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Xie S, Zhou N, Su N, Xiao Z, Wei S, Yang Y, Liu J, Li W, Zhang B. Noncoding RNA-associated competing endogenous RNA networks in trastuzumab-induced cardiotoxicity. Noncoding RNA Res 2024;9:744-758. [PMID: 38577019 PMCID: PMC10990741 DOI: 10.1016/j.ncrna.2024.02.004] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 04/06/2024] Open

Affiliation(s)

Suifen Xie Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
Ni Zhou Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
Nan Su Department of Ophthalmology, The First People's Hospital of Lanzhou City, Lanzhou, 730050, Gansu Province, China
Zijun Xiao Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China
Shanshan Wei Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China
Yuanying Yang Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China
Jian Liu Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China
Wenqun Li Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China
Bikui Zhang Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China Institute of Clinical Pharmacy, Central South University, Changsha, Hunan, 410011, China

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Sun Y, Liu X, Shan X, Wang Y, Zhong C, Lu C, Guan B, Yao S, Huo Y, Sun R, Wei M, Dong Z. Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis. Gene 2024;911:148346. [PMID: 38452877 DOI: 10.1016/j.gene.2024.148346] [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: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]

Affiliation(s)

Yuyan Sun Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
Xuxiao Liu Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
Xin Shan Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
Yiwo Wang Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
Chongyu Zhong Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
Chaofa Lu Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
Bin Guan Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
Shun Yao Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
Yujia Huo Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
Runkai Sun Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
Min Wei Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
Zhiguo Dong Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.

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Travis G, McGowan EM, Simpson AM, Marsh DJ, Nassif NT. PTEN, PTENP1, microRNAs, and ceRNA Networks: Precision Targeting in Cancer Therapeutics. Cancers (Basel) 2023;15:4954. [PMID: 37894321 PMCID: PMC10605164 DOI: 10.3390/cancers15204954] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open

Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Guo W, Wu F, Feng X, Wang Q, Lu Y, Xu J. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. Int J Mol Sci 2023;24:15039. [PMID: 37894720 PMCID: PMC10606207 DOI: 10.3390/ijms242015039] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open

Affiliation(s)

Xin Tang Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Qimeng Li Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Xiaoju Feng Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Bo Yang Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Xiu Zhong Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Yang Zhou Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Qi Wang Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Yan Mao Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Wubin Xie Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Tianhong Liu Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Qi Tang Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Wei Guo Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Fengkai Wu Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Xuanjun Feng Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Qingjun Wang Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Yanli Lu Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Jie Xu Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.) State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China

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Deng W, Lu Y, Hu P, Zhang Q, Li S, Yang D, Zhao N, Qian K, Liu F. Integrated Analysis of Non-Coding RNA and mRNA Expression Profiles in Exosomes from Lung Tissue with Sepsis-Induced Acute Lung Injury. J Inflamm Res 2023;16:3879-3895. [PMID: 37674532 PMCID: PMC10478974 DOI: 10.2147/jir.s419491] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/19/2023] [Indexed: 09/08/2023] Open

Affiliation(s)

Wei Deng Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Yanhua Lu Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Ping Hu Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Qingqing Zhang Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Shuangyan Li Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Dong Yang Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Ning Zhao Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Kejian Qian Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
Fen Liu Department of Critical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China Medical Innovation Center, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China

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Mahmoudi E, Cairns MJ. CircRNA and Ageing. Subcell Biochem 2023;102:249-70. [PMID: 36600136 DOI: 10.1007/978-3-031-21410-3_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]

Yang W, Lu S, Peng L, Zhang Z, Zhang Y, Guo D, Ma F, Hua Y, Chen X. Integrated analysis of necroptosis-related genes for evaluating immune infiltration and colon cancer prognosis. Front Immunol 2022;13:1085038. [PMID: 36618366 PMCID: PMC9814966 DOI: 10.3389/fimmu.2022.1085038] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open

Abstract

Background

Colon cancer (CC) is the second most common gastrointestinal malignancy. About one in five patients have already developed distant metastases at the time of initial diagnosis, and up to half of patients develop distant metastases from initial local disease, which leads to a poor prognosis for CC patients. Necroptosis plays a key role in promoting tumor growth in different tumors. The purpose of this study was to construct a prognostic model composed of necroptosis-related genes (NRGs) in CC.

Methods

The Cancer Genome Atlas was used to obtain information on clinical features and gene expression. Gene expression differential analysis, weighted gene co-expression network analysis, univariate Cox regression analysis and the least absolute shrinkage and selection operator regression algorithm were utilized to identify prognostic NRGs. Thereafter, a risk scoring model was established based on the NRGs. Biological processes and pathways were identified by gene ontology and gene set enrichment analysis (GSEA). Further, protein-protein interaction and ceRNA networks were constructed based on mRNA-miRNA-lncRNA. Finally, the effect of necroptosis related risk score on different degrees of immune cell infiltration was evaluated.

Results

CALB1, CHST13, and SLC4A4 were identified as NRGs of prognostic significance and were used to establish a risk scoring model. The time-dependent receiver operating characteristic curve analysis revealed that the model could well predict the 1-, 3-, and 5-year overall survival (OS). Further, GSEA suggested that the NRGs may participate in biological processes, such as the WNT pathway and JAK-Stat pathway. Eight key hub genes were identified, and a ceRNA regulatory network, which comprised 1 lncRNA, 5 miRNAs and 3 mRNAs, was constructed. Immune infiltration analysis revealed that the low-risk group had significantly higher immune-related scores than the high-risk group. A nomogram of the model was constructed based on the risk score, necroptosis, and the clinicopathological features (age and TNM stage). The calibration curves implied that the model was effective at predicting the 1-, 3-, and 5-year OS of CC.

Conclusion

Our NRG-based prognostic model can assist in the evaluation of CC prognosis and the identification of therapeutic targets for CC.

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Cao H, Rao X, Jia J, Yan T, Li D. Identification of tubulointerstitial genes and ceRNA networks involved in diabetic nephropathy via integrated bioinformatics approaches. Hereditas 2022;159:36. [PMID: 36154667 PMCID: PMC9511769 DOI: 10.1186/s41065-022-00249-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open

Abstract

Background

Diabetic nephropathy (DN) is the major cause of end-stage renal disease worldwide. The mechanism of tubulointerstitial lesions in DN is not fully elucidated. This article aims to identify novel genes and clarify the molecular mechanisms for the progression of DN through integrated bioinformatics approaches.

Method

We downloaded microarray datasets from Gene Expression Omnibus (GEO) database and identified the differentially expressed genes (DEGs). Enrichment analyses, construction of Protein–protein interaction (PPI) network, and visualization of the co-expressed network between mRNAs and microRNAs (miRNAs) were performed. Additionally, we validated the expression of hub genes and analyzed the Receiver Operating Characteristic (ROC) curve in another GEO dataset. Clinical analysis and ceRNA networks were further analyzed.

Results

Totally 463 DEGs were identified, and enrichment analyses demonstrated that extracellular matrix structural constituents, regulation of immune effector process, positive regulation of cytokine production, phagosome, and complement and coagulation cascades were the major enriched pathways in DN. Three hub genes (CD53, CSF2RB, and LAPTM5) were obtained, and their expression levels were validated by GEO datasets. Pearson analysis showed that these genes were negatively correlated with the glomerular filtration rate (GFR). After literature searching, the ceRNA networks among circRNAs/IncRNAs, miRNAs, and mRNAs were constructed. The predicted RNA pathway of NEAT1/XIST-hsa-miR-155-5p/hsa-miR-486-5p-CSF2RB provides an important perspective and insights into the molecular mechanism of DN.

Conclusion

In conclusion, we identified three genes, namely CD53, CSF2RB, and LAPTM5, as hub genes of tubulointerstitial lesions in DN. They may be closely related to the pathogenesis of DN and the predicted RNA regulatory pathway of NEAT1/XIST-hsa-miR-155-5p/hsa-miR-486-5p-CSF2RB presents a biomarker axis to the occurrence and development of DN.

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Marques TM, Gama-Carvalho M. Network Approaches to Study Endogenous RNA Competition and Its Impact on Tissue-Specific microRNA Functions. Biomolecules 2022;12:332. [PMID: 35204832 DOI: 10.3390/biom12020332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open

Chen X, Lin B, Luo M, Chu W, Li P, Liu H, Xi Z, Fan R. Identifying circRNA- and lncRNA-associated-ceRNA networks in the hippocampi of rats exposed to PM_2.5 using RNA-seq analysis. Genomics 2020;113:193-204. [PMID: 33338629 DOI: 10.1016/j.ygeno.2020.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/04/2020] [Accepted: 12/13/2020] [Indexed: 11/16/2022]

Wang D, Yang N, Xie S. Sex-biased ceRNA networks reveal that OSCAR can promote proliferation and migration of lung adenocarcinoma in women. Clin Exp Pharmacol Physiol 2020;47:1350-1359. [PMID: 32246488 DOI: 10.1111/1440-1681.13318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022]

Liu H, Yu W, Wu J, Li Z, Li H, Zhou J, Hu J, Lu Y. Identification and characterization of circular RNAs during wood formation of poplars in acclimation to low nitrogen availability. Planta 2020;251:47. [PMID: 31925576 DOI: 10.1007/s00425-020-03338-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]

Abstract

Circular RNA (circRNA) identification and expression profiles, and construction of circRNAs-miRNAs-mRNAs networks indicates that circRNAs are involved in wood formation of poplars in acclimation to low nitrogen availability. Circular RNAs (circRNAs) are covalently closed non-coding RNAs that play pivotal roles in various biological processes. However, circRNAs' roles in wood formation of poplars in acclimation to low nitrogen (N) availability are currently unknown. Here, we undertook a systematic identification and characterization of circRNAs in the wood of Populus × canescens exposed to either 50 (low N) or 500 (normal N) µM NH₄NO₃ using rRNA-depleted RNA-sequencing. A total of 2,509 unique circRNAs were identified, and 163 (ca. 6.5%) circRNAs were significantly differentially expressed (DE) under low N condition. We observed a positive correlation between the expression patterns of DE circRNAs and their hosting protein-coding genes. Moreover, circRNAs-miRNAs-mRNAs' networks were identified in the wood of poplars under low N availability. For instance, upregulated several circRNAs, such as circRNA1226, circRNA 1732, and circRNA392 induced increases in nuclear factor Y, subunit A1-A (NFYA1-A), NFYA1-B, and NFYA10 transcript levels via the mediation of miR169b members, which is in line with reduced xylem width and cell layers of the xylem in the wood of low N-supplied poplars. Upregulation of circRNA1006, circRNA1344, circRNA1941, circRNA901, and circRNA146 caused increased transcript level of MYB61 via the mediation of a miR5021 member, corresponding well to the higher lignin concentration in the wood of low N-treated poplars. Overall, these results indicated that DE circRNAs play an essential role in regulating gene expression via circRNAs-miRNAs-mRNAs' networks to modulate wood anatomical and chemical properties of poplars in acclimation to low N availability.

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Liang Y, Zhu H, Chen J, Lin W, Li B, Guo Y. Construction of relapse-related lncRNA-mediated ceRNA networks in Hodgkin lymphoma. Arch Med Sci 2020;16:1411-1418. [PMID: 33224341 PMCID: PMC7667426 DOI: 10.5114/aoms.2020.98839] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 02/02/2019] [Indexed: 12/22/2022] Open

Wang Z, Xu P, Chen B, Zhang Z, Zhang C, Zhan Q, Huang S, Xia ZA, Peng W. Identifying circRNA-associated-ceRNA networks in the hippocampus of Aβ1-42-induced Alzheimer's disease-like rats using microarray analysis. Aging (Albany NY) 2019;10:775-788. [PMID: 29706607 PMCID: PMC5940119 DOI: 10.18632/aging.101427] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022]

Cheng W, Li XW, Xiao YQ, Duan SB. Non-coding RNA-Associated ceRNA Networks in a New Contrast-Induced Acute Kidney Injury Rat Model. Mol Ther Nucleic Acids 2019;17:102-12. [PMID: 31234008 DOI: 10.1016/j.omtn.2019.05.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 12/22/2022]

Mitra A, Pfeifer K, Park KS. Circular RNAs and competing endogenous RNA (ceRNA) networks. Transl Cancer Res 2018;7:S624-S628. [PMID: 30159229 DOI: 10.21037/tcr.2018.05.12] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]