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Zhao H, Lou G, Shao Y, Wang T, Wang H, Guo Q, Yang W, Liu H, Liao S. Competing Endogenous RNAs Crosstalk in Hippocampus: A Potential Mechanism for Neuronal Developing Defects in Down Syndrome. J Mol Neurosci 2024; 74:32. [PMID: 38536538 DOI: 10.1007/s12031-024-02205-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/02/2024] [Indexed: 07/20/2024]
Abstract
Down syndrome (DS) is the most example of aneuploidy, resulting from an additional copy of all or part of chromosome 21. Competing endogenous RNAs (ceRNAs) play important roles in neuronal development and neurological defects. This study aimed to identify hub genes and synergistic crosstalk among ceRNAs in the DS fetal hippocampus as potential targets for the treatment of DS-related neurodegenerative diseases. We profiled differentially expressed long non-coding RNAs (DElncRNAs), differentially expressed circular RNAs (DEcircRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in hippocampal samples from patients with or without DS. Functional enrichment analysis and gene set enrichment analysis were performed, and chromosome 21-related ceRNA and protein-protein interaction networks were constructed. Additionally, the correlations between lncRNA-mRNA and miRNA-mRNA expression in the samples and HEK293T cells were validated. Our finding of changes in the expression of some key genes and ncRNAs on chromosome 21 in DS might not fully conform to the gene dosage hypothesis. Moreover, we found that four lncRNAs (MIR99AHG, PLCB4, SNHG14, GIGYF2) and one circRNA (hsa_circ_0061697) may competitively bind with three miRNAs (hsa-miR-548b-5p, miR-730-5p, and hsa-miR-548i) and subsequently regulate five mRNAs (beta-1,3-galactosyltransferase 5 [B3GALT5], helicase lymphoid-specific [HELLS], thrombospondin-2 [THBS2], glycinamide ribonucleotide transformylase [GART], clathrin heavy chain like 1 [CLTCL1]). These RNAs, whether located on chromosome 21 or not, interact with each other and might activate the PI3K/Akt/mTOR and Wnt signaling pathways, which are involved in autophagosome formation and tau hyperphosphorylation, possibly leading to adverse consequences of trisomy 21. These findings provide researchers with a better understanding of the fundamental molecular mechanisms underlying DS-related progressive defects in neuronal development.
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Affiliation(s)
- Huiru Zhao
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Guiyu Lou
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yupu Shao
- Experimental Center, Department of Basic Medicine, Henan Medical College, Zhengzhou, China
| | - Tao Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongdan Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiannan Guo
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenke Yang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongyan Liu
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Shixiu Liao
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People's Hospital, Medical Genetics Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou, China.
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Zhang X, Yang S, Chen W, Dong X, Zhang R, Ye H, Mei X, Liu H, Fang Y, He C. Circular RNA circYPEL2: A Novel Biomarker in Cervical Cancer. Genes (Basel) 2021; 13:genes13010038. [PMID: 35052380 PMCID: PMC8774301 DOI: 10.3390/genes13010038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 01/16/2023] Open
Abstract
Cervical cancer (CC) is one of the most threatening diseases in women. Circular RNAs (circRNAs) have been reported to be cancer hallmarks, but typical circRNAs in CC were rarely indicated. Through high-throughput sequencing in CC and normal cervix tissues, circYPEL2 (hsa_circ_0005600) was proposed as a candidate circRNA. CircYPEL2 exhibited significantly high expression in CC tissue and strong stability in CC cell lines. Furthermore, knockdown and overexpression of circYPEL2 indicated the potential involvement in CC proliferation, migration and invasion. Finally, the downstream regulatory genes of circYPEL2 were investigated by knockdown experiment in CC cell lines with high-throughput sequencing. In summary, our work identified circYPEL2 as a potential biomarker for clinical research of cervical cancer.
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Affiliation(s)
- Xinyang Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.Z.); (S.Y.); (W.C.); (X.D.); (X.M.)
| | - Siqi Yang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.Z.); (S.Y.); (W.C.); (X.D.); (X.M.)
| | - Wenbo Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.Z.); (S.Y.); (W.C.); (X.D.); (X.M.)
| | - Xin Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.Z.); (S.Y.); (W.C.); (X.D.); (X.M.)
| | - Rongyu Zhang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (H.Y.); (C.H.)
| | - Haidong Ye
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (H.Y.); (C.H.)
| | - Xiangfei Mei
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.Z.); (S.Y.); (W.C.); (X.D.); (X.M.)
| | - Huan Liu
- University of Science and Technology of China, Hefei 230026, China
- Correspondence: (H.L.); (Y.F.)
| | - Yu Fang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (H.Y.); (C.H.)
- Correspondence: (H.L.); (Y.F.)
| | - Chunjiang He
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (H.Y.); (C.H.)
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