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Identification of the Novel Methylated Genes' Signature to Predict Prognosis in INRG High-Risk Neuroblastomas. JOURNAL OF ONCOLOGY 2021; 2021:1615201. [PMID: 34557229 PMCID: PMC8455188 DOI: 10.1155/2021/1615201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Neuroblastomas are the most frequent extracranial pediatric solid tumors. The prognosis of children with high-risk neuroblastomas has remained poor in the past decade. A powerful signature is required to identify factors associated with prognosis and improved treatment selection. Here, we identified a strong methylation signature that favored the earlier diagnosis of neuroblastoma in patients. METHODS Gene methylation (GM) data of neuroblastoma patients from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) were analyzed using a multivariate Cox regression analysis (MCRA) and univariate Cox proportional hazards regression analysis (UCPHRA). RESULTS The methylated genes' signature consisting of eight genes (NBEA, DDX28, TMED8, LOC151174, EFNB2, GHRHR, MIMT1, and SLC29A3) was selected. The signature divided patients into low- and high-risk categories, with statistically significant survival rates (median survival time: 25.08 vs. >128.80 months, log-rank test, P < 0.001) in the training group, and the validation of the signature's risk stratification ability was carried out in the test group (log-rank test, P < 0.01, median survival time: 30.48 vs. >120.36 months). The methylated genes' signature was found to be an independent predictive factor for neuroblastoma by MCRA. Functional enrichment analysis suggested that these methylated genes were related to butanoate metabolism, beta-alanine metabolism, and glutamate metabolism, all playing different significant roles in the process of energy metabolism in neuroblastomas. CONCLUSIONS The set of eight methylated genes could be used as a new predictive and prognostic signature for patients with INRG high-risk neuroblastomas, thus assisting in treatment, drug development, and predicting survival.
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Gebremedhn S, Ali A, Hossain M, Hoelker M, Salilew-Wondim D, Anthony RV, Tesfaye D. MicroRNA-Mediated Gene Regulatory Mechanisms in Mammalian Female Reproductive Health. Int J Mol Sci 2021; 22:938. [PMID: 33477832 PMCID: PMC7832875 DOI: 10.3390/ijms22020938] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/12/2022] Open
Abstract
Mammalian reproductive health affects the entire reproductive cycle starting with the ovarian function through implantation and fetal growth. Various environmental and physiological factors contribute to disturbed reproductive health status leading to infertility problems in mammalian species. In the last couple of decades a significant number of studies have been conducted to investigate the transcriptome of reproductive tissues and organs in relation to the various reproductive health issues including endometritis, polycystic ovarian syndrome (PCOS), intrauterine growth restriction (IUGR), preeclampsia, and various age-associated reproductive disorders. Among others, the post-transcriptional regulation of genes by small noncoding miRNAs contributes to the observed transcriptome dysregulation associated with reproductive pathophysiological conditions. MicroRNAs as a class of non-coding RNAs are also known to be involved in various pathophysiological conditions either in cellular cytoplasm or they can be released to the extracellular fluid via membrane-bounded extracellular vesicles and proteins. The present review summarizes the cellular and extracellular miRNAs and their association with the etiology of major reproductive pathologies including PCOS, endometritis, IUGR and age-associated disorders in various mammalian species.
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Affiliation(s)
- Samuel Gebremedhn
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, 3051 Rampart Rd, Fort Collins, CO 80523, USA; (S.G.); (A.A.); (R.V.A.)
| | - Asghar Ali
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, 3051 Rampart Rd, Fort Collins, CO 80523, USA; (S.G.); (A.A.); (R.V.A.)
| | - Munir Hossain
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Michael Hoelker
- Institute of Animal Sciences, Department of Animal Breeding and Husbandry, University of Bonn, 53115 Bonn, Germany; (M.H.); (D.S.-W.)
| | - Dessie Salilew-Wondim
- Institute of Animal Sciences, Department of Animal Breeding and Husbandry, University of Bonn, 53115 Bonn, Germany; (M.H.); (D.S.-W.)
| | - Russell V. Anthony
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, 3051 Rampart Rd, Fort Collins, CO 80523, USA; (S.G.); (A.A.); (R.V.A.)
| | - Dawit Tesfaye
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, 3051 Rampart Rd, Fort Collins, CO 80523, USA; (S.G.); (A.A.); (R.V.A.)
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Zhang X, Zhang Y, Meng Q, Sun H, Wu S, Xu J, Yun J, Yang X, Li B, Zhu H, Xue L, Li X, Chen R. MicroRNA-382-5p is involved in pulmonary inflammation induced by fine particulate matter exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114278. [PMID: 32146367 DOI: 10.1016/j.envpol.2020.114278] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/31/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Exposure to atmospheric particulate matter (PM) has been related to the increasing incidence and mortality of pulmonary diseases, where microRNAs (miRNAs) play significant roles in these biological and pathological processes. In the present study, we found that miR-382-5p played an anti-inflammatory role in pulmonary inflammation induced by fine particulate matter (PM2.5) or diesel exhaust particles (DEPs) in vitro and in vivo. The expression level of miR-382-5p was downregulated, while its target gene, namely CXCL12, was elevated in HBE cells after exposure to PM2.5 or DEPs. Mechanistically, PM2.5 or DEPs exposure increased CXCL12/MMP9 expression via miR-382-5p inhibition, subsequently triggered pulmonary inflammation. Furthermore, antagonizing the function of CXCL12 significantly reduced the expression of MMP9 and local inflammation induced by PM2.5 or DEPs. PM2.5 or DEPs caused apoptosis and G1 phase arrest could be partially restored by overexpression of miR-382-5p and antagonism of CXCL12. In a murine model, enhanced miR-382-5p expression effectively reduced expression levels of CXCL12, MMP9 and inflammatory cytokines, hereby protected lung tissues against PM2.5 or DEPs-induced lesions. Collectively, the miR-382-5p/CXCL12/MMP9 pathway may provide a mechanism, which mediates inflammatory response to PM2.5 or DEPs exposure.
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Affiliation(s)
- Xinwei Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Yanshu Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, 063000, Hebei Province, China
| | - Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Hao Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Jie Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Jun Yun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Xi Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Bin Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Hao Zhu
- School of Public Health, North China University of Science and Technology, Tangshan, 063000, Hebei Province, China
| | - Ling Xue
- School of Public Health, North China University of Science and Technology, Tangshan, 063000, Hebei Province, China
| | - Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China; Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, 511436, China.
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