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Huang X, Ma Z, Qin W. Screening and Bioinformatics Analyses of Key miRNAs Associated with Toll-like Receptor Activation in Gastric Cancer Cells. Medicina (B Aires) 2023; 59:medicina59030511. [PMID: 36984512 PMCID: PMC10053384 DOI: 10.3390/medicina59030511] [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: 02/09/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Background and Objectives: To screen key miRNAs and their target genes related to Toll-like receptor (TLR) activation in gastric cancer (GC) cells and analyze them bioinformatically. Materials and Methods: Venn diagrams were obtained to screen miRNAs that were upregulated/downregulated in both GSE54129 and GSE164174. The miRTarBase database was used to predict the target genes of upregulated miRNAs. The differentially expressed genes in the regulatory network were analyzed. miR-16-5p expression in different tissue samples and the variations in the methylation states of four hub genes were measured. Results: We found that GSE54129 included 21 normal gastric tissues and 111 gastric cancer tissues, GSE164174 included 1417 normal gastric tissues and 1423 gastric cancer tissues. Venn diagram analysis results showed that compared with the control group, a total of 68 DEmiRNAs were upregulated in the GSE54129 and GSE164174 datasets, and no common downregulated DEmiRNAs were found. On further analysis of the GSE108345 dataset, we obtained the competing endogenous RNA (ceRNA) network associated with the activation of TLRs, and listed the top 10 lncRNA–miRNA–mRNA networks, including 10 miRNAs, 86 mRNA and 134 lncRNAs. Cytological HuBBA scores yielded a total of 1 miRNA, 16 mRNAs and 45 lncRNAs, of which miR-16-5p scored the highest as it was considered a key miRNA for TLR activation in GC cells, which are important in response against microorganisms. The results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that endocytosis, microRNAs in cancer and the PI3K-Akt signaling pathway are related to TLR signaling. The results of in vivo experiments indicated that miR-16-5p was highly expressed in gastric cancer cells and tissues. Conclusions: Hsa-miR-16-5p’s target genes mainly play a role by regulating the expression of four genes—MCL1, AP2B1, LAMB1, and RAB11FIP2. The findings provide a scientific basis for the development of immunotherapy for GC.
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Affiliation(s)
- Xiong Huang
- Department of General Surgery, The Eighth People’s Hospital of Shanghai, Shanghai 200233, China
- Correspondence: ; Tel.: +86-021-34284588
| | - Zhen Ma
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Qin
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
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Vosough P, Khatami SH, Hashemloo A, Tajbakhsh A, Karimi-Fard F, Taghvimi S, Taheri-Anganeh M, Soltani Fard E, Savardashtaki A, Movahedpour A. Exosomal lncRNAs in gastrointestinal cancer. Clin Chim Acta 2023; 540:117216. [PMID: 36592922 DOI: 10.1016/j.cca.2022.117216] [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: 08/24/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Gastrointestinal cancer (GIC) remains a leading cause of morbidity and mortality worldwide. Unfortunately, these cancers are diagnosed in advanced metastatic stages due to lack of reliable biomarkers that are sufficiently specific and sensitive in early disease. There has been growing evidence that circulating exosomes can be used to diagnose cancer non-invasively with limited risks and side effects. Furthermore, exosomal long non-coding RNAs (lncRNAs) are emerging as a new class of promising biomarkers in cancer. This review provides an overview of the extraction and detection of exosomal lncRNAs with a focus on their potential role in GIC.
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Affiliation(s)
- Parisa Vosough
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Sina Taghvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Husna AA, Rahman MM, Chen HW, Hasan MN, Nakagawa T, Miura N. Long non-coding RNA and transfer RNA-derived small fragments in exosomes are potential biomarkers for canine oral melanoma. Vet Comp Oncol 2022; 20:653-663. [PMID: 35388611 DOI: 10.1111/vco.12818] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/26/2022]
Abstract
Novel small non-coding RNAs (sRNAs) represent an emerging line of research in both human and canine oncology, due to their diverse regulatory and functional roles. Novel sRNAs are regarded as distinct from microRNAs, although both are part of the exosomal cargo. Recently, we reported on exosomal miRNAs as biomarkers for canine melanoma; however, it is unknown if novel sRNAs hold similar potential. Accordingly, we aimed to identify and validate novel sRNAs as potential biomarkers of canine oral melanoma, as part of our larger project on sequencing small exosomal RNA for this disease. Next generation sequencing revealed several differentially expressed novel sRNAs in exosomes from two melanoma cell lines (KMeC and LMeC) when compared with reference exosomes (from tumor-free dogs). Among these novel sRNAs, long noncoding RNA fragments, tRNA-derived fragments, snoRNAs, and snRNAs were abundantly expressed. We selected four novel sRNAs upregulated in each cell line, and validated their aberrant expression with qPCR. In analysis using plasma-derived exosomes from melanoma patients, six out of the eight selected novel sRNAs showed significantly elevated expression. Receiver operating curve (ROC) analysis showed that one long non-coding RNA-derived small fragment (ENSCAFT00000069599.1) and one transfer RNA-derived small fragment (tRNA-Ala-TGC-5-1) have more than 85% sensitivity and specificity for differentiating melanoma patients from tumor-free dogs. Therefore, we consider that novel sRNAs may serve as candidate biomarkers to facilitate more accurate diagnosis of canine oral melanoma in clinical settings. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Al Asmaul Husna
- The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan.,Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Md Mahfuzur Rahman
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Hui-Wen Chen
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Md Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Takayuki Nakagawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoki Miura
- The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan.,Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
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Ma W, Xue N, Zhang J, Wang D, Yao X, Lin L, Xu Q. circUBAP2 regulates osteosarcoma progression via the miR‑204‑3p/HMGA2 axis. Int J Oncol 2021; 58:298-311. [PMID: 33650644 PMCID: PMC7864148 DOI: 10.3892/ijo.2021.5178] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Circular RNA (circRNA/circ)-ubiquitin associated protein 2 (UBAP2), a newly recognized circRNA, serves a functional role in several types of tumor, including ovarian cancer, colorectal cancer and osteosarcoma. However, the precise roles and molecular mechanism under-lying circUBAP2 in osteosarcoma (OS) are not completely understood. In the present study, the expression levels of circUBAP2, microRNA (miR)-204-3p and (HMGA2) were evaluated via reverse transcription-quantitative PCR in OS tissues and cells. OS cell proliferation, migration, invasion and apoptosis were assessed by performing Cell Counting Kit-8, Transwell and flow cytometry assays, respectively. HMGA2 protein expression levels were determined via western blot-ting. Dual-luciferase reporter assays were performed to verify the interaction between circUBAP2 and miR-204-3p, and between miR-204-3p and HMGA2. An RNA immunoprecipitation (RIP) assay was conducted to confirm the interaction between circUBAP2 and miR-204-3p. The results demonstrated that circUBAP2 expression was significantly upregulated in OS tissues and cell lines compared with para-cancerous tissues and hFOB1.19 cells, respectively. In addition, high circUBAP2 expression levels in patients with OS were associated with a lower survival rate compared with lower expression levels in patients with OS. The functional assays revealed that circUBAP2 knockdown significantly inhibited OS cell proliferation, migration and invasion, but increased OS cell apoptosis compared with the small interfering RNA-negative control (si-NC) group. The dual-luciferase reporter and RIP assay results confirmed that circUBAP2 bound to miR-204-3p. Moreover, miR-204-3p expression was significantly downregulated in OS tissues compared with paracancerous tissues, and miR-204-3p expression was negatively correlated with circUBAP2 expression in OS tissues. Collectively, the results demonstrated that miR-204-3p was associated with circUBAP2 knockdown-mediated inhibition of OS cell malignant behavior. Moreover, miR-204-3p was also identified as one of the direct targets of HMGA2. Collectively, the results indicated that compared with the si-NC group, circUBAP2 knockdown significantly inhibited OS cell malignant behavior by binding to miR-204-3p, which subsequently regulated HMGA2 expression. Therefore, the present study demonstrated that circUBAP2 expression was upregulated in OS, and circUBAP2 regulated OS cell malignant behavior via the miR-204-3p/HMGA2 axis.
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Affiliation(s)
- Weiguo Ma
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Ning Xue
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Junhua Zhang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Dan Wang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Xiaobin Yao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Lin Lin
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
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