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Li HC, Yang CH, Lo SY. Long noncoding RNAs in hepatitis B virus replication and oncogenesis. World J Gastroenterol 2022; 28:2823-2842. [PMID: 35978877 PMCID: PMC9280728 DOI: 10.3748/wjg.v28.i25.2823] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/16/2022] [Accepted: 05/22/2022] [Indexed: 02/06/2023] Open
Abstract
Several diverse long noncoding RNAs (lncRNAs) have been identified to be involved in hepatitis B virus (HBV) replication and oncogenesis, especially those dysregulated in HBV-related hepatocellular carcinoma (HCC). Most of these dysregulated lncRNAs are modulated by the HBV X protein. The regulatory mechanisms of some lncRNAs in HBV replication and oncogenesis have been characterized. Genetic polymorphisms of several lncRNAs affecting HBV replication or oncogenesis have also been studied. The prognosis of HCC remains poor. It is important to identify novel tumor markers for early diagnosis and find more therapeutic targets for effective treatments of HCC. Some dysregulated lncRNAs in HBV-related HCC may become biomarkers for early diagnosis and/or the therapeutic targets of HCC. This mini-review summarizes these findings briefly, focusing on recent developments.
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Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
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Zhou S, Liu Y, Dong J, Yang Q, Xu N, Yang Y, Gu Z, Ai X. Transcriptome analysis of goldfish (Carassius auratus) in response to Gyrodactylus kobayashii infection. Parasitol Res 2020; 120:161-171. [PMID: 33094386 DOI: 10.1007/s00436-020-06827-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Gyrodactylid monogeneans are widespread parasites of teleost fishes, and infection with these parasites results in high host morbidity and mortality in aquaculture. To comprehensively elucidate the immune mechanisms against Gyrodactylus kobayashii, the transcriptome profiles of goldfish (Carassius auratus) skin after challenge with G. kobayashii were first investigated using next-generation sequencing. Approximately 21 million clean reads per library were obtained, and the average percentage of these clean reads mapped to the reference genome was 82.25%. A total of 556 differentially expressed genes (DEGs), including 344 upregulated and 212 downregulated genes, were identified, and 380 DEGs were successfully annotated and assigned to 95 signaling pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG). In addition, 14 pathways associated with immune response were identified mainly including mTOR signaling pathway, cytokine-cytokine receptor interaction, intestinal immune network for IgA production, toll-like receptor signaling pathway, and phagosome. Twelve genes were selected and validated using qRT-PCR. A similar trend of these genes between RNA-Seq and qRT-PCR was observed, indicating that RNA-Seq data was reliable. Besides, the ALP activity and NO content in serum were significantly higher in the infected goldfish compared with the non-infected goldfish. In summary, this study provides better understandings of immune defense mechanisms of goldfish against G. kobayashii, which will support future molecular research on gyrodactylids and facilitate the prevention and treatment of gyrodactylosis in aquaculture.
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Affiliation(s)
- Shun Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China.,Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430223, China.,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China
| | - Yongtao Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China.,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China
| | - Jing Dong
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China.,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China
| | - Qiuhong Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China.,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China
| | - Ning Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China.,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China
| | - Yibin Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China.,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China
| | - Zemao Gu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430223, China
| | - Xiaohui Ai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 8 Wuda Park Road 1, Wuhan, 430223, Hubei Province, China. .,Hu Bei Province Engineering and Technology Research Center of Aquatic Product Quality and Safety, Wuhan, 430223, China.
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Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma Using cis-eQTL Analysis. J Clin Med 2020; 9:jcm9041137. [PMID: 32316112 PMCID: PMC7231141 DOI: 10.3390/jcm9041137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
Ovarian clear cell adenocarcinoma (Ov-CCA) has a higher prevalence in the Japanese ancestry than other populations. The ancestral disparities in Ov-CCA prevalence suggests the presence of Ov-CCA-specific genetic alterations and may provide an opportunity to identify the novel genes associated with Ov-CCA tumorigenesis. Using 94 previously reported genes as the phenotypic trait, we conducted multistep expression quantitative trait loci (eQTL) analysis with the HapMap3 project datasets. Four single-nucleotide polymorphisms (SNPs) (rs4873815, rs12976454, rs11136002, and rs13259097) that had different allele frequencies in the Japanese ancestry and seven genes associated in cis (APBA3, C8orf58, KIAA1967, NAPRT1, RHOBTB2, TNFRSF10B, and ZNF707) were identified. In silico functional annotation analysis and in vitro promoter assay validated the regulatory effect of rs4873815-TT on ZNF707 and rs11136002-TT on TNFRSF10B. Furthermore, ZNF707 was highly expressed in Ov-CCA and had a negative prognostic value in disease recurrence in our sample cohort. This prognostic power was consistently observed in The Cancer Genome Atlas (TCGA) clear cell renal cell carcinoma dataset, suggesting that ZNF707 may have prognostic value in clear cell histology regardless of tissue origin. In conclusion, rs4873815-TT/ZNF707 may have clinical significance in the prognosis and tumorigenesis of Ov-CCA, which may be more relevant to clear cell histology. Besides, this study may underpin the evidence that cis-eQTL analysis based on ancestral disparities can facilitate the discovery of causal genetic alterations in complex diseases, such as cancer.
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Zhang H, Chen X, Zhang J, Wang X, Chen H, Liu L, Liu S. Long non‑coding RNAs in HBV‑related hepatocellular carcinoma (Review). Int J Oncol 2019; 56:18-32. [PMID: 31746420 DOI: 10.3892/ijo.2019.4909] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/02/2019] [Indexed: 12/25/2022] Open
Abstract
Hepatitis B virus (HBV)‑related hepatocellular carcinoma (HCC) is a global health problem that accounts for more than half of total liver cancer cases in developing countries. Despite the growing number of researches conducted, the molecular mechanism underlying the development of HCC remains elusive. Long non‑coding RNAs (lncRNAs), which are non‑coding RNAs >200 nt in length that were previously considered to be transcriptional noise, have been found to be dysregulated in HBV‑related HCC with the help of high‑throughput omics techniques. Subsequent investigations revealed that aberrant expression of lncRNAs may affect the risk of HBV‑related HCC through diverse mechanisms, including epigenetic silencing of transcriptional activation, alternative splicing, molecular sponging, modulating protein stability, and by serving as precursors of miRNAs. Although the sensitivity and specificity of lncRNAs must be further validated, a number of circulating lncRNAs have been identified as useful biomarkers for HBV‑related HCC. In addition to these findings, recent studies also unveiled that certain genetic polymorphisms in lncRNAs may affect the occurrence and prognosis of HBV‑related HCC. The aim of the present review was to provide an overview of the mechanisms underlying the involvement of lncRNAs in HBV‑related HCC. Subsequently, lncRNAs found to be dysregulated in HBV‑related HCC were focused on and current findings on circulating lncRNAs and their genetic polymorphisms were discussed.
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Affiliation(s)
- Hao Zhang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Sichuan 610000, P.R. China
| | - Xuebing Chen
- Department of Infectious Diseases, People's Hospital of Deyang City, Deyang, Sichuan 618000, P.R. China
| | - Jian Zhang
- Department of Pathology, People's Hospital of Deyang City, Deyang, Sichuan 618000, P.R. China
| | - Xianwei Wang
- Department of Pathology, People's Hospital of Deyang City, Deyang, Sichuan 618000, P.R. China
| | - Huijuan Chen
- Department of Pathology, People's Hospital of Deyang City, Deyang, Sichuan 618000, P.R. China
| | - Lin Liu
- Department of Pathology, People's Hospital of Deyang City, Deyang, Sichuan 618000, P.R. China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Sichuan 610000, P.R. China
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