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Abudurousuli K, Talihati Z, Hailati S, Han MY, Nuer M, Khan N, Maihemuti N, Dilimulati D, Nueraihemaiti N, Simayi J, Zhou W. Investigation of target genes and potential mechanisms related to compound Xiao-ai-fei honey ointment based on network pharmacology and bioinformatics analysis. Medicine (Baltimore) 2023; 102:e34629. [PMID: 37565919 PMCID: PMC10419591 DOI: 10.1097/md.0000000000034629] [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: 05/12/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Compound Xiao-ai-fei honey ointment (CXHO) is an anticancer preparation with a long history in Uyghur folk medicine in China and has been used for the treatment of gastric cancer (GC) in Xinjiang, China. Nevertheless, the mechanism of its anticancer effect remains to be investigated. METHODS Bioactive ingredients of CXHO were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. Target genes of ingredients were acquired via the PubChem and Swiss target prediction database. Gene expression profiling of GC was obtained from GSE54129 in the GEO database and analyzed using the limma package in R. The hub genes associated with CXHO in GC were validated using the TIMER2.0 database, GEPIA2 database and Auto Dock tools. The effect of CXHO on migration of GC cells was detected by Transwell chamber assay and Wound healing assay. The effect of CXHO on expression levels of MMP2/MMP9 and NF-κb, PI3K/AKT signaling pathway was detected by Western blot assay. RESULTS Forty-five bioactive ingredients and their 819 related genes were found. A total of 462 differentially expressed genes were identified between GC patients and healthy controls. Seventeen common target genes were identified as hub genes CXHO against GC. Among them, MMP2 and MMP9 were significantly associated with tumor immune infiltrates and had good binding affinity with effective ingredients. Moreover, we validated the mRNA and protein expression levels and prognostic value of MMP2 and MMP9 by different databases. In addition, Kyoto encyclopedia of genes and genomes and gene ontology analyses showed that the 17 common target genes were mainly involved in steroid hormone biosynthesis and cancer-related pathways. Experimental results showed that CXHO inhibited migration of GC cells and down regulated the expression levels of MMP2/MMP9, NF-κb. In addition, CXHO can inhibited PI3K/AKT signaling pathway. CONCLUSION We identified and experimental validated 2 pivotal target genes of CXHO against GC and preliminarily analyzed the potential mechanisms by which CXHO inhibits the development of GC. All these findings support CXHO as a promising drug for the treatment of GC.
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Affiliation(s)
- Kayisaier Abudurousuli
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Ziruo Talihati
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Sendaer Hailati
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Meng Yuan Han
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Muhadaisi Nuer
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Nawaz Khan
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Nulibiya Maihemuti
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Dilihuma Dilimulati
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Nuerbiye Nueraihemaiti
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Jimilihan Simayi
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
| | - Wenting Zhou
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi, P.R. China
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Sarcopenia and a 5-mRNA risk module as a combined factor to predict prognosis for patients with stomach adenocarcinoma. Genomics 2021; 114:361-377. [PMID: 34933074 DOI: 10.1016/j.ygeno.2021.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 11/18/2021] [Accepted: 12/04/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Sarcopenia is an important factor affecting the prognostic outcomes in adult cancer patients. Gastric cancer is considered an age-related disease and is one of the leading causes of global cancer mortality. We aimed to establish an effective age-related model at a molecular level to predict the prognosis of patients with gastric cancer. METHODS TCGA STAD (stomach adenocarcinoma) and NCBI GEO database were utilized in this study to explore the expression, clinical relevance and prognostic value of age-related mRNAs in stomach adenocarcinoma through an integrated bioinformatics analysis. WGCNA co-expression network, Univariate Cox regression analysis, LASSO regression and Multivariate Cox regression analysis were implemented to construct an age-related prognostic signature. RESULTS As a result, sarcopenia is not only an unfavorable factor for OS (overall survival) in patients with tumor of gastric (HR: 1.707, 95%CI: 1.437-2.026), but also increases the risk of postoperative complications in patients with gastric cancer (OR: 2.904, 95%CI: 2.150-3.922). A panel of 5 mRNAs (DCBLD1, DLC1, IGFBP1, RNASE1 and SPC24) were identified to dichotomize patients with significantly different OS and independently predicted the OS in TCGA STAD (HR = 3.044, 95%CI = 2.078-4.460, P < 0.001). CONCLUSION The study provided novel insights to understand STAD at a molecular level and indicated that the 5 mRNAs might act as independent promising prognosis biomarkers for STAD. Sarcopenia and the 5-mRNA risk module as a combined factor to predict prognosis may play an important role in clinical diagnosis.
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Li AL, Chou CY, Chen CL, Wu KL, Lin SC, Chen HC, Wang MC, Chang CC, Hsu BG, Wu MS, Ma N, Huang CC. The MicroRNA Prediction Models as Ancillary Diagnosis Biomarkers for Urothelial Carcinoma in Patients With Chronic Kidney Disease. Front Med (Lausanne) 2021; 8:726214. [PMID: 34660637 PMCID: PMC8517232 DOI: 10.3389/fmed.2021.726214] [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: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022] Open
Abstract
Urothelial carcinoma is a common urological cancer in chronic kidney disease patients. Cystoscopy and urine cytology are the clinical diagnostic tools for UC. However, cystoscopy is an invasive procedure, while urine cytology showed low sensitivity for low-grade urothelial tumors. High accuracy with non-invasive tools for UC is needed for CKD patients. Our study collected a total of 272 urine and 138 plasma samples to detect the miRNA expression levels for establishing UC signatures from CKD patients. Seventeen candidate miRNAs of biofluids were selected and confirmed by qRT-PCR. Our results showed that urinary miR-1274a and miR-30a-5p expression levels were significantly lower but miR-19a-5p expression levels were higher in UC when compared with CKD. In plasma samples, miR-155-5p, miR-19b-1-5p, miR-378, and miR-636 showed significantly lower expression in UC compared to those with CKD. The Kaplan-Meier curve showed that lower expression of miR-19a, miR-19b, miR-636 and miR-378, and higher expression of miR-708-5p were associated with poor prognosis in patients with bladder cancer. In addition, we produced classifiers for predicting UC by multiple logistic regression. The urine signature was developed with four miRNAs, and the AUC was 0.8211. Eight miRNA expression levels from both urine and plasma samples were examined, and the AUC was 0.8595. Two miRNA classifiers and the nomograms could improve the drawbacks of current UC biomarker screenings for patients with CKD.
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Affiliation(s)
- An-Lun Li
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Che-Yi Chou
- Division of Nephrology, Department of Internal Medicine, Asia University Hospital, Taichung, Taiwan
| | - Chien-Lung Chen
- Department of Nephrology, Landseed International Hospital, Taoyuan, Taiwan
| | - Kun-Lin Wu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.,Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Chun Chen
- Division of Nephrology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Cheng Kung University Hospital, Tainan, Taiwan
| | - Chia-Chu Chang
- Division of Nephrology, Department of Internal Medicine, Kuang Tien General Hospital, Taichung, Taiwan.,Department of Nutrition, Hungkuang University, Taichung, Taiwan
| | - Bang-Gee Hsu
- Division of Nephrology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, Taipei Medical University and Hospitals, Taipei, Taiwan
| | - Nianhan Ma
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chiu-Ching Huang
- Division of Nephrology and The Kidney Institute, China Medical University and Hospitals, Taichung, Taiwan
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Prognostic Value and Immune Infiltrates of ABCA8 and FABP4 in Stomach Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4145164. [PMID: 32685482 PMCID: PMC7338980 DOI: 10.1155/2020/4145164] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/01/2020] [Accepted: 06/06/2020] [Indexed: 12/21/2022]
Abstract
Background Stomach adenocarcinoma (STAD) is a common malignancy worldwide with poor prognosis. Therefore, it is important to identify a valuable prognostic biomarker for STAD. The aim of present study was to identify novel prognostic biomarkers for STAD and evaluate the potential role of hub genes in STAD. Methods Gene Expression Profiling Interactive Analysis (GEPIA) and Cancer RNA-Seq Nexus were performed to identify differentially expressed genes (DEGs). Subsequently, hub genes were selected by a Venn diagram, and the expression of key genes was confirmed by UALCAN database. Furthermore, survival analysis of these hub genes was performed using Oncolnc and Human Protein Atlas (HPA) database. Gene alteration status of hub genes was assessed by cBioPortal. Finally, we investigated the association between hub genes and immune cell infiltration in STAD through the Tumor Immune Estimation Resource (TIMER) and GEPIA database. Results Three common hub genes were obtained, including 2 downregulated DEGs (ABCA8 and FABP4) and one upregulated DEG (SLC52A3). Furthermore, increased expression of ABCA8 and FABP4 and decreased expression of SLC52A3 were correlated with poor prognosis. Meanwhile, three hub genes showed genetic alterations in various datasets of STAD. Finally, our results showed that ABCA8 and FABP4 displayed a positive correlation with immune infiltration, especially in M2 macrophages. Conclusions The results of this study suggest that ABCA8 and FABP4 may be used as prognostic biomarkers and correlated with immune infiltration in STAD.
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Pereira A, Moreira F, Vinasco-Sandoval T, Cunha A, Vidal A, Ribeiro-dos-Santos AM, Pinto P, Magalhães L, Assumpção M, Demachki S, Santos S, Assumpção P, Ribeiro-dos-Santos Â. miRNome Reveals New Insights Into the Molecular Biology of Field Cancerization in Gastric Cancer. Front Genet 2019; 10:592. [PMID: 31275362 PMCID: PMC6593062 DOI: 10.3389/fgene.2019.00592] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play an important role in gastric carcinogenesis and have been associated with gastric field cancerization; however, their role is not fully understood in this process. We performed the miRNome sequencing of non-cancerous, adjacent to tumor and gastric cancer samples to understand the involvement of these small RNAs in gastric field cancerization. METHODS We analyzed samples of patients without cancer as control (non-cancerous gastric samples) and adjacent to cancer and gastric cancer paired samples, and considered miRNAs with |log2(fold change)| > 2 and Padj < 0.05 to be statistically significant. The identification of target genes, functional analysis and enrichment in KEGG pathways were realized in the TargetCompare, miRTargetLink, and DAVID tools. We also performed receiver operating characteristic (ROC) curves and miRNAs that had an AUC > 0.85 were considered to be potential biomarkers. RESULTS We found 14 miRNAs exclusively deregulated in gastric cancer, of which six have potential diagnostic value for advanced disease. Nine miRNAs with known tumor suppressor activities (TS-miRs) were deregulated exclusively in adjacent tissue. Of these, five have potential diagnostic value for the early stages of gastric cancer. Functional analysis of these TS-miRs revealed that they regulate important cellular signaling pathways (PI3K-Akt, HIF-1, Ras, Rap1, ErbB, and MAPK signaling pathways), that are involved in gastric carcinogenesis. Seven miRNAs were differentially expressed in both gastric cancer and adjacent regarding to non-cancerous tissues; among them, hsa-miR-200a-3p and hsa-miR-873-5p have potential diagnostic value for early and advanced stages of the disease. Only hsa-miR-196a-5p was differentially expressed between adjacent to cancer and gastric cancer tissues. In addition, the other miRNAs identified in this study were not differentially expressed between adjacent to cancer and gastric cancer, suggesting that these tissues are very similar and that share these molecular changes. CONCLUSION Our results show that gastric cancer and adjacent tissues have a similar miRNA expression profile, indicating that studied miRNAs are intimately associated with field cancerization in gastric cancer. The overexpression of TS-miRs in adjacent tissues may be a barrier against tumorigenesis within these pre-cancerous conditions prior to the eventual formation or relapse of a tumor. Additionally, these miRNAs have a great accuracy in discriminating non-cancerous from adjacent to tumor and cancer tissues and can be potentially useful as biomarkers for gastric cancer.
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Affiliation(s)
- Adenilson Pereira
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Fabiano Moreira
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Tatiana Vinasco-Sandoval
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Adenard Cunha
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Amanda Vidal
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - André M. Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
| | - Pablo Pinto
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
| | - Mônica Assumpção
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Samia Demachki
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Sidney Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Paulo Assumpção
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
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