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Tao SS, Fang X, Xu LZ, Zhang RD, Luo QQ, Tang J, Dai XF, Xu SZ, Yang XK, Pana HF. Association of gene polymorphisms and the decreased expression of long non-coding RNA LOC553103 with rheumatoid arthritis. Postgrad Med J 2024:qgae055. [PMID: 38656404 DOI: 10.1093/postmj/qgae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/14/2024] [Accepted: 04/06/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are involved in many key bioprocesses, including the occurrence and development of rheumatoid arthritis (RA). We aimed to analyze the association of genetic variants of long non-coding RNA LOC553103 and its peripheral blood mononuclear cells (PBMC) expression with RA. METHODS We enrolled 457 RA patients and 551 healthy controls and conducted a case-control study to analyze the relationship between LOC553103 gene rs272879 and the susceptibility of RA by TaqMan single nucleotide polymorphism genotyping. Among them, we sampled 92 cases and 92 controls, respectively, to detect the PBMC level of LOC553103 using quantitative real-time polymerase chain reaction technology. We explored the association between LOC553103 rs272879 and its PBMC expression levels in 71 RA patients. Mann-Whitney, Chi-square, and Spearman correlation analysis were used for statistical analysis and P-value <.05 was considered statistically significant. RESULTS The genotype frequency of LOC553103 rs272879 CC was increased, and CG was decreased in RA patients compared to the control group (χ2 = 6.772, P = .034). The LOC553103 expression level in PBMC of RA patients was downregulated compared to healthy control (Z = -4.497, P < .001). Moreover, negative correlations were observed between the PBMC level of LOC553103 and erythrocyte sedimentation rate (rs = -0.262, P = .018), white blood cell count (rs = -0.382, P = .004), platelet (rs = -0.293, P = .030), and disease activity score in 28 joints (rs = -0.271, P = .016) in RA patients. CONCLUSIONS This study provides the first evidence supporting an association between LOC553103 gene polymorphisms and susceptibility of RA and a relationship of PBMC level of LOC553103 with clinical manifestations and laboratory indicators of RA patients.
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Affiliation(s)
- Sha-Sha Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Preventive Medicine Experimental Teaching Center, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xi Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Liang-Zi Xu
- Department of Clinical Medicine, First Clinical Medical College, Anhui Medical University, Hefei, Anhui 230032, China
| | - Ruo-Di Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Qing-Qing Luo
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jian Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiao-Fan Dai
- Department of Public Affairs Administration, School of Health Service Management, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Shu-Zhen Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiao-Ke Yang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Hai-Feng Pana
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
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Salnikov MY, MacNeil KM, Mymryk JS. The viral etiology of EBV-associated gastric cancers contributes to their unique pathology, clinical outcomes, treatment responses and immune landscape. Front Immunol 2024; 15:1358511. [PMID: 38596668 PMCID: PMC11002251 DOI: 10.3389/fimmu.2024.1358511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Epstein-Barr virus (EBV) is a pathogen known to cause a number of malignancies, often taking years for them to develop after primary infection. EBV-associated gastric cancer (EBVaGC) is one such malignancy, and is an immunologically, molecularly and pathologically distinct entity from EBV-negative gastric cancer (EBVnGC). In comparison with EBVnGCs, EBVaGCs overexpress a number of immune regulatory genes to help form an immunosuppressive tumor microenvironment (TME), have improved prognosis, and overall have an "immune-hot" phenotype. This review provides an overview of the histopathology, clinical features and clinical outcomes of EBVaGCs. We also summarize the differences between the TMEs of EBVaGCs and EBVnGCs, which includes significant differences in cell composition and immune infiltration. A list of available EBVaGC and EBVnGC gene expression datasets and computational tools are also provided within this review. Finally, an overview is provided of the various chemo- and immuno-therapeutics available in treating gastric cancers (GCs), with a focus on EBVaGCs.
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Affiliation(s)
- Mikhail Y. Salnikov
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Katelyn M. MacNeil
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
- Department of Otolaryngology, Western University, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
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Cheng S, Liu Y, He B, Zhang J, Yang Y, Wang X, Li Z. Chlamydia trachomatis upregulates lncRNA CYTOR to mediate autophagy through miR-206/MAPK1 axis. Pathog Dis 2024; 82:ftae011. [PMID: 38821518 PMCID: PMC11210502 DOI: 10.1093/femspd/ftae011] [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: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/30/2024] [Indexed: 06/02/2024] Open
Abstract
Chlamydia trachomatis infection can be regulated by autophagy-related genes. LncRNA CYTOR has been proven to be involved in autophagy. In this research, we investigated the role of CYTOR in autophagy induced by C. trachomatis and the potential mechanisms. After C. trachomatis infection, CYTOR and MAPK1 were up-regulated and miR-206 was down-regulated, meanwhile, the autophagy-related protein Beclin1 and LC3-Ⅱ/LC3-Ⅰ ratio were increased. Interference with CYTOR or overexpression with miR-206 downregulated the autophagy-related protein Beclin1 and the number of autophagic spots LC3, decreased the protein ratio of LC3-II/LC3-I, and upregulated the expression of P62 protein. The luciferase reporter assay confirmed that CYTOR acted as a sponge for miR-206 to target MAPK1. In addition, CYTOR promoted autophagy induced by C. trachomatis infection through the MAPK1/ERK signaling pathway activation. Taken together, we have identified a novel molecular mechanism that the CYTOR/miR-206/MAPK1 axis was involved in the regulation of autophagy in C. trachomatis infection. This work provides an experimental basis for elucidating the pathogenesis of C. trachomatis for the treatment, prevention and control of related infectious diseases.
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Affiliation(s)
- Shan Cheng
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
| | - Yi Liu
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
| | - Bei He
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
| | - Jinrong Zhang
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
| | - Yewei Yang
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
| | - Xinglv Wang
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
| | - Zhongyu Li
- Institute of Pathogenic Biology, School of Nursing, Hengyang Medical College, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, University of South China, Hengyang 421001 Hunan, China
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Wang Q, Liu Z, Zeng X, Zheng Y, Lan L, Wang X, Lai Z, Hou X, Gao L, Liang L, Tang S, Zhang Z, Leng J, Fan X. Integrated analysis of miRNA-mRNA expression of newly emerging swine H3N2 influenza virus cross-species infection with tree shrews. Virol J 2024; 21:4. [PMID: 38178220 PMCID: PMC10768296 DOI: 10.1186/s12985-023-02260-3] [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: 08/10/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Cross-species transmission of zoonotic IAVs to humans is potentially widespread and lethal, posing a great threat to human health, and their cross-species transmission mechanism has attracted much attention. miRNAs have been shown to be involved in the regulation of IAVs infection and immunity, however, few studies have focused on the molecular mechanisms underlying miRNAs and mRNAs expression after IAVs cross-species infection. METHODS We used tree shrews, a close relative of primates, as a model and used RNA-Seq and bioinformatics tools to analyze the expression profiles of DEMs and DEGs in the nasal turbinate tissue at different time points after the newly emerged swine influenza A virus SW2783 cross-species infection with tree shrews, and miRNA-mRNA interaction maps were constructed and verified by RT-qPCR, miRNA transfection and luciferase reporter assay. RESULTS 14 DEMs were screened based on functional analysis and interaction map, miR-760-3p, miR-449b-2, miR-30e-3p, and miR-429 were involved in the signal transduction process of replication and proliferation after infection, miR-324-3p, miR-1301-1, miR-103-1, miR-134-5p, miR-29a, miR-31, miR-16b, miR-34a, and miR-125b participate in negative feedback regulation of genes related to the immune function of the body to activate the antiviral immune response, and miR-106b-3p may be related to the cross-species infection potential of SW2783, and the expression level of these miRNAs varies in different days after infection. CONCLUSIONS The miRNA regulatory networks were constructed and 14 DEMs were identified, some of them can affect the replication and proliferation of viruses by regulating signal transduction, while others can play an antiviral role by regulating the immune response. It indicates that abnormal expression of miRNAs plays a crucial role in the regulation of cross-species IAVs infection, which lays a solid foundation for further exploration of the molecular regulatory mechanism of miRNAs in IAVs cross-species infection and anti-influenza virus targets.
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Affiliation(s)
- Qihui Wang
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
| | - Zihe Liu
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Xia Zeng
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Yu Zheng
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Li Lan
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Xinhang Wang
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Zhenping Lai
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China
| | - Xiaoqiong Hou
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
| | - Lingxi Gao
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China
| | - Liang Liang
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Shen Tang
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Zengfeng Zhang
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Jing Leng
- Department of Immunology, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China.
- Key Laboratory of Characteristic Experimental Animal Models of Guangxi, Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
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Shen D, Hong Y, Feng Z, Chen X, Cai Y, Peng Q, Tu J. Development of dynamical network biomarkers for regulation in Epstein-Barr virus positive peripheral T cell lymphoma unspecified type. Front Genet 2022; 13:966247. [PMID: 36544484 PMCID: PMC9760704 DOI: 10.3389/fgene.2022.966247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: This study was performed to identify key regulatory network biomarkers including transcription factors (TFs), miRNAs and lncRNAs that may affect the oncogenesis of EBV positive PTCL-U. Methods: GSE34143 dataset was downloaded and analyzed to identify differentially expressed genes (DEGs) between EBV positive PTCL-U and normal samples. Gene ontology and pathway enrichment analyses were performed to illustrate the potential function of the DEGs. Then, key regulators including TFs, miRNAs and lncRNAs involved in EBV positive PTCL-U were identified by constructing TF-mRNA, lncRNA-miRNA-mRNA, and EBV encoded miRNA-mRNA regulatory networks. Results: A total of 96 DEGs were identified between EBV positive PTCL-U and normal tissues, which were related to immune responses, B cell receptor signaling pathway, chemokine activity. Pathway analysis indicated that the DEGs were mainly enriched in cytokine-cytokine receptor interaction and chemokine signaling pathway. Based on the TF network, hub TFs were identified regulate the target DEGs. Afterwards, a ceRNA network was constructed, in which miR-181(a/b/c/d) and lncRNA LINC01744 were found. According to the EBV-related miRNA regulatory network, CXCL10 and CXCL11 were found to be regulated by EBV-miR-BART1-3p and EBV-miR-BHRF1-3, respectively. By integrating the three networks, some key regulators were found and may serve as potential network biomarkers in the regulation of EBV positive PTCL-U. Conclusion: The network-based approach of the present study identified potential biomarkers including transcription factors, miRNAs, lncRNAs and EBV-related miRNAs involved in EBV positive PTCL-U, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of EBV positive PTCL-U.
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Affiliation(s)
- Dan Shen
- Department of Oncology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yin Hong
- Department of Cardiothoracic Surgery, Suzhou BenQ Hospital, Suzhou, China
| | - Zhengyang Feng
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangying Chen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuxing Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Jian Tu, ; Qiliang Peng,
| | - Jian Tu
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Jian Tu, ; Qiliang Peng,
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Yang Z, Luo W, Huang Z, Guo M, He X, Fan Z, Wang Q, Qin Q, Yang M, Lee X. Genome-Wide Analysis of Differentially Expressed mRNAs and lncRNAs in Koi Carp Infected with Koi Herpesvirus. Viruses 2022; 14:v14112555. [PMID: 36423164 PMCID: PMC9694643 DOI: 10.3390/v14112555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) constitute an emerging group of ncRNAs that modulate gene expression at the transcriptional or translational level. Koi herpesvirus (KHV), also known as Cyprinus herpesvirus type 3 (CyHV-3) and characterized by high pathogenicity and high mortality, has caused substantial economic losses in the common carp and koi carp fisheries industry. In this work, we sequenced the lncRNA and mRNA of host koi carp infected with KHV. A total of 20,178 DEmRNAs were obtained, of which 5021 mRNAs were upregulated and 15,157 mRNAs were downregulated. Both KEGG pathways and GO terms were enriched in many important immune pathways. The KEGG analysis showed that DEGs were significantly enriched in many important immune pathways, such as apoptosis, NOD-like receptor signaling pathway, Jak-STAT signaling pathway, TNF signaling pathway, IL-17 signaling pathway, NF-kappa B signaling pathway, and so on. Furthermore, a total of 32,697 novel lncRNA transcripts were obtained from koi carp immune tissues; 9459 of these genes were differentially expressed. Through antisense, cis-acting, and trans-acting analyses, the target genes of differentially expressed lncRNAs (DElncRNAs) were predicted. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DElncRNA expression pattern was consistent with the differential mRNA expression pattern. The lncRNA-mRNA network analysis, which included many immune pathways, showed that after KHV infection, the expression of most lncRNAs and their target mRNAs were downregulated, suggesting that these lncRNAs engage in a positive regulatory relationship with their target mRNAs. Considering that many studies have shown that herpesviruses can escape the immune system by negatively regulating these immune pathways, we speculated that these lncRNAs play a significant role in KHV's escape from host immunity. Furthermore, 10 immune-related genes and 20 lncRNAs were subsequently verified through RT-qPCR, to confirm the accuracy of the high-throughput sequencing results. In this study, we aimed to explore lncRNA functions in the immune response of lower vertebrates and provide a theoretical basis for the study of noncoding RNAs in teleosts. Therefore, exploring lncRNA expression in KHV-infected koi carp helped us better understand the biological role played by lncRNA-dependent pathways in aquaculture animal viral infection.
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Affiliation(s)
- Zimin Yang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wei Luo
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhihong Huang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Min Guo
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaochuan He
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zihan Fan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qing Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, China
| | - Qiwei Qin
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Min Yang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (M.Y.); (X.L.)
| | - Xuezhu Lee
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (M.Y.); (X.L.)
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Wang D, Zhu N, Xie F, Qin M, Wang Y. Long non-coding RNA IGFBP7-AS1 promotes odontogenic differentiation of stem cells from human exfoliated deciduous teeth through autophagy: An in vitro study. Arch Oral Biol 2022; 141:105492. [DOI: 10.1016/j.archoralbio.2022.105492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/02/2022]
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Liu J, Yin J, Wang Y, Cai L, Geng R, Du M, Zhong Z, Ni S, Huang X, Yu H, Bai J. A comprehensive prognostic and immune analysis of enhancer RNA identifies IGFBP7-AS1 as a novel prognostic biomarker in Uterine Corpus Endometrial Carcinoma. Biol Proced Online 2022; 24:9. [PMID: 35836132 PMCID: PMC9284715 DOI: 10.1186/s12575-022-00172-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNA) have been implicated in a hand of studies that supported an involvement and co-operation in Uterine Corpus Endometrial Carcinoma (UCEC). Enhancer RNAs (eRNA), a functional subtype of lncRNA, have a key role throughout the genome to guide protein production, thus potentially associated with diseases. METHODS In this study, we mainly applied the Cancer Genome Atlas (TCGA) dataset to systematically discover crucial eRNAs involving UCEC. For the key eRNAs in UCEC, we employed RT-qPCR to compare eRNA expression levels in tumor tissues and paired normal adjacent tissues from UCEC patients for validation. Furthermore, the relationships between the key eRNAs and immune activities were measured from several aspects, including the analysis for tumor microenvironment, immune infiltration cells, immune check point genes, tumor mutation burden, and microsatellite instability, as well as m6A related genes. Finally, the key eRNAs were verified by a comprehensive pan-cancer analysis. RESULTS IGFBP7 Antisense RNA 1 (IGFBP7-AS1) was identified as the key eRNA for its expression patterns of low levels in tumor tissues and favorable prognostic value in UCEC correlated with its target gene IGFBP7. In RT-qPCR analysis, IGFBP7-AS1 and IGFBP7 had down-regulated expression in tumor tissues, which was consistent with previous analysis. Moreover, IGFBP7-AS1 was found closely related with immune response in relevant immune analyses. Besides, IGFBP7-AS1 and its target gene IGFBP7 correlated with a multi-omics pan-cancer analysis. CONCLUSIONS Finally, we suggested that IGFBP7-AS1 played a key role in impacting on clinical outcomes of UCEC patients for its possible influence on immune activity.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jian Yin
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Yuanyuan Wang
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Lixin Cai
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Rui Geng
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Mulong Du
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Zihang Zhong
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Senmiao Ni
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Xiaohao Huang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
| | - Hao Yu
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China.
| | - Jianling Bai
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China.
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Herbert A, Fedorov A, Poptsova M. Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus. Int J Mol Sci 2022; 23:ijms23063079. [PMID: 35328502 PMCID: PMC8955656 DOI: 10.3390/ijms23063079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/24/2022] [Accepted: 03/09/2022] [Indexed: 12/27/2022] Open
Abstract
Z-DNA binding protein (ZBP1) very much represents the nuclear option. By initiating inflammatory cell death (ICD), ZBP1 activates host defenses to destroy infectious threats. ZBP1 is also able to induce noninflammatory regulated cell death via apoptosis (RCD). ZBP1 senses the presence of left-handed Z-DNA and Z-RNA (ZNA), including that formed by expression of endogenous retroelements. Viruses such as the Epstein–Barr “kissing virus” inhibit ICD, RCD and other cell death signaling pathways to produce persistent infection. EBV undergoes lytic replication in plasma cells, which maintain detectable levels of basal ZBP1 expression, leading us to suggest a new role for ZBP1 in maintaining EBV latency, one of benefit for both host and virus. We provide an overview of the pathways that are involved in establishing latent infection, including those regulated by MYC and NF-κB. We describe and provide a synthesis of the evidence supporting a role for ZNA in these pathways, highlighting the positive and negative selection of ZNA forming sequences in the EBV genome that underscores the coadaptation of host and virus. Instead of a fight to the death, a state of détente now exists where persistent infection by the virus is tolerated by the host, while disease outcomes such as death, autoimmunity and cancer are minimized. Based on these new insights, we propose actionable therapeutic approaches to unhost EBV.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
- Correspondence:
| | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
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Zou C, Liao J, Hu D, Su Y, Lin H, Lin K, Luo X, Zheng X, Zhang L, Huang T, Lin X. SNHG8 Promotes the Progression of Epstein-Barr Virus-Associated Gastric Cancer via Sponging miR-512-5p and Targeting TRIM28. Front Oncol 2021; 11:734694. [PMID: 34722282 PMCID: PMC8554152 DOI: 10.3389/fonc.2021.734694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/23/2021] [Indexed: 11/18/2022] Open
Abstract
SNHG8, a family member of small nucleolar RNA host genes (SNHG), has been reported to act as an oncogene in gastric carcinoma (GC). However, its biological function in Epstein–Barr virus (EBV)-associated gastric cancer (EBVaGC) remains unclear. This study investigated the role of SNHG8 in EBVaGC. Sixty-one cases of EBVaGC, 20 cases of non-EBV-infected gastric cancer (EBVnGC), and relative cell lines were studied for the expression of SNHG8 and BHRF1 (BCL2 homolog reading frame 1) encoded by EBV with Western blot and qRT-PCR assays. The relationship between the expression levels of SNHG8 and the clinical outcome in 61 EBVaGC cases was analyzed. Effects of overexpression or knockdown of BHRF1, SNHG8, or TRIM28 on cell proliferation, migration, invasion, and cell cycle and the related molecules were determined by several assays, including cell proliferation, colony assay, wound healing assay, transwell invasion assay, cell circle with flow cytometry, qRT-PCR, and Western blot for expression levels. The interactions among SNHG8, miR-512-5p, and TRIM28 were determined with Luciferase reporter assay, RNA immunoprecipitation (RIP), pull-down assays, and Western blot assay. The in vivo activity of SNHG8 was assessed with SNHG8 knockdown tumor xenografts in zebrafish. Results demonstrated that the following. (1) BHRF1 and SNHG8 were overexpressed in EBV-encoded RNA 1-positive EBVaGC tissues and cell lines. BHRF1 upregulated the expressions of SNHG8 and TRIM28 in AGS. (2) SNHG8 overexpression had a significant correlation with tumor size and vascular tumor thrombus. Patients with high SNHG8 expression had poorer overall survival (OS) compared to those with low SNHG8 expression. (3) SNHG8 overexpression promoted EBVaGC cell proliferation, migration, and invasion in vitro and in vivo, cell cycle arrested at the G2/M phase via the activation of BCL-2, CCND1, PCNA, PARP1, CDH1, CDH2 VIM, and Snail. (4) Results of dual-luciferase reporter assay, RNA immunoprecipitation, and pull-down assays indicated that SNHG8 sponged miR-512-5p, which targeted on TRIM28 and promoted cancer malignant behaviors of EBVaGC cells. Our data suggest that BHRF1 triggered the expression of SNHG8, which sponged miR-512-5p and upregulated TRIM28 and a set of effectors (such as BCL-2, CCND1, CDH1, CDH2 Snail, and VIM) to promote EBVaGC tumorigenesis and invasion. SNHG8 could be an independent prognostic factor for EBVaGC and sever as target for EBVaGC therapy.
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Affiliation(s)
- Changyan Zou
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Jinrong Liao
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Dan Hu
- Department of Pathology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Ying Su
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Huamei Lin
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Keyu Lin
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Xingguan Luo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Xiongwei Zheng
- Department of Pathology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Lurong Zhang
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
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