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Huo X, Wang K, Yao B, Song L, Li Z, He W, Li Y, Ma J, Wang L, Wu Z. Function and regulation of miR-186-5p, miR-125b-5p and miR-1260a in chordoma. BMC Cancer 2023; 23:1152. [PMID: 38012562 PMCID: PMC10680222 DOI: 10.1186/s12885-023-11238-x] [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: 12/28/2022] [Accepted: 07/30/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The function and regulation of miRNAs in progression of chordoma were unclear. METHODS Five miRNAs were identified by the machine learning method from the miRNA expression array. CCk-8 assay, EDU assay, wound healing migration assay, and trans-well assay were used to reveal the effect of the miRNAs in chordoma cell lines. Moreover, bioinformation analysis and the mRNA expression array between the primary chordomas and recurrent chordomas were used to find the target protein genes of miRNAs. Furthermore, qRT-PCR and luciferase reporter assay were used to verify the result. RESULTS miR-186-5p, miR-30c-5p, miR-151b, and miR-125b-5p could inhibit proliferation, migration, and invasion of chordoma while miR-1260a enhances proliferation, migration, and invasion of chordoma. Recurrent chordoma has a worse disease-free outcome than the primary chordoma patients. AMOT, NPTX1, RYR3, and P2RX5 were the target protein mRNAs of miR-186-5p; NPTX1 was the target protein mRNAs of miR-125b-5p; and AMOT and TNFSF14 were the target protein mRNAs of miR-1260a. CONCLUSIONS miR-186-5p, miR-125b-5p, miR-1260a, and their target protein mRNAs including AMOT, NPTX1, RYR3, P2RX5, TNFSF14 may be the basement of chordoma research.
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Affiliation(s)
- Xulei Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China
| | - Ke Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China.
| | - Bohan Yao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China
| | - Lairong Song
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China
| | - Zirun Li
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wenyan He
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, TianJin, China
| | - Junpeng Ma
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China
| | - Liang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nansihuanxilu 119, Fengtai District, Beijing, 100070, China.
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Wu J, Lu F, Yu B, Wang W, Ye X. The oncogenic role of SNRPB in human tumors: A pan-cancer analysis. Front Mol Biosci 2022; 9:994440. [PMID: 36275630 PMCID: PMC9582665 DOI: 10.3389/fmolb.2022.994440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
Purpose: The purpose of this study was to explore the oncogenic role of small nuclear ribonucleoprotein polypeptides B and B1 (SNRPB) in human tumors. Materials and methods: Study cases were acquired from The Cancer Genome Atlas database, the Gene Expression Omnibus database, The Human Protein Atlas, and the Clinical Proteomic Tumor Analysis Consortium. We then used the R package and several online tools to analyze and visualize the role of SNRPB across tumors. Results: We found that the expression of SNRPB was significantly increased in 28 of 33 tumors, and higher expression was observed in late pathological and TNM stages. Significantly decreased levels of SNRPB promoter methylation were observed in 12 tumors. SNRPB was found to be a risk factor for decreased overall survival in 10 tumors (p < 0.05), a risk factor for decreased disease-specific survival in 8 tumors (p < 0.05), and a risk factor for decreased progression-free interval in 7 tumors (p < 0.05). The PPI network of SNRPB and the top 100 coexpressed genes revealed that CDK1, CDC6, AURKB, CCNB1, CCNA2, and CDC45 were the most closely interacting genes across tumors. The GO and KEGG enrichment analyses revealed that SNRPB and the above genes were mainly enriched with respect to functions in cell cycle-related genetic material replication, assembly, and distribution. SNRPB was significantly associated with immune cell infiltration and the expression of immunomodulation-related genes in several but not all tumors. Conclusion and limitations: The expression of SNRPB was significantly elevated in almost all tumors, and the decreased promoter methylation level may contribute to the elevated expression of SNRPB. SNRPB may facilitate the progression of pathological and TNM stages and is a risk factor for unfavorable prognosis across tumors. However, our research was based on data obtained from public databases, without further validation of our findings at the cellular and animal levels. Therefore, further studies are needed to clarify the oncogenic mechanism of SNRPB and its potential as a therapeutic target.
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Affiliation(s)
- Juan Wu
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Feng Lu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bin Yu
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenjun Wang
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqun Ye
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Xiaoqun Ye,
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Wang Y, Shen L, Li G, Chen J, Ge R. Upregulation of XIAP promotes lung adenocarcinoma brain metastasis by modulating ceRNA network. Front Oncol 2022; 12:946253. [PMID: 35992856 PMCID: PMC9389361 DOI: 10.3389/fonc.2022.946253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulation of XIAP has been shown to affect the progression of a variety of cancers, including lung adenocarcinoma (LUAD). However, the function and mechanisms of XIAP in lung adenocarcinoma with brain metastasis (LUAD-BM) remains poorly understood. In this study, we analyzed the differential mRNA of 58 lung adenocarcinomas samples and 28 lung adenocarcinomas with brain metastases in GEO database. 191 differentially expressed mRNAs were significantly associated with immune response, the proliferation of the immune cell, cell-cell adhesion. Subsequent analyzed by lasso and SVM found that XIAP was significantly elevated in LUAD-BM and significantly associated with LUAD grade and metastasis. Then we constructed a molecular regulatory network of ncRNA-miRNA-mRNA ceRNA by Cystoscope based on the correlation obtained from Starbase. It was found that SBF2-AS1 or RUNDC3A-AS1, has-miR-338-3p and XIAP may have a regulatory relationship. Furthermore, we also initially found that XIAP was closely correlation with T cells, B cells, Mast cells, macrophages, and dendritic cells. In conclusion, we found that XIAP was significantly higher expressed in LUAD-BM compared with LUAD without brain metastasis, suggesting that XIAP may play an important role in the future prediction and clinical treatment of LUAD-BM.
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Affiliation(s)
- Yingjing Wang
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Lu Shen
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Geng Li
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Jiayi Chen
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Rong Ge
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
- *Correspondence: Rong Ge,
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Hatmal MM, Al-Hatamleh MAI, Olaimat AN, Alshaer W, Hasan H, Albakri KA, Alkhafaji E, Issa NN, Al-Holy MA, Abderrahman SM, Abdallah AM, Mohamud R. Immunomodulatory Properties of Human Breast Milk: MicroRNA Contents and Potential Epigenetic Effects. Biomedicines 2022; 10:biomedicines10061219. [PMID: 35740242 PMCID: PMC9219990 DOI: 10.3390/biomedicines10061219] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Infants who are exclusively breastfed in the first six months of age receive adequate nutrients, achieving optimal immune protection and growth. In addition to the known nutritional components of human breast milk (HBM), i.e., water, carbohydrates, fats and proteins, it is also a rich source of microRNAs, which impact epigenetic mechanisms. This comprehensive work presents an up-to-date overview of the immunomodulatory constituents of HBM, highlighting its content of circulating microRNAs. The epigenetic effects of HBM are discussed, especially those regulated by miRNAs. HBM contains more than 1400 microRNAs. The majority of these microRNAs originate from the lactating gland and are based on the remodeling of cells in the gland during breastfeeding. These miRNAs can affect epigenetic patterns by several mechanisms, including DNA methylation, histone modifications and RNA regulation, which could ultimately result in alterations in gene expressions. Therefore, the unique microRNA profile of HBM, including exosomal microRNAs, is implicated in the regulation of the genes responsible for a variety of immunological and physiological functions, such as FTO, INS, IGF1, NRF2, GLUT1 and FOXP3 genes. Hence, studying the HBM miRNA composition is important for improving the nutritional approaches for pregnancy and infant's early life and preventing diseases that could occur in the future. Interestingly, the composition of miRNAs in HBM is affected by multiple factors, including diet, environmental and genetic factors.
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Affiliation(s)
- Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
- Correspondence: (M.M.H.); (R.M.)
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman 11942, Jordan;
| | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Khaled A. Albakri
- Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Enas Alkhafaji
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan;
| | - Nada N. Issa
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Murad A. Al-Holy
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Salim M. Abderrahman
- Department of Biology and Biotechnology, Faculty of Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Atiyeh M. Abdallah
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar;
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
- Correspondence: (M.M.H.); (R.M.)
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