflammatory response, aggregation and chemotaxis of leukocyte, and response to lipopolysaccharide by mediating IL-17 signaling pathway, NF-kappa B signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway. Immune infiltration analysis shows 25 immune cells are significantly elevated in UC samples. Moreover, these signature genes exhibit a strong correlation with various immune cells and a mild to moderate correlation with the Mayo score. CONCLUSION S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14 have been identified as credible potential biomarkers for the diagnosis and therapy of UC. The immune response mediated by these signature biomarkers plays a crucial role in the occurrence and advancement of UC by means of the reciprocal interaction between the signature biomarkers and immune-infiltrated cells.
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Affiliation(s)
- Yuanming Yang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Yiwei Hua
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Huan Zheng
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Rui Jia
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zhining Ye
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Guifang Su
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Yueming Gu
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Kai Zhan
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Kairui Tang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Shuhao Qi
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Haomeng Wu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China
| | - Shumin Qin
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China.
| | - Shaogang Huang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China; Yang Chunbo academic experience inheritance studio of Guangdong provincial hospital of Chinese Medicine, Guangzhou, 510006, China.
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Zhan K, Pan H, Zhou Z, Tang W, Ye Z, Huang S, Luo L. Biological role of long non-coding RNA KCNQ1OT1 in cancer progression. Biomed Pharmacother 2023; 169:115876. [PMID: 37976888 DOI: 10.1016/j.biopha.2023.115876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a type of RNAs that are more than 200 nucleotides without protein-coding potential. In recent years, more and more attention has been paid to the role of lncRNAs in cancer pathogenesis. LncRNA KCNQ1 overlapping transcript 1 (KCNQ1OT1) is located on chromosome 11p15.5 with a total length of 91 kb and is highly expressed in various malignancies, which is closely related to tumor growth, lymph node metastasis, survival cycle and recurrence rate. In addition, KCNQ1OT1 is involved in the regulation of PI3K/AKT and Wnt/β-catenin signaling pathways. In this review, the mechanism and related progress of KCNQ1OT1 in different cancers were reviewed. It was found that KCNQ1OT1 can stabilize mRNA expression through sponging miRNA, which not only induced tumor cell proliferation, migration, invasion, drug resistance, epithelial-mesenchymal transition (EMT) and inhibited cell apoptosis in vitro, but also promoted tumor growth and metastasis in vivo. Therefore, as a new biomarker and therapeutic target, KCNQ1OT1 has broad prospects for the diagnosis and treatment of different cancers.
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Affiliation(s)
- Kai Zhan
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523000, China
| | - Huafeng Pan
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhang Zhou
- Department of Anesthesiology, Wuhan Fourth Hospital, Wuhan 430000, China
| | - Wenqian Tang
- Department of Health Management Center, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430070, China
| | - Zhining Ye
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523000, China
| | - Shaogang Huang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523000, China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Lei Luo
- Department of Health Management Center, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430070, China.
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Wu LH, Ye ZN, Peng P, Xie WR, Xu JT, Zhang XY, Xia HHX, He XX. Efficacy and Safety of Washed Microbiota Transplantation to Treat Patients with Mild-to-Severe COVID-19 and Suspected of Having Gut Microbiota Dysbiosis: Study Protocol for a Randomized Controlled Trial. Curr Med Sci 2021; 41:1087-1095. [PMID: 34846698 PMCID: PMC8630278 DOI: 10.1007/s11596-021-2475-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 11/02/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Coronavirus disease 2019 (COVID-19) is often accompanied by gastrointestinal symptoms, which are related to gut microbiota dysbiosis (GMD). Whether washed microbiota transplantation (WMT) is an effective treatment for COVID-19 patients suspected of having GMD by restoring the gut microbiota is unknown. This study is designed to explore the efficacy and safety of WMT in COVID-19 patients suspected of having GMD. METHODS This is a randomized, multicenter, single-blind prospective study. COVID-19 patients suspected of having GMD will be randomly divided to receive routine treatment only or to receive routine treatment and WMT. The frequency of WMT will be once a day for three consecutive days. Laboratory and imaging examinations will be performed at admission, 1 and 2 weeks after treatment, and on the day of discharge. Then a telephone follow-up will be conducted at 1st week, 2nd week, and 6th month after discharge. The clinical efficacy and safety of WMT in COVD-19 patients suspected of having GMD and the effects of WMT on the organ function, homeostasis, inflammatory response, intestinal mucosal barrier function, and immunity of the patients will be evaluated. RESULTS By following the proposed protocol, WMT is expected to be efficacious and safe for the treatment of COVID-19 patients suspected of having GMD, and the therapeutic effect is expected to be associated with improvement of the intestinal mucosal barrier function, inflammatory response, and immunity. CONCLUSION The findings from this study may offer a new approach for the prevention and treatment of COVID-19 patients suspected of having GMD.
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Affiliation(s)
- Li-hao Wu
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
- Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
| | - Zhi-ning Ye
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
- Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
| | - Ping Peng
- Guangzhou Eighth People’s Hospital, Guangzhou, 510060 China
| | - Wen-rui Xie
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
- Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
| | - Jia-ting Xu
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
- Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
| | - Xue-yuan Zhang
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
- Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
| | - Harry Hua-xiang Xia
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
| | - Xing-xiang He
- Department of Gastroenterology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
- Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080 China
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