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Huang X, Li Y, Li J, Jiang Y, Cui W, Zhou H, Tang L. The long noncoding RNA loc107053557 acts as a gga-miR-3530-5p sponge to suppress the replication of vvIBDV through regulating STAT1 expression. Virulence 2024; 15:2333237. [PMID: 38528779 PMCID: PMC10984138 DOI: 10.1080/21505594.2024.2333237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/16/2024] [Indexed: 03/27/2024] Open
Abstract
Infectious bursal disease virus (IBDV) causes immunosuppression and high mortality in young chickens. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are important regulators during viral infection. However, detailed the regulatory mechanisms of lncRNA-miRNA-mRNA have not yet been described in IBDV infection. Here, we analysed the role of lncRNA53557/gga-miR-3530-5p/STAT1 axis in very virulent IBDV (vvIBDV) infection. Evidently upregulated expression of lncRNA53557 was observed in bursa of Fabricius and DT40 cells. Meanwhile, overexpression of lncRNA53557 promoted STAT1 expression and inhibited vvIBDV replication and vice versa, indicating that the upregulation of lncRNA53557 was part of the host antiviral defence. The subcellular fractionation assay confirmed that lncRNA53557 can be localized in the cytoplasm. Further, dual-luciferase reporter, RNA pulldown, FISH and RT-qPCR assays revealed that lncRNA53557 were directly bound to gga-miR-3530-5p and had a negative regulatory relationship between them. Subsequent mechanistic analysis showed that lncRNA53557 acted as a competing endogenous RNA (ceRNA) of gga-miR-3530-5p to relieve the repressive effect of gga-miR-3530-5p on its target STAT1, as well as Mx1, OASL, and ISG15, thereby suppressing vvIBDV replication. The study reveals that a network of enriched lncRNAs and lncRNA-associated ceRNA is involved in the regulation of IBDV infection, offering new insight into the mechanisms underlying IBDV-host interaction.
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Affiliation(s)
- Xuewei Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, P.R. China
| | - Yue Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Jiaxuan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
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2
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Chi X, Huang G, Wang L, Zhang X, Liu J, Yin Z, Guo G, Chen Y, Wang S, Chen JL. A small protein encoded by PCBP1-AS1 is identified as a key regulator of influenza virus replication via enhancing autophagy. PLoS Pathog 2024; 20:e1012461. [PMID: 39137200 DOI: 10.1371/journal.ppat.1012461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Many annotated long noncoding RNAs (lncRNAs) contain small open reading frames (sORFs), some of which have been demonstrated to encode small proteins or micropeptides with fundamental biological importance. However, functions of lncRNAs-encoded small proteins or micropeptides in viral pathogenesis remain largely unexplored. Here, we identified a 110-amino acid small protein as a key regulator of influenza A virus (IAV) replication. This small protein that we call PESP was encoded by the putative lncRNA PCBP1-AS1. It was observed that both PCBP1-AS1 and PESP were significantly upregulated by IAV infection. Furthermore, they were markedly induced by treatment with either type I or type III interferon. Overexpression of either PCBP1-AS1 or PESP alone significantly enhanced IAV replication. In contrast, shRNA-mediated knockdown of PCBP1-AS1 or CRISPR/Cas9-mediated knockout of PESP markedly inhibited the viral production. Moreover, the targeted deletion or mutation of the sORF within the PCBP1-AS1 transcript, which resulted in the disruption of PESP expression, significantly diminished the capacity of PCBP1-AS1 to enhance IAV replication, underscoring the indispensable role of PESP in the facilitation of IAV replication by PCBP1-AS1. Interestingly, overexpression of PESP enhanced the IAV-induced autophagy by increasing the expression of ATG7, an essential autophagy effector enzyme. We also found that the 7-22 amino acids at the N-terminus of PESP were crucial for its functionality in modulating ATG7 expression and action as an enhancer of IAV replication. Additionally, HSP90AA1, a protein identified previously as a facilitator of autophagy, was found to interact with PESP, resulting in the stabilization of PESP and consequently an increase in the production of IAV. These data reveal a critical lncRNA-encoded small protein that is induced and exploited by IAV during its infection, and provide a significant insight into IAV-host interaction network.
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Affiliation(s)
- Xiaojuan Chi
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guiying Huang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liwei Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinge Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayin Liu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhihui Yin
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guijie Guo
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Song Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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3
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Jiang Y, Cai L, Jia S, Xie W, Wang X, Li J, Cui W, Li G, Xia X, Tang L. Guanylate-binding protein 1 inhibits inflammatory factors produced by H5N1 virus through Its GTPase activity. Poult Sci 2024; 103:103800. [PMID: 38743966 PMCID: PMC11108968 DOI: 10.1016/j.psj.2024.103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
The combination of inflammatory factors resulting from an influenza A virus infection is one of the main causes of death in host animals. Studies have shown that guinea pig guanosine monophosphate binding protein 1 (guanylate-binding protein 1, gGBP1) can downregulate cytokine production induced by the influenza virus. Therefore, exploring the innate immune defense mechanism of GBP1 in the process of H5N1 influenza virus infection has important implications for understanding the pathogenic mechanism, disease prevention, and the control of influenza A virus infections. We found that, in addition to inhibiting the early replication of influenza virus, gGBP1 also inhibited the production of CCL2 and CXCL10 cytokines induced by the influenza virus as well as the proliferation of mononuclear macrophages induced by these cytokines. These findings further confirmed that gGBP1 inhibited the production of cytokines through its GTPase activity and cell proliferation through its C-terminal α-helix structure. This study revealed the effect of gGBP1 on the production of cellular inflammatory factors during influenza virus infection and determined the key amino acid residues that assist in the inhibitory processes mediated by gGBP1.
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Affiliation(s)
- Yanping Jiang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Limeng Cai
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shuo Jia
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Weichun Xie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Xueying Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Jiaxuan Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Wen Cui
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Guiwei Li
- Institute of Rural Revitalization Science and Technology, Heilongjiang Academy of Agricultural Science, Harbin 150023, China
| | - Xianzhu Xia
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun 130000, China
| | - Lijie Tang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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Rai A, Bhagchandani T, Tandon R. Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195023. [PMID: 38513793 DOI: 10.1016/j.bbagrm.2024.195023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts of size >200 bp that do not translate into proteins. Emerging data revealed that viral infection results in systemic changes in the host at transcriptional level. These include alterations in the lncRNA expression levels and triggering of antiviral immune response involving several effector molecules and diverse signalling pathways. Thus, lncRNAs have emerged as an essential mediatory element at distinct phases of the virus infection cycle. The complete eradication of the viral disease requires more precise and novel approach, thus manipulation of the lncRNAs could be one of them. This review shed light upon the existing knowledge of lncRNAs wherein the implication of differentially expressed lncRNAs in blood-borne, air-borne, and vector-borne viral diseases and its promising therapeutic applications under clinical settings has been discussed. It further enhances our understanding of the complex interplay at host-pathogen interface with respect to lncRNA expression and function.
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Affiliation(s)
- Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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5
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Zhu S, Chen X, He D, Zhang M, Man X, Tang Y, Diao Y. Role of long non-coding RNA DLY6E in regulating TMUV infection. Virus Res 2024; 343:199350. [PMID: 38438020 PMCID: PMC10982077 DOI: 10.1016/j.virusres.2024.199350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Long non-coding RNA (lncRNA) is a type of RNA with a length greater than 200 nt and lacking coding ability. In recent years, a considerable number of lncRNAs have been found to have important functions. The lncRNA plays an important role in growth and development, body metabolism, immune function, and regulation of viral replication. A lncRNA, MSTRG8505.2, was screened and named lncRNA DLY6E, which was a new duck-derived lncRNA. The lncRNADLY6E in this study has a complex secondary structure, specifically distributed in the heart, liver and other organs. The expression of lncRNA DLY6E was significantly up-regulated after TMUV infection, which was time-dependent and non-dose-dependent. Overexpression of three structural proteins and seven non-structural proteins of TMUV in DEF cells showed no significant difference in the expression of lncRNADLY6E. Meanwhile, using lipopolysaccharides (LPS) and poly (I:C) to stimulate DEF cells, the results showed that the induced expression of lncRNA DLY6E was associated with the dsRNA-related TLR3/RIG-I/MDA5 pathway rather than the LPS activated signaling pathway. To further explore the function of lncRNA DLY6E, an eukaryotic expression vector was constructed. Overexpression of lncRNA DLY6E in DEF cells can increase the replication of TMUV. After overexpression of lncRNADLY6E, the transcriptional level of its target gene LY6E was detected, and the results showed that lncRNADLY6E did not act through its target gene. Overexpression of lncRNA DLY6E significantly inhibited the mRNA levels of OAS, Mx and PKR, suggesting that lncRNA DLY6E may promote the virus by inhibiting the transcription of antiviral proteins in innate immunity. This phenomenon provides new ideas for the prevention and control of TMUV, which is worth further thinking and exploration.
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Affiliation(s)
- Siming Zhu
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Xin Chen
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Dalin He
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Meijuan Zhang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Xinhong Man
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China.
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China.
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6
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Saleh RO, Jasim SA, Kadhum WR, Hjazi A, Faraz A, Abid MK, Yumashev A, Alawadi A, Aiad IAZ, Alsalamy A. Exploring the detailed role of interleukins in cancer: A comprehensive review of literature. Pathol Res Pract 2024; 257:155284. [PMID: 38663179 DOI: 10.1016/j.prp.2024.155284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 05/12/2024]
Abstract
The cancer cells that are not normal can grow into tumors, invade surrounding tissues, and travel to other parts of the body via the lymphatic or circulatory systems. Interleukins, a vital class of signaling proteins, facilitate cell-to-cell contact within the immune system. A type of non-coding RNA known as lncRNAs mediates its actions by regulating miRNA-mRNA roles (Interleukins). Because of their dual function in controlling the growth of tumors and altering the immune system's response to cancer cells, interleukins have been extensively studied concerning cancer. Understanding the complex relationships between interleukins, the immune system, the tumor microenvironment, and the components of interleukin signaling pathways that impact the miRNA-mRNA axis, including lncRNAs, has advanced significantly in cancer research. Due to the significant and all-encompassing influence of interleukins on the immune system and the development and advancement of cancers, lncRNAs play a crucial role in cancer research by modulating interleukins. Their diverse effects on immune system regulation, tumor growth encouragement, and tumor inhibition make them appealing candidates for potential cancer treatments and diagnostics. A deeper understanding of the relationship between the biology of interleukin and lncRNAs will likely result in more effective immunotherapy strategies and individualized cancer treatments.
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Affiliation(s)
- Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq
| | - Saade Abdalkareem Jasim
- Pharmacy Department, Al-Huda University College, Anbar, Iraq; Biotechnology Department, College of Applied Science, Fallujah University, Anbar, Iraq.
| | - Wesam R Kadhum
- Department of Pharmacy, Kut University College, Kut, Wasit 52001, Iraq; Advanced Research Center, Kut University College, Kut, Wasit 52001, Iraq
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Faraz
- Department of Basic Medical Sciences, College of Medicine, Majmaah University, Majmaah 11952, Saudi Arabia.
| | - Mohammed Kadhem Abid
- Department of Anesthesia, College of Health & Medical Technology, Al-Ayen University, Thi-Qar, Iraq
| | - Alexey Yumashev
- Department of Prosthetic Dentistry, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Iraq
| | - Ibrahim Ahmed Zaki Aiad
- Department of Pediatrics, General Medicine Practice Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia
| | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
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7
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Wang M, Yao X, Tong X, Qi D, Ye X. Lnc-RPS6P3 Inhibits Influenza A Virus Replication and Attenuates the Inhibitory Effect of NS1 on Innate Immune Response. Microorganisms 2024; 12:654. [PMID: 38674599 PMCID: PMC11052439 DOI: 10.3390/microorganisms12040654] [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: 02/20/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Host factors play important roles in influenza A virus (IAV) replication. In order to identify novel host factors involved in IAV replication, we compared the differentially expressed genes in A549 cells after IAV infection. We found that lncRNA lnc-RPS6P3 was up-regulated upon viral infection and poly(I:C) and IFN-β treatment, indicating it was an interferon-stimulated gene. Functional analysis demonstrated that overexpression of lnc-RPS6P3 inhibited IAV replication while knockdown of lnc-RPS6P3 promoted viral infection in A549 cells. Lnc-RPS6P3 inhibited both transcription and replication of IAV. Further study showed that lnc-RPS6P3 interacted with viral NP and interfered with NP self-oligomerization and, consequently, inhibited vRNP activity. In addition, lnc-RPS6P3 interacted with viral NS1 and reduced the interaction of NS1 and RIG-I; it also attenuated the inhibitory effect of NS1 on IFN-β stimulation. In conclusion, we revealed that lnc-RPS6P3 is an interferon-stimulated gene that inhibits IAV replication and attenuates the inhibitory effect of NS1 on innate immune response.
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Affiliation(s)
- Mingge Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Xinli Yao
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomei Tong
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Dandan Qi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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LIU JUN, LI WENLI, LU RUYUE, XU JIAQING, JIANG CHUNHUI, DUAN JUNLIN, ZHANG LINGZHI, WANG GUANFU, CHEN JIAXI. Investigation of the feasibility of NRAV as a biomarker for hepatocellular carcinoma. Oncol Res 2024; 32:717-726. [PMID: 38560576 PMCID: PMC10972727 DOI: 10.32604/or.2023.043575] [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: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 04/04/2024] Open
Abstract
The long non-coding RNA, Negative Regulator of Antiviral Response (NRAV) has been identified as a participant in both respiratory virus replication and immune checkpoints, however, its involvement in pan-cancer immune regulation and prognosis, particularly those of hepatocellular carcinoma (HCC), remains unclear. To address this knowledge gap, we analyzed expression profiles obtained from The Cancer Genome Atlas (TCGA) database, comparing normal and malignant tumor tissues. We found that NRAV expression is significantly upregulated in tumor tissues compared to adjacent nontumor tissues. Kaplan-Meier (K-M) analysis revealed the prognostic power of NRAV, wherein overexpression was significantly linked to reduced overall survival in a diverse range of tumor patients. Furthermore, noteworthy associations were observed between NRAV, immune checkpoints, immune cell infiltration, genes related to autophagy, epithelial-mesenchymal transition (EMT), pyroptosis, tumor mutational burden (TMB), and microsatellite instability (MSI) across different cancer types, including HCC. Moreover, NRAV upregulation expression was associated with multiple pathological stages by clinical observations. Furthermore, our investigation revealed a substantial elevation in the expression of NRAV in both HCC tumor tissues and cells compared to normal tissues and cells. The inhibition of NRAV resulted in the inhibition of cell proliferation, migration, and invasion in HCC cells, while also influencing the expression of CD274 (PD-L1) and CD44, along with various biomarkers associated with EMT, autophagy, and pyroptosis. The aforementioned results propose NRAV as a promising prognostic biomarker for HCC.
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Affiliation(s)
- JUN LIU
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
- Department of Clinical Laboratory, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, China
| | - WENLI LI
- Department of Clinical Laboratory, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, China
| | - RUYUE LU
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
| | - JIAQING XU
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
| | - CHUNHUI JIANG
- School of Basic Medical Sciences Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - JUNLIN DUAN
- Department of Clinical Laboratory, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, China
| | - LINGZHI ZHANG
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - GUANFU WANG
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - JIAXI CHEN
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
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9
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Wang X, Cheng J, Shen L, Chen M, Sun K, Li J, Li M, Ma C, Wei L. Rab5c promotes RSV and ADV replication by autophagy in respiratory epithelial cells. Virus Res 2024; 341:199324. [PMID: 38242290 PMCID: PMC10830860 DOI: 10.1016/j.virusres.2024.199324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Respiratory system diseases caused by respiratory viruses are common and exert tremendous pressure on global healthcare system. In our previous studies, we found that Long non-coding RNA NRAV (Lnc NRAV) and its target molecule Rab5c plays a significant role in respiratory virus infection. However, the mechanism by which Rab5c affects virus replication remains unclear. Rab5c, a protein mainly localized on the cell membranes and in early endosomes and phagosomes, participates in endocytosis mediated by clathrin and regulates the fusion of early endosome, maturation of early phagosomes, and autophagy. Therefore, we inferred that Rab5c impacts virus replication, which might be related to endocytosis or autophagy. We selected RSV (respiratory syncytial virus) as a representative enveloped virus and ADV (Adenovirus) as a representative non-enveloped virus to explore the possible mechanism of RSV and ADV replication promoted by Rab5c in A549 cells and in Rab5c-overexpressing mice. Here, we confirmed that the activated Rab5c promotes RSV and ADV replication and the inactivated Rab5c inhibits their replication. However, Rab5c promoting RSV and ADV replication is not mediated by endocytosis rather by autophagy in respiratory epithelial cells. Our study showed that Rab5c upregulates LC3-Ⅱ (microtubule-associated protein 1 light chain 3 beta) protein expression levels by interacting with Beclin1, a key autophagy molecule, which can induce autophagy and promote replication of ADV and RSV. This study enriches the understanding of the interaction between respiratory viruses and Rab5c, providing new insights for virus prevention and treatment.
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Affiliation(s)
- Xiuli Wang
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China; Clinical Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jing Cheng
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China
| | - Linchao Shen
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China
| | - Meixi Chen
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China; Clinical Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Keran Sun
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China
| | - Jian Li
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China; Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Miao Li
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China
| | - Cuiqing Ma
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China
| | - Lin Wei
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China; Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, Hebei, China.
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10
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Chattopadhyay P, Mehta P, Soni J, Tardalkar K, Joshi M, Pandey R. Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients. NAR Genom Bioinform 2024; 6:lqae023. [PMID: 38426128 PMCID: PMC10903533 DOI: 10.1093/nargab/lqae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
A plethora of studies have demonstrated the roles of lncRNAs in modulating disease severity and outcomes during infection. However, the spatio-temporal expression of these lncRNAs is poorly understood. In this study, we used single-cell RNA-seq to understand the spatio-temporal expression dynamics of lncRNAs across healthy, SARS-CoV-2-infected, and recovered individuals and their functional role in modulating the disease and recovery. We identified 203 differentially expressed lncRNAs, including cell type-specific ones like MALAT1, NEAT1, ZFAS1, SNHG7, SNHG8, and SNHG25 modulating immune function in classical monocyte, NK T, proliferating NK, plasmablast, naive, and activated B/T cells. Interestingly, we found invariant lncRNAs (no significant change in expression across conditions) regulating essential housekeeping functions (for example, HOTAIR, NRAV, SNHG27, SNHG28, and UCA1) in infected and recovered individuals. Despite similar repeat element abundance, variant lncRNAs displayed higher Alu content, suggesting increased interactions with proximal and distal genes, crucial for immune response modulation. The comparable repeat abundance but distinct expression levels of variant and invariant lncRNAs highlight the significance of investigating the regulatory mechanisms of invariant lncRNAs. Overall, this study offers new insights into the spatio-temporal expression patterns and functional roles of lncRNAs in SARS-CoV-2-infected and recovered individuals while highlighting the importance of invariant lncRNAs in the disease context.
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Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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11
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Sefatjoo Z, Mohebbi SR, Hosseini SM, Shoraka S, Saeedi Niasar M, Baghaei K, Meyfour A, Sadeghi A, Malekpour H, Asadzadeh Aghdaei H, Zali MR. Evaluation of long non-coding RNAs EGOT, NRAV, NRIR and mRNAs ISG15 and IFITM3 expressions in COVID-19 patients. Cytokine 2024; 175:156495. [PMID: 38184893 DOI: 10.1016/j.cyto.2023.156495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/26/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Individuals with Coronavirus Disease 2019 (COVID-19) may show no symptoms to moderate or severe complications. This variation may be due to differences in the strength of the immune response, including a delayed interferon (IFN) response in asymptomatic patients and higher IFN levels in severe patients. Some long non-coding RNAs (lncRNAs), as regulators of the IFN pathway, may contribute to the emergence of different COVID-19 symptoms. This study aimed to comparatively investigate the relationship between lncRNAs (eosinophil granule ontogeny transcript (EGOT), negative regulator of antiviral response (NRAV), and negative regulator of interferon response (NRIR)), alongside interferon-stimulated genes (ISGs) like ISG-15 and interferon-induced transmembrane protein 3 (IFITM3) in COVID-19 patients with asymptomatic, moderate, and severe symptoms. Buffy coat samples were collected from 17 asymptomatic, 23 moderate, 22 severe patients, and 44 healthy controls. Quantitative real-time PCR was utilized to determine the expression levels. In a comparison between COVID-19 patients and healthy individuals, higher expression levels of EGOT and NRAV were observed in severe and moderate patients. NRIR expression was increased across all patient groups. Meanwhile, ISG15 expression decreased in all patient groups, and the moderate group showed a significant decrease in IFITM3 expression. Comparing COVID-19 patient groups, EGOT expression was significantly higher in moderate COVID-19 patients compared to asymptomatic patients. NRAV was higher in moderate and severe patients compared to asymptomatic. NRIR levels did not differ significantly between the COVID-19 patient groups. ISG15 was higher in moderate and severe patients compared to asymptomatic. IFITM3 expression was significantly higher in severe patients compared to the moderate group. In severe COVID-19 patients, EGOT expression was positively correlated with NRAV levels. EGOT and NRAV showed a significant positive correlation in asymptomatic patients, and both were positively correlated with IFITM3 expression. This study suggests that EGOT, NRAV, NRIR, ISG15, and IFITM3 may serve as diagnostic biomarkers for COVID-19. The lncRNA NRAV may be a good biomarker in a prognostic panel between asymptomatic and severe patients in combination with other high-sensitivity biomarkers. EGOT, NRAV, and ISG15 could also be considered as specific biomarkers in a prognostic panel comparing asymptomatic and moderate patients with other high-sensitivity biomarkers.
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Affiliation(s)
- Zahra Sefatjoo
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Shahrzad Shoraka
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Saeedi Niasar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Habib Malekpour
- Research and Development Center, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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12
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Wang RY, Yang JL, Xu N, Xu J, Yang SH, Liang DM, Li JZ, Zhu H. Lipid metabolism-related long noncoding RNA RP11-817I4.1 promotes fatty acid synthesis and tumor progression in hepatocellular carcinoma. World J Gastroenterol 2024; 30:919-942. [PMID: 38516243 PMCID: PMC10950635 DOI: 10.3748/wjg.v30.i8.919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/24/2023] [Accepted: 01/27/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common types of tumors. The influence of lipid metabolism disruption on the development of HCC has been demonstrated in published studies. AIM To establish an HCC prognostic model for lipid metabolism-related long non-coding RNAs (LMR-lncRNAs) and conduct in-depth research on the specific role of novel LMR-lncRNAs in HCC. METHODS Correlation and differential expression analyses of The Cancer Genome Atlas data were used to identify differentially expressed LMR-lncRNAs. Quantitative real-time polymerase chain reaction analysis was used to evaluate the expression of LMR-lncRNAs. Nile red staining was employed to observe intracellular lipid levels. The interaction between RP11-817I4.1, miR-3120-3p, and ATP citrate lyase (ACLY) was validated through the performance of dual-luciferase reporter gene and RIP assays. RESULTS Three LMR-lncRNAs (negative regulator of antiviral response, RNA transmembrane and coiled-coil domain family 1 antisense RNA 1, and RP11-817I4.1) were identified as predictive markers for HCC patients and were utilized in the construction of risk models. Additionally, proliferation, migration, and invasion were reduced by RP11-817I4.1 knockdown. An increase in lipid levels in HCC cells was significantly induced by RP11-817I4.1 through the miR-3120-3p/ACLY axis. CONCLUSION LMR-lncRNAs have the capacity to predict the clinical characteristics and prognoses of HCC patients, and the discovery of a novel LMR-lncRNAs, RP11-817I4.1, revealed its role in promoting lipid accumulation, thereby accelerating the onset and progression of HCC.
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Affiliation(s)
- Ren-Yong Wang
- Second Affiliated Hospital of Kunming Medical University, Kunming 650106, Yunnan Province, China
| | - Jia-Ling Yang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu Province, China
| | - Ning Xu
- Second Affiliated Hospital of Kunming Medical University, Kunming 650106, Yunnan Province, China
| | - Jia Xu
- Wuhan Blood Center, Wuhan 430030, Hubei Province, China
| | - Shao-Hua Yang
- Second Affiliated Hospital of Kunming Medical University, Kunming 650106, Yunnan Province, China
| | - Dao-Ming Liang
- Second Affiliated Hospital of Kunming Medical University, Kunming 650106, Yunnan Province, China
| | - Jin-Ze Li
- Department of Gastrointestinal Surgery, The Third People's Hospital of Hubei Province, Wuhan 430071, Hubei Province, China
| | - Hong Zhu
- Second Affiliated Hospital of Kunming Medical University, Kunming 650106, Yunnan Province, China
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13
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Zhang Y, Gao Y, Li F, Qi Q, Li Q, Gu Y, Zheng Z, Hu B, Wang T, Zhang E, Xu H, Liu L, Tian T, Jin G, Yan C. Long non-coding RNA NRAV in the 12q24.31 risk locus drives gastric cancer development through glucose metabolism reprogramming. Carcinogenesis 2024; 45:23-34. [PMID: 37950445 DOI: 10.1093/carcin/bgad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) serve as vital candidates to mediate cancer risk. Here, we aimed to identify the risk single-nucleotide polymorphisms (SNPs)-induced lncRNAs and to investigate their roles in gastric cancer (GC) development. Through integrating the differential expression analysis of lncRNAs in GC tissues and expression quantitative trait loci analysis in normal stomach tissues and GC tissues, as well as genetic association analysis based on GC genome-wide association studies and an independent validation study, we identified four lncRNA-related SNPs consistently associated with GC risk, including SNHG7 [odds ratio (OR) = 1.16, 95% confidence interval (CI): 1.09-1.23], NRAV (OR = 1.11, 95% CI: 1.05-1.17), LINC01082 (OR = 1.16, 95% CI: 1.08-1.22) and FENDRR (OR = 1.16, 95% CI: 1.07-1.25). We further found that a functional SNP rs6489786 at 12q24.31 increases binding of MEOX1 or MEOX2 at a distal enhancer and results in up-regulation of NRAV. The functional assays revealed that NRAV accelerates GC cell proliferation while inhibits GC cell apoptosis. Mechanistically, NRAV decreases the expression of key subunit genes through the electron transport chain, thereby driving the glucose metabolism reprogramming from aerobic respiration to glycolysis. These findings suggest that regulating lncRNA expression is a crucial mechanism for risk-associated variants in promoting GC development.
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Affiliation(s)
- Yan Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yun Gao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fengyuan Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Qi
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qian Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuanliang Gu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhonghua Zheng
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Beiping Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tianpei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Public Health Institute of Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Liu
- Institute of Digestive Endoscopy, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
- Public Health Institute of Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Immunology, Key Laboratory of Immunological Environment and Disease, Nanjing Medical University, Nanjing, China
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Wuxi, China
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14
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Jasim SA, Aziz DZ, Mustafa YF, Margiana R, Al-Alwany AA, Hjazi A, Alawadi A, Yumashev A, Alsalamy A, Fenjan MN. Role of genetically engineered mesenchymal stem cell exosomes and LncRNAs in respiratory diseases treatment. Pathol Res Pract 2024; 254:155135. [PMID: 38295461 DOI: 10.1016/j.prp.2024.155135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
The term acute respiratory disease encompasses a wide range of acute lung diseases, which in recent years have been ranked among the top three deadly diseases in the world. Since conventional treatment methods, including the use of anti-inflammatory drugs, have had no significant effect on the treatment process of these diseases, the attention of the medical community has been drawn to alternative methods. Mesenchymal stem cells (MSC) are multipotential stem/progenitor cells that have extensive immunomodulatory and anti-inflammatory properties and also play a critical role in the microenvironment of injured tissue. MSC secretomes (containing large extracellular vesicles, microvesicles, and exosomes) are a newly introduced option for cell-free therapies that can circumvent the hurdles of cell-based therapies while maintaining the therapeutic role of MSC themselves. The therapeutic capabilities of MSCs have been showed in many acute respiratory diseases, including chronic respiratory disease (CRD), novel coronavirus 2019 (COVID -19), and pneumonia. MSCs offer novel therapeutic approaches for chronic and acute lung diseases due to their anti-inflammatory and immunomodulatory properties. In this review, we summarize the current evidence on the efficacy and safety of MSC-derived products in preclinical models of lung diseases and highlight the biologically active compounds present in the MSC secretome and their mechanisms involved in anti-inflammatory activity and tissue regeneration.
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Affiliation(s)
| | - Dhifaf Zeki Aziz
- College of Science, Department of pathological Analyses, University of Kufa, Al-Najaf, Iraq.
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq.
| | - Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.
| | | | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Saudi Arabia.
| | - Ahmed Alawadi
- College of technical engineering, the Islamic University, Najaf, Iraq; College of technical engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; College of technical engineering, the Islamic University of Babylon, Babylon, Iraq
| | - Alexey Yumashev
- Department of Prosthetic Dentistry, Sechenov First Moscow State Medical University, Russia.
| | - Ali Alsalamy
- College of technical engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq.
| | - Mohammed N Fenjan
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Iraq.
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15
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Cheng J, Tao J, Li B, Shi Y, Liu H. The lncRNA HCG4 regulates the RIG-I-mediated IFN production to suppress H1N1 swine influenza virus replication. Front Microbiol 2024; 14:1324218. [PMID: 38274760 PMCID: PMC10808666 DOI: 10.3389/fmicb.2023.1324218] [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: 10/19/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Influenza A virus (IAV) non-structural protein 1 (NS1) is a virulence factor that allows the virus to replicate efficiently by suppressing host innate immune responses. Previously, we demonstrated that the serine (S) at position 42 of NS1 in H1N1 swine influenza virus (SIV) is a critical residue in interferon (IFN) resistance, thus facilitating viral infections. Here, by lncRNA-seq, a total of 153 differentially expressed lncRNAs were identified, and the lncRNA HCG4 was selected due to its significantly higher expression after infection with the NS1 S42P mutant virus. Overexpression of HCG4 enhanced IFN-β production and suppressed SIV infection, highlighting the potential antiviral activity of HCG4 against SIV. Further investigation suggested that HCG4 served as a positive feedback mediator for RIG-I signaling. It alleviated the inhibitory effect on RIG-I K63-linked ubiquitination by NS1 protein, thereby resulting in an increase in RIG-I-mediated IFN production. Taken together, our findings demonstrate that HCG4 modulates the innate immune response to SIV infection through K63-linked RIG-I ubiquitination, providing insights into the role of lncRNAs in controlling viral infections.
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Affiliation(s)
- Jinghua Cheng
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Jie Tao
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Benqiang Li
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Ying Shi
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Huili Liu
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
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16
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Banerjee S, Sarkar R, Mukherjee A, Mitra S, Gope A, Chawla-Sarkar M. Rotavirus-induced lncRNA SLC7A11-AS1 promotes ferroptosis by targeting cystine/glutamate antiporter xCT (SLC7A11) to facilitate virus infection. Virus Res 2024; 339:199261. [PMID: 37923170 PMCID: PMC10684390 DOI: 10.1016/j.virusres.2023.199261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Rotavirus (RV) is the primary etiological agent of virus-associated gastroenteritis in infants, causing 200,000 childhood death annually. Despite the availability of vaccines, rotaviral diarrhea continues to be a severe issue in underdeveloped nations in Asia and Africa. The situation demands continual studies on host-rotavirus interactions to understand disease pathogenesis and develop effective antiviral therapeutics. Long non-coding RNAs (lncRNAs), which are a subset of non-coding RNAs of more than 200 nucleotides in length, are reported to play a regulatory function in numerous viral infections. Virus infection often alters the host transcriptome including lncRNA that are differentially expressed either to play an antiviral role or to be advantageous towards virus propagation. In the current study, qPCR array-based expression profiling of host lncRNAs was performed in rotavirus-infected HT-29 cells that identified the lncRNA SLC7A11-AS1 to be upregulated during RV infection. Knockdown of SLC7A11-AS1 conspicuously reduced RV titers implying its pro-viral significance. RV-induced SLC7A11-AS1 downregulates the gene SLC7A11/xCT that encodes the light chain subunit of the system XC- cystine-glutamate exchange transporter, leading to decrease in intracellular glutathione level and increase in lipid peroxidation, which are signature features of ferroptotic pathway. Ectopic expression of xCT also abrogated RV infection by reversing the virus optimized levels of intracellular GSH and lipid ROS levels. Cumulatively, the study reveals that RV infection triggers ferroptotic cell death via SLC7A11-AS1/xCT axis to facilitate its own propagation.
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Affiliation(s)
- Shreya Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rakesh Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Arpita Mukherjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Animesh Gope
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India.
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17
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Chen B, Guo G, Wang G, Zhu Q, Wang L, Shi W, Wang S, Chen Y, Chi X, Wen F, Maarouf M, Huang S, Yang Z, Chen JL. ATG7/GAPLINC/IRF3 axis plays a critical role in regulating pathogenesis of influenza A virus. PLoS Pathog 2024; 20:e1011958. [PMID: 38227600 PMCID: PMC10817227 DOI: 10.1371/journal.ppat.1011958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/26/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024] Open
Abstract
Autophagy-related protein 7 (ATG7) is an essential autophagy effector enzyme. Although it is well known that autophagy plays crucial roles in the infections with various viruses including influenza A virus (IAV), function and underlying mechanism of ATG7 in infection and pathogenesis of IAV remain poorly understood. Here, in vitro studies showed that ATG7 had profound effects on replication of IAV. Depletion of ATG7 markedly attenuated the replication of IAV, whereas overexpression of ATG7 facilitated the viral replication. ATG7 conditional knockout mice were further employed and exhibited significantly resistant to viral infections, as evidenced by a lower degree of tissue injury, slower body weight loss, and better survival, than the wild type animals challenged with either IAV (RNA virus) or pseudorabies virus (DNA virus). Interestingly, we found that ATG7 promoted the replication of IAV in autophagy-dependent and -independent manners, as inhibition of autophagy failed to completely block the upregulation of IAV replication by ATG7. To determine the autophagy-independent mechanism, transcriptome analysis was utilized and demonstrated that ATG7 restrained the production of interferons (IFNs). Loss of ATG7 obviously enhanced the expression of type I and III IFNs in ATG7-depleted cells and mice, whereas overexpression of ATG7 impaired the interferon response to IAV infection. Consistently, our experiments demonstrated that ATG7 significantly suppressed IRF3 activation during the IAV infection. Furthermore, we identified long noncoding RNA (lncRNA) GAPLINC as a critical regulator involved in the promotion of IAV replication by ATG7. Importantly, both inactivation of IRF3 and inhibition of IFN response caused by ATG7 were mediated through control over GAPLINC expression, suggesting that GAPLINC contributes to the suppression of antiviral immunity by ATG7. Together, these results uncover an autophagy-independent mechanism by which ATG7 suppresses host innate immunity and establish a critical role for ATG7/GAPLINC/IRF3 axis in regulating IAV infection and pathogenesis.
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Affiliation(s)
- Biao Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Guijie Guo
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Guoqing Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Qianwen Zhu
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Lulu Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Wenhao Shi
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Song Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Xiaojuan Chi
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Faxin Wen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Zhou Yang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
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18
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Yao X, Zhong L, Wang M, Wang M, Han Y, Wang Y, Zhou J, Song J, Li Y, Xu Y. Up-regulated lncRNA CYLD as a ceRNA of miR-2383 facilitates bovine viral diarrhea virus replication by promoting CYLD expression to counteract RIG-I-mediated type-I IFN production. Int J Biol Macromol 2023; 253:127351. [PMID: 37839600 DOI: 10.1016/j.ijbiomac.2023.127351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/17/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Bovine viral diarrhea virus (BVDV) is one of the most important pathogens of cattle, causing numerous economic losses to the cattle industry. To date, many potential mechanisms of BVDV evading or subverting innate immunity are still unknown. In this study, an lnc-CYLD/miR-2383/CYLD axis involved in BVDV-host interactions was screened from RNA-seq-based co-expression networks analysis of long noncoding RNAs, microRNAs and mRNAs in BVDV-infected bovine cells, and underlying mechanisms of lnc-CYLD/miR-2383/CYLD axis regulating BVDV replication were explored. Results showed that BVDV-induced up-regulation of the lnc-CYLD competed for binding to the miR-2383, and then promoted CYLD expression, thereby inhibiting RIG-I-mediated type-I interferon (IFN) production, which was subsequently confirmed by treatment with lnc-CYLD overexpression and miR-2383 inhibitor. However, miR-2383 transfection and small interfering RNA-mediated lnc-CYLD knockdown inhibited CYLD expression and enhanced RIG-I-mediated type-I IFN production, inhibiting BVDV replication. In addition, interaction relationship between lnc-CYLD and miR-2383, and colocalization relationship of lnc-CYLD, miR-2383 and CYLD were confirmed by dual-luciferase assay and in situ hybridization assay. Conclusively, up-regulation of the lnc-CYLD as a competing endogenous RNA binds to the miR-2383 to reduce inhibitory effect of the miR-2383 on the CYLD expression, playing an important role in counteracting type-I IFN-dependent antiviral immunity to facilitate BVDV replication.
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Affiliation(s)
- Xin Yao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China; Key Laboratory for Animal Disease Control and Pharmaceutical Development of Heilongjiang Province, Northeast Agricultural University, Harbin, China
| | - Linhan Zhong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Mengmeng Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Mei Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yanyan Han
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yixin Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jiaying Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jingge Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yuan Li
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China.
| | - Yigang Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China; Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics and Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China.
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19
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Lê-Bury G, Chen Y, Rhen JM, Grenier JK, Singhal A, Russell DG, Boliar S. HIV-1 active and latent infections induce disparate chromatin reorganization and transcriptional regulation of mRNAs and lncRNAs in SupT1 cells. mBio 2023; 14:e0261923. [PMID: 38038477 PMCID: PMC10746154 DOI: 10.1128/mbio.02619-23] [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: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE HIV-1 infection of T-lymphocytes depends on co-opting cellular transcriptional and translational machineries for viral replication. This requires significant changes in the cellular microenvironment. We have characterized and compared the changes in cellular chromatin structures as well as gene expression landscapes in T cells that are either actively or latently infected with HIV-1. Our results reveal that chromatin accessibility and expression of both protein-coding mRNAs and non-coding lncRNAs are uniquely regulated in HIV-1-infected T cells, depending on whether the virus is actively transcribing or remains in a transcriptionally silent, latent state. HIV-1 latent infection elicits more robust changes in the cellular chromatin organization than active viral infection. Our analysis also identifies the effects of such epigenomic changes on the cellular gene expression and subsequent biological pathways. This study comprehensively characterizes the cellular epigenomic and transcriptomic states that support active and latent HIV-1 infection in an in vitro model of SupT1 cells.
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Affiliation(s)
- Gabrielle Lê-Bury
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yao Chen
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jordan M. Rhen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcription Regulation and Expression Facility, Cornell University, Ithaca, New York, USA
| | - Amit Singhal
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore, Singapore
| | - David G. Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Saikat Boliar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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20
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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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21
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Mohapatra S, Tripathi S, Sharma V, Basu A. Regulation of microglia-mediated inflammation by host lncRNA Gm20559 upon flaviviral infection. Cytokine 2023; 172:156383. [PMID: 37801852 DOI: 10.1016/j.cyto.2023.156383] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Japanese Encephalitis Virus (JEV) and West Nile Viruses (WNV) are neurotropic flaviviruses which cause neuronal death and exaggerated glial activation in the central nervous system. Role of host long non coding RNAs in shaping microglial inflammation upon flavivirus infections has been unexplored. This study attempted to decipher the role of lncRNA Gm20559 in regulating microglial inflammatory response in context of flaviviruses. METHODS Antisense oligonucleotide LNA Gapmers designed against lncRNA Gm20559 and non-specific site (negative control) were used for Gm20559 knockdown in JEV and WNV-infected N9 microglial cells. Upon establishing successful Gm20559 knockdown, expression of various proinflammatory cytokines, chemokines, interferon-stimulated genes (ISGs) and RIG-I were checked by qRT-PCR and cytometric bead array. Western Blotting was done to analyse the phosphorylation level of various inflammatory markers and viral non-structural protein expression. Plaque Assays were employed to quantify viral titres in microglial supernatant upon knocking down Gm20559. Effect of microglial supernatant on HT22 neuronal cells was assessed by checking expression of apoptotic protein and viral non-structural protein by Western Blotting. RESULTS Upregulation in Gm20559 expression was observed in BALB/c pup brains, primary microglia as well as N9 microglia cell line upon both JEV and WNV infection. Knockdown of Gm20559 in JEV and WNV-infected N9 cell led to the reduction of major proinflammatory cytokines - IL-1β, IL-6, IP-10 and IFN-β. Inhibition of Gm20559 upon JEV infection in N9 microglia also led to downregulation of RIG-I and OAS-2, which was not the case in WNV-infected N9 microglia. Phosphorylation level of P38 MAPK was reduced in case of JEV-infected N9 microglia and not WNV-infected N9 microglia. Whereas phosphorylation of NF-κB pathway was unchanged upon Gm20559 knockdown in both JEV and WNV-infected N9 microglia. However, treating HT22 cells with JEV and WNV-infected microglial supernatant with and without Gm20559 could not trigger cell death or influence viral replication. CONCLUSION Knockdown studies on lncRNA Gm20559 suggests its pivotal role in maintaining the inflammatory milieu of microglia in flaviviral infection by modulating the expression of various pro-inflammatory cytokines. However, Gm20559-induced increased microglial proinflammatory response upon flavivirus infection fails to trigger neuronal death.
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Affiliation(s)
- Stuti Mohapatra
- National Brain Research Centre, Manesar, Haryana 122052, India
| | - Shraddha Tripathi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Telangana 500078, India
| | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Telangana 500078, India.
| | - Anirban Basu
- National Brain Research Centre, Manesar, Haryana 122052, India.
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22
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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23
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Amin HM, Szabo B, Abukhairan R, Zeke A, Kardos J, Schad E, Tantos A. In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F). Int J Mol Sci 2023; 24:16032. [PMID: 38003223 PMCID: PMC10671326 DOI: 10.3390/ijms242216032] [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: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
For several histone lysine methyltransferases (HKMTs), RNA binding has been already shown to be a functionally relevant feature, but detailed information on the RNA interactome of these proteins is not always known. Of the six human KMT2 proteins responsible for the methylation of the H3K4 residue, two-SETD1A and SETD1B-contain RNA recognition domains (RRMs). Here we investigated the RNA binding capacity of SETD1A and identified a broad range of interacting RNAs within HEK293T cells. Our analysis revealed that similar to yeast Set1, SETD1A is also capable of binding several coding and non-coding RNAs, including RNA species related to RNA processing. We also show direct RNA binding activity of the individual RRM domain in vitro, which is in contrast with the RRM domain found in yeast Set1. Structural modeling revealed important details on the possible RNA recognition mode of SETD1A and highlighted some fundamental differences between SETD1A and Set1, explaining the differences in the RNA binding capacity of their respective RRMs.
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Affiliation(s)
- Harem Muhamad Amin
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Department of Biology, College of Science, University of Sulaimani, Sulaymaniyah 46001, Kurdistan Region, Iraq
| | - Beata Szabo
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - Rawan Abukhairan
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - Andras Zeke
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary;
| | - Eva Schad
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - Agnes Tantos
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
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24
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Moallemi Rad L, Safarzadeh A, Taheri M, Ghafouri-Fard S, Eghbali A. Construction of ceRNA network and identification of hub differentially expressed genes associated with breast cancer using reanalysis of microarray dataset: A systems biology approach. Pathol Res Pract 2023; 251:154838. [PMID: 37804544 DOI: 10.1016/j.prp.2023.154838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023]
Abstract
The interaction between long non-coding RNAs (lncRNAs), miRNAs and mRNAs has implications in the pathogenesis of different cancer, including breast cancer. In the current study, we developed an in-silico approach to ascertain the competing endogenous RNA (ceRNA) network in breast cancer. Our approach led to identification of 1816 differentially expressed (DE) mRNAs, including 1039 downregulated DEmRNAs (such as LEP and ADIPOQ) and 777 upregulated DEmRNAs (such as COL11A1 and COL10A1), 19 DElncRNAs, including 15 downregulated DElncRNAs (such as CARMN and COPG2IT1) and 4 upregulated DElncRNAs (such as MALAT1 and NRAV) and 27 DEmiRNAs, including 15 downregulated DEmiRNAs (such as MIR452 and MIR224) and 12 upregulated DEmiRNAs (such as MIR6787 and MIR21). Pathway analysis revealed down-regulation of PPAR, Fatty acid metabolism, Adipocytokine, Vascular smooth muscle contraction and Metabolism of xenobiotics by cytochrome P450, while up-regulation of Pyrimidine metabolism, p53 signaling pathway, Cell cycle, Oocyte meiosis and RNA transport pathways in breast cancer. Finally, we constructed an lncRNA/miRNA/mRNA ceRNA network consisted of 2 lncRNAs, 15 mRNAs, and 4 miRNAs. This network represents an appropriate target for design of anti-cancer modalities and documentation of novel markers for breast cancer.
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Affiliation(s)
- Lina Moallemi Rad
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Arash Safarzadeh
- Photochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ahmad Eghbali
- Anesthesiology Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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25
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Arora H, Prajapati B, Seth P. Potential role of lncRNA in impairing cellular properties of human neural progenitor cells following exposure to Zika virus E protein. Exp Neurol 2023; 368:114493. [PMID: 37479020 DOI: 10.1016/j.expneurol.2023.114493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Zika virus (ZIKV) infection during the first trimester of the pregnancy may lead to Congenital zika syndrome in the neonates. The viral infection hampers foetal brain development and causes microcephaly. Human neural progenitor cells (hNPCs) play an important role in brain development, however they are highly susceptible to ZIKV infection. In this study, we elucidated the molecular mechanisms that lead to cellular alterations in hNPCs due to ZIKV E-protein. We investigated proliferation, differentiation, migration and inflammation in hNPCs, which may lead to microcephaly. In our study, we found that ZIKV E-protein causes cell cycle arrest, decrease in proliferation and increase in mitotic length of the dividing hNPCs. We observed CyclinD1 and upstream molecules (p21 and p53) of the pathway are dysregulated, and intracellular calcium at basal level as well as upon ATP stimulation were reduced following over expression of ZIKV E-protein. ZIKV E-protein transfected hNPCs exhibited pre-mature differentiation with pro-neural genes upregulated. Furthermore, ZIKV E-protein disrupted migrational properties of hNPCs and caused elevated levels of inflammatory chemokines and cytokines. To gain insights into molecular mechanisms of these effects on hNPCs, we explored the possible involvement of long non coding RNAs in ZIKV neuropathogenesis. We have shortlisted lncRNAs associated with differentially expressed genes from publicly available transcriptomic data and found some of those lncRNAs are differentially expressed upon E-protein transfection of hNPCs. Gene ontology analysis suggest these lncRNAs play an important role in regulation of viral life cycle, host's defence response and cell proliferation.
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Affiliation(s)
- Himali Arora
- Cellular and Molecular Neuroscience, Neurovirology Section, National Brain Research Centre, Manesar, Gurugram, Haryana, India
| | - Bharat Prajapati
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Pankaj Seth
- Cellular and Molecular Neuroscience, Neurovirology Section, National Brain Research Centre, Manesar, Gurugram, Haryana, India.
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26
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Li J, Li J, Teng P, Yang F, Zhang J, Sun B, Chen W. Long noncoding RNA 1392 regulates MDA5 by interaction with ELAVL1 to inhibit coxsackievirus B5 infection. Virol Sin 2023; 38:699-708. [PMID: 37543144 PMCID: PMC10590689 DOI: 10.1016/j.virs.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) modulate many aspects of biological and pathological processes. Recent studies have shown that host lncRNAs participate in the antiviral immune response, but functional lncRNAs in coxsackievirus B5 (CVB5) infection remain unknown. Here, we identified a novel cytoplasmic lncRNA, LINC1392, which was highly inducible in CVB5 infected RD cells in a time- and dose-dependent manner, and also can be induced by the viral RNA and IFN-β. Further investigation showed that LINC1392 promoted several important interferon-stimulated genes (ISGs) expression, including IFIT1, IFIT2, and IFITM3 by activating MDA5, thereby inhibiting the replication of CVB5 in vitro. Mechanistically, LINC1392 bound to ELAV like RNA binding protein 1 (ELAVL1) and blocked ELAVL1 interaction with MDA5. Functional study revealed that the 245-835 nt locus of LINC1392 exerted the antiviral effect and was also an important site for ELAVL1 binding. In mice, LINC1392 could inhibit CVB5 replication and alleviated the histopathological lesions of intestinal and brain tissues induced by viral infection. Our findings collectively reveal that the novel LINC1392 acts as a positive regulator in the IFN-I signaling pathway against CVB5 infection. Elucidating the underlying mechanisms on how lncRNA regulats the host innate immunity response towards CVB5 infection will lay the foundation for antiviral drug research.
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Affiliation(s)
- Jing Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jinwei Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Peiying Teng
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Fan Yang
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jihong Zhang
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Bo Sun
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Wei Chen
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
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27
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Thatai AKS, Ammankallu S, Devasahayam Arokia Balaya R, Soman SP, Nisar M, Babu S, John L, George A, Anto CK, Sanjeev D, Kandiyil MK, Raj SS, Awasthi K, Vinodchandra SS, Prasad TSK, Raju R. VirhostlncR: A comprehensive database to explore lncRNAs and their targets in viral infections. Comput Biol Med 2023; 164:107279. [PMID: 37572440 DOI: 10.1016/j.compbiomed.2023.107279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 08/14/2023]
Abstract
Long non-coding-RNAs (lncRNAs) are an expanding set of cis-/trans-regulatory RNA genes that outnumber the protein-coding genes. Although being increasingly discovered, the functional role of the majority of lncRNAs in diverse biological conditions is undefined. Increasing evidence supports the critical role of lncRNAs in the emergence, regulation, and progression of various viral infections including influenza, hepatitis, coronavirus, and human immunodeficiency virus. Hence, the identification of signature lncRNAs would facilitate focused analysis of their functional roles accounting for their targets and regulatory mechanisms associated with infections. Towards this, we compiled 2803 lncRNAs identified to be modulated by 33 viral strains in various mammalian cell types and are provided through the resource named VirhostlncR (http://ciods.in/VirhostlncR/). The information on each of the viral strains, their multiplicity of infection, duration of infection, host cell name and cell types, fold change of lncRNA expression, and their specific identification methods are integrated into VirhostlncR. Based on the current datasets, we report 150 lncRNAs including differentiation antagonizing non-protein coding RNA (DANCR), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), maternally expressed gene 3 (MEG3), nuclear paraspeckle assembly transcript 1 (NEAT1), and plasmacytoma variant translocation 1 (PVT1) to be perturbed by two or more viruses. Analysis of viral protein interactions with human transcription factors (TFs) or TF-containing protein complexes identified that distinct viruses can transcriptionally regulate many of these lncRNAs through multiple protein complexes. Together, we believe that the current dataset will enable priority selection of lncRNAs for identification of their targets and serve as an effective platform for the analysis of noncoding RNA-mediated regulations in viral infections.
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Affiliation(s)
- Arun Kumar Sumaithangi Thatai
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Shruthi Ammankallu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Rex Devasahayam Arokia Balaya
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Sreelakshmi Pathappillil Soman
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Sreeranjini Babu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Anju George
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Christy Kallely Anto
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Mrudula Kinarulla Kandiyil
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Sini S Raj
- Department of Computer Science, University of Kerala, Thiruvananthapuram, 695 581, Kerala, India.
| | - Kriti Awasthi
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - S S Vinodchandra
- Department of Computer Science, University of Kerala, Thiruvananthapuram, 695 581, Kerala, India.
| | - Thottethodi Subrahmanya Keshava Prasad
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Omics Analytics Pvt. Ltd., Yenepoya Incubator, Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Rajesh Raju
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India; Omics Analytics Pvt. Ltd., Yenepoya Incubator, Deralakatte, Mangalore, 575 018, Karnataka, India.
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28
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Hu J, Zhang L, Zheng X, Wang G, Chen X, Hu Z, Chen Y, Wang X, Gu M, Hu S, Liu X, Jiao X, Peng D, Liu X. Long noncoding RNA #61 exerts a broad anti-influenza a virus effect by its long arm rings. Antiviral Res 2023; 215:105637. [PMID: 37196902 DOI: 10.1016/j.antiviral.2023.105637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Emerging evidence has demonstrated the critical role of long noncoding RNAs (lncRNAs) in regulating gene expression. However, the functional significance and mechanisms underlying influenza A virus (IAV)-host lncRNA interactions are still elusive. Here, we identified a functional lncRNA, LncRNA#61, as a broad anti-IAV factor. LncRNA#61 is highly upregulated by different subtypes of IAV, including human H1N1 virus and avian H5N1 and H7N9 viruses. Furthermore, nuclear-enriched LncRNA#61 can translocate from the nucleus to the cytoplasm soon after IAV infection. Forced LncRNA#61 expression dramatically impedes viral replication of various subtypes of IAV, including human H1N1 virus and avian H3N2/N8, H4N6, H5N1, H6N2/N8, H7N9, H8N4, H10N3, H11N2/N6/N9 viruses. Conversely, abolishing LncRNA#61 expression substantially favored viral replication. More importantly, LncRNA#61 delivered by the lipid nanoparticle (LNP)-encapsulated strategy shows good performance in restraining viral replication in mice. Interestingly, LncRNA#61 is involved in multiple steps of the viral replication cycle, including virus entry, viral RNA synthesis and the virus release period. Mechanistically, the four long ring arms of LncRNA#61 mainly mediate its broad antiviral effect and contribute to its inhibition of viral polymerase activity and nuclear aggregation of key polymerase components. Therefore, we defined LncRNA#61 as a potential broad-spectrum antiviral factor for IAV. Our study further extends our understanding of the stunning and unanticipated biology of lncRNAs as well as their close interaction with IAV, providing valuable clues for developing novel broad anti-IAV therapeutics targeting host lncRNAs.
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Affiliation(s)
- Jiao Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Lei Zhang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xinxin Zheng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Guoqing Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xia Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Zenglei Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Yu Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Min Gu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Daxin Peng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China.
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Zhang Z, Yu T, Li H, Du L, Jin Z, Peng X, Yan Y, Zhou J, Gu J. Long Noncoding RNA AROD Inhibits Host Antiviral Innate Immunity via the miR-324-5p-CUEDC2 Axis. Microbiol Spectr 2023; 11:e0420622. [PMID: 37036350 PMCID: PMC10269697 DOI: 10.1128/spectrum.04206-22] [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: 10/17/2022] [Accepted: 03/12/2023] [Indexed: 04/11/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs that are involved in multiple biological processes. Here, we report a mechanism through which the lnc-AROD-miR-324-5p-CUEDC2 axis regulates the host innate immune response, using influenza A virus (IAV) as a model. We identified that host lnc-AROD without protein-coding capability is composed of 975 nucleotides. Moreover, lnc-AROD inhibited interferon-β expression, as well as interferon-stimulated genes ISG15 and MxA. Furthermore, in vivo assays confirmed that lnc-AROD overexpression increased flu virus pathogenicity and mortality in mice. Mechanistically, lnc-AROD interacted with miR-324-5p, leading to decreased binding of miR-324-5p to CUEDC2. Collectively, our findings demonstrated that lnc-AROD is a critical regulator of the host antiviral response via the miR-324-5p-CUEDC2 axis, and lnc-AROD functions as competing endogenous RNA. Our results also provided evidence that lnc-AROD serves as an inhibitor of the antiviral immune response and may represent a potential drug target. IMPORTANCE lnc-AROD is a potential diagnostic and discriminative biomarker for different cancers. However, so far the mechanisms of lnc-AROD regulating virus replication are not well understood. In this study, we identified that lnc-AROD is downregulated during RNA virus infection. We demonstrated that lnc-AROD enhanced CUEDC2 expression, which in turn inhibited innate immunity and favored IAV replication. Our studies indicated that lnc-AROD functions as a competing endogenous RNA that binds miR-324-5p and reduces its inhibitory effect on CUEDC2. Taken together, our findings reveal that lnc-AROD plays an important role during the host antiviral immune response.
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Affiliation(s)
- Zixiao Zhang
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Tianqi Yu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Haimin Li
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Liuyang Du
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Zian Jin
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Xiran Peng
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Yan Yan
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
- Collaborative Innovation Center and State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jinyan Gu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University Center for Veterinary Sciences, Hangzhou, China
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30
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Jiang S, Hu J, Bai Y, Hao R, Liu L, Chen H. Transcriptome-wide 5-methylcytosine modification profiling of long non-coding RNAs in A549 cells infected with H1N1 influenza A virus. BMC Genomics 2023; 24:316. [PMID: 37308824 DOI: 10.1186/s12864-023-09432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND In recent years, accumulating evidences have revealed that influenza A virus (IAV) infections induce significant differential expression of host long noncoding RNAs (lncRNAs), some of which play important roles in the regulation of virus-host interactions and determining the virus pathogenesis. However, whether these lncRNAs bear post-translational modifications and how their differential expression is regulated remain largely unknown. In this study, the transcriptome-wide 5-methylcytosine (m5C) modification of lncRNAs in A549 cells infected with an H1N1 influenza A virus was analyzed and compared with uninfected cells by Methylated RNA immunoprecipitation sequencing (MeRIP-Seq). RESULTS Our data identified 1317 upregulated m5C peaks and 1667 downregulated peaks in the H1N1 infected group. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the differentially modified lncRNAs were associated with protein modification, organelle localization, nuclear export and other biological processes. Furthermore, conjoint analysis of the differentially modified (DM) and differentially expressed (DE) lncRNAs identified 143 'hyper-up', 81 'hypo-up', 6 'hypo-down' and 4 'hyper-down' lncRNAs. GO and KEGG analyses revealed that these DM and DE lncRNAs were predominantly associated with pathogen recognition and disease pathogenesis pathways, indicating that m5C modifications could play an important role in the regulation of host response to IAV replication by modulating the expression and/or stability of lncRNAs. CONCLUSION This study presented the first m5C modification profile of lncRNAs in A549 cells infected with IAV and demonstrated a significant alteration of m5C modifications on host lncRNAs upon IAV infection. These data could give a reference to future researches on the roles of m5C methylation in virus infection.
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Affiliation(s)
- Shengqiang Jiang
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Jing Hu
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Yang Bai
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Ruiwei Hao
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Long Liu
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, Hubei, P. R. China
| | - Hongying Chen
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China.
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31
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Wang K, Gong M, Zhao S, Lai C, Zhao L, Cheng S, Xia M, Li Y, Wang K, Sun H, Zhu P, Zhou Y, Ao Q, Deng X. A novel lncRNA DFRV plays a dual function in influenza A virus infection. Front Microbiol 2023; 14:1171423. [PMID: 37303776 PMCID: PMC10248499 DOI: 10.3389/fmicb.2023.1171423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/27/2023] [Indexed: 06/13/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been associated with a variety of biological activities, including immune responses. However, the function of lncRNAs in antiviral innate immune responses are not fully understood. Here, we identified a novel lncRNA, termed dual function regulating influenza virus (DFRV), elevating in a dose- and time-dependent manner during influenza A virus (IAV) infection, which was dependent on the NFκB signaling pathway. Meanwhile, DFRV was spliced into two transcripts post IAV infection, in which DFRV long suppress the viral replication while DFRV short plays the opposite role. Moreover, DFRV regulates IL-1β and TNF-α via activating several pro-inflammatory signaling cascades, including NFκB, STAT3, PI3K, AKT, ERK1/2 and p38. Besides, DFRV short can inhibit DFRV long expression in a dose-dependent manner. Collectively, our studies reveal that DFRV may act as a potential dual-regulator to preserve innate immune homeostasis in IAV infection.
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Affiliation(s)
- Keyu Wang
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Meiliang Gong
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Sumin Zhao
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Chengcai Lai
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lingna Zhao
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine and Institute for Immunology, Tsinghua University, Beijing, China
| | - Sijie Cheng
- Center for Disease Prevention and Control, Changde, Hunan, China
| | - Min Xia
- Department of Vascular Cell Biology, Max Plank Institute for Molecular Biomedicine, Münster, Germany
| | - Yuru Li
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Kun Wang
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Heqiang Sun
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Pingjun Zhu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu Zhou
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qiangguo Ao
- Department of Nephrology, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xinli Deng
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
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Ning H, Chiu SH, Xu X, Ma Y, Chen JL, Yang G. The Immunosuppressive Roles of PD-L1 during Influenza A Virus Infection. Int J Mol Sci 2023; 24:ijms24108586. [PMID: 37239931 DOI: 10.3390/ijms24108586] [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: 04/03/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical benefits of targeting programmed death-ligand 1 (PD-L1) in various cancers represent a strategy for the treatment of immunosuppressive diseases. Here, it was demonstrated that the expression levels of PD-L1 in cells were greatly upregulated in response to H1N1 influenza A virus (IAV) infection. Overexpression of PD-L1 promoted viral replication and downregulated type-I and type-III interferons and interferon-stimulated genes. Moreover, the association between PD-L1 and Src homology region-2, containing protein tyrosine phosphatase (SHP2), during IAV/H1N1 infection was analyzed by employing the SHP2 inhibitor (SHP099), siSHP2, and pNL-SHP2. The results showed that the expressions of PD-L1 mRNA and protein were decreased under SHP099 or siSHP2 treatment, whereas the cells overexpressing SHP2 exhibited the opposite effects. Additionally, the effects of PD-L1 on the expression of p-ERK and p-SHP2 were investigated in PD-L1-overexpressed cells following WSN or PR8 infection, determining that the PD-L1 overexpression led to the decreased expression of p-SHP2 and p-ERK induced by WSN or PR8 infection. Taken together, these data reveal that PD-L1 could play an important role in immunosuppression during IAV/H1N1 infection; thus, it may serve as a promising therapeutic target for development of novel anti-IAV drugs.
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Affiliation(s)
- Hongya Ning
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences (College of Bee Science), Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Shih-Hsin Chiu
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences (College of Bee Science), Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Xiaodong Xu
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences (College of Bee Science), Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Yanmei Ma
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences (College of Bee Science), Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences (College of Bee Science), Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Guihong Yang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences (College of Bee Science), Fujian Agricultural and Forestry University, Fuzhou 350002, China
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Asemi R, Rajabpoor Nikoo N, Asemi Z, Shafabakhsh R, Hajijafari M, Sharifi M, Homayoonfal M, Davoodvandi A, Hakamifard A. Modulation of long non-coding RNAs by resveratrol as a potential therapeutic approach in cancer: A comprehensive review. Pathol Res Pract 2023; 246:154507. [PMID: 37196467 DOI: 10.1016/j.prp.2023.154507] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
LncRNAs, or long non-coding RNAs, are a subset of RNAs that play a regulatory role in a wide range of biological functions, including RNA processing, epigenetic regulation, and signal transduction. Recent research indicates that lncRNAs play a key role in the development and spread of cancer by being dysregulated in the disease. In addition, lncRNAs have been linked to the overexpression of certain proteins that are involved in tumor development and progression. Resveratrol has anti-inflammatory and anti-cancer properties that it exerts through regulating different lncRNAs. By the regulation of tumor-supportive and tumor-suppressive lncRNAs, resveratrol acts as an anti-cancer agent. By downregulating the tumor-supportive lncRNAs DANCR, MALAT1, CCAT1, CRNDE, HOTAIR, PCAT1, PVT1, SNHG16, AK001796, DIO3OS, GAS5 and H19, and upregulating MEG3, PTTG3P, BISPR, PCAT29, GAS5, LOC146880, HOTAIR, PCA3, NBR2, this herbal remedy causes apoptosis and cytotoxicity. For the purpose of using polyphenols in cancer therapy, it would be helpful to have more in-depth knowledge about lncRNA modulation via resveratrol. Here, we discuss the current knowledge and future promise of resveratrol as modulators of lncRNAs in different cancers.
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Affiliation(s)
- Reza Asemi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
| | - Nesa Rajabpoor Nikoo
- Department of Gynecology and Obstetrics, Tehran University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Mohammad Hajijafari
- Department of Anesthesiology, School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Mehran Sharifi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
| | - Mina Homayoonfal
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Amirhossein Davoodvandi
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Islamic Republic of Iran.
| | - Atousa Hakamifard
- Department of Infectious Diseases, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
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Zhang Y, Chi X, Hu J, Wang S, Zhao S, Mao Y, Peng B, Chen J, Wang S. LncRNA LINC02574 Inhibits Influenza A Virus Replication by Positively Regulating the Innate Immune Response. Int J Mol Sci 2023; 24:ijms24087248. [PMID: 37108410 PMCID: PMC10138361 DOI: 10.3390/ijms24087248] [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: 02/22/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Studies have shown that long noncoding RNAs (lncRNAs) play crucial roles in regulating virus infection, host immune response, and other biological processes. Although some lncRNAs have been reported to be involved in antiviral immunity, many lncRNAs have unknown functions in interactions between the host and various viruses, especially influenza A virus (IAV). Herein, we demonstrate that the expression of lncRNA LINC02574 can be induced by IAV infection. Treatment with viral genomic RNA, poly (I:C), or interferons (IFNs) significantly stimulated LINC02574 expression, while RIG-I knockdown and IFNAR1 knockout significantly decreased LINC02574 expression after viral infection or IFN treatment. In addition, inhibition of LINC02574 expression in A549 cells enhanced IAV replication, while overexpression of LINC02574 inhibited viral production. Interestingly, knockdown of LINC02574 attenuated the expression of type I and type III IFNs and multiple ISGs, as well as the activation of STAT1 triggered by IAV infection. Moreover, LINC02574 deficiency impaired the expression of RIG-I, TLR3, and MDA5, and decreased the phosphorylation level of IRF3. In conclusion, the RIG-I-dependent interferon signaling pathway can induce LINC02574 expression. Moreover, the data reveal that LINC02574 inhibits IAV replication by positively regulating the innate immune response.
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Affiliation(s)
- Yanwei Zhang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaojuan Chi
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingyun Hu
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shulin Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Senhong Zhao
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanan Mao
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Benqun Peng
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jilong Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Song Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Lin S, Yin HT, Zhao ZM, Chen ZK, Zhou XMI, Zhang ZD, Guo XJ, Zhao WG, Wu P. LincRNA_XR209691.3 could promote Bombyx mori nucleopolyhedrovirus replication by interacting with BmHSP70. INSECT MOLECULAR BIOLOGY 2023; 32:160-172. [PMID: 36482511 DOI: 10.1111/imb.12821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Long non-coding RNAs (lncRNAs), a class of transcripts exceeding 200 nucleotides and lacking protein coding potential, have been proven to play important roles in viral infection and host immunity. Bombyx mori nucleopolyhedrovirus (BmNPV) is an important pathogen, which causes the silkworm disease and leads to a huge challenge to the sericultural industry. At present, research on the roles of insect lncRNAs in host-virus interaction are relatively few. In this study, we explored the function of lincRNA_XR209691.3 that was significantly up-regulated in the silkworm fat body upon BmNPV infection. Firstly, the subcellular localization experiment confirmed that lincRNA_XR209691.3 was present in both the nucleus and cytoplasm. Enhancing the expression of lincRNA_XR209691.3 in BmN cells could promote the proliferation of BmNPV, while inhibition of lincRNA_XR209691.3 by RNA interference suppresses the proliferation of BmNPV. Combining RNA pull-down and mass spectrometry, we identified the host and BmNPV proteins that could interact with lincRNA_XR209691.3. Next, by using truncation experiment and RNA immunoprecipitation (RIP) assay, it was found that lincRNA_XR209691.3 could bind to the Actin domain of BmHSP70. Subsequently, overexpression of lncRNA_XR209691.3 in BmN cells promoted the expression of BmHSP70, while knockdown of BmHsp70 suppressed the replication of BmNPV. Based on the above results, it is speculated that lincRNA_XR209691.3 could promote the proliferation of BmNPV through interaction with BmHSP70, possibly by improving the stability of BmHSP70 and thereby enhancing the expression of BmHSP70. Our results shed light on the lncRNA function in insect-pathogen interactions and provide a new clue to elucidate the molecular mechanism of BmNPV infection.
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Affiliation(s)
- Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Hao Tong Yin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhi Meng Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zi Kang Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xue MIng Zhou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zheng Dong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xi Jie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Wei Guo Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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Tang X, Zhang R, Gao L, Lv X, Sun Y, Ma J. LncRNA 8244-ssc-miR-320-CCR7 Regulates IFN-β during SVA Infecting PK-15 Cells. Microorganisms 2023; 11:microorganisms11030688. [PMID: 36985261 PMCID: PMC10059919 DOI: 10.3390/microorganisms11030688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/10/2023] Open
Abstract
Seneca Valley virus (SVV), a member of the Picornaviridae family, is an oncolytic RNA virus that can cause idiopathic vesicular disease and increase mortality in newborn piglets. Although research on the pathogenic characteristics, epidemiology, pathogenic mechanism, and clinical diagnosis of SVA has increased due to its emergence and prevalence, the interaction between SVA and its host lncRNA has not been fully studied. This study used qualcomm sequencing to analyze differentially expressed lncRNAs and found that during SVA infection, lncRNA 8244 was significantly down-regulated in both PK-15 cells and piglets. Further analysis through quantitative real-time PCR and dual luciferase experiments demonstrated that lncRNA8244 could compete with ssc-miR-320 to regulate the expression of CCR7. The lncRNA824-ssc-miR-320-CCR7 axis activated the TLR-mediated signaling pathway, which recognized viral molecules and induced the expression of IFN-β. These findings provide new insight into the interaction between lncRNA and SVA infection, which could lead to a better understanding of SVA pathogenesis and contribute to the prevention and control of SVA disease.
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Affiliation(s)
- Xiaoyu Tang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ruiyu Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Long Gao
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaocheng Lv
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuan Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Y.S.); (J.M.)
| | - Jingyun Ma
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Y.S.); (J.M.)
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Nicknam A, Khojasteh Pour S, Hashemnejad MA, Hussen BM, Safarzadeh A, Eslami S, Taheri M, Ghafouri-Fard S, Jamali E. Expression analysis of Rho GTPase-related lncRNAs in breast cancer. Pathol Res Pract 2023; 244:154429. [PMID: 36996609 DOI: 10.1016/j.prp.2023.154429] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]
Abstract
The Rho GTPases have prominent roles in cell cycle transition and cell migration. Some members of this family have been found to be mutated in cancers. Moreover, alterations in expression levels and/or activity of these proteins have been reported in many types of cancers. Thus, Rho GTPases are involved in the carcinogenesis. Rho GTPases regulate growth, motility, invasiveness and metastatic ability of breast cancer cells. Long non-coding RNAs (lncRNAs) have been revealed to exert significant effect in the regulation of these proteins via direct routes or through sequestering microRNAs that inhibit Rho GTPases. We aimed to assess expression levels of four Rho GTPase-related lncRNAs, namely NORAD, RAD51-AS1, NRAV and DANCR in breast cancer samples versus non-cancerous specimens from the same individuals. Expression levels of NORAD were shown to be elevated in tumoral tissues compared with non-tumoral tissues (Expression ratio (95% CI)= 5.85 (3.16-10.83), Standard error of mean (SEM)= 0.44, P value< 0.0001). NRAV expression was also higher in tumoral tissues compared with control tissues (Expression ratio=2.85 (1.52-5.35), SEM= 0.45, P value= 0.0013). Similar to these lncRNAs, RHOA was demonstrated to be up-regulated in malignant tissues (Expression ratio=6.58 (3.17-13.63), SEM= 0.52, P value< 0.0001). Although expression ratio values showed up-regulation of RAD51-AS1 and DANCR in cancerous tissues (Expression ratio (95% CI)= 2.2 (1.05-4.6) and 1.35 (0.72-2.53), respectively), P values did not reach significance level (P values=0.0706 and 0.3746, respectively). There were significant associations between expression level of NRAV gene in tumor tissues and a number of parameters including age, histological tumor grade and tubule formation. Taken together, the current study shows dysregulation of a number of RHOA-related lncRNAs in breast cancer in association with abnormal up-regulation of this member of Rho GTPase family and suggests conduction of additional functional studies to unravel their mode of participation in the breast carcinogenesis.
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Affiliation(s)
- Amir Nicknam
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Amin Hashemnejad
- Clinical Research Developmental Unit (CRDU) of Shahid Rajaei Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Arash Safarzadeh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Qiu H, Yang B, Chen Y, Zhu Q, Wen F, Peng M, Wang G, Guo G, Chen B, Maarouf M, Fang M, Chen JL. Influenza A Virus-Induced circRNA circMerTK Negatively Regulates Innate Antiviral Responses. Microbiol Spectr 2023; 11:e0363722. [PMID: 36847523 PMCID: PMC10100971 DOI: 10.1128/spectrum.03637-22] [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: 09/09/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
Circular RNAs (circRNAs) are an important subclass of noncoding RNAs implicated in the regulation of multiple biological processes. However, the functional involvement of circRNAs in the pathogenesis of influenza A viruses (IAVs) remains largely unknown. Here, we employed RNA sequencing (RNA-Seq) to examine the differentially expressed circRNAs in mouse lung tissues challenged or not challenged with IAV to evaluate the impact of viral infection on circRNAs in vivo. We observed that 413 circRNAs exhibited significantly altered levels following IAV infection. Among these, circMerTK, the derivative of myeloid-epithelial-reproductive tyrosine kinase (MerTK) pre-mRNA, was highly induced by IAV. Interestingly, circMerTK expression was also increased upon infection with multiple DNA and RNA viruses in human and animal cell lines, and thus it was selected for further studies. Poly(I:C) and interferon β (IFN-β) stimulated circMerTK expression, while RIG-I knockout and IFNAR1 knockout cell lines failed to elevate circMerTK levels after IAV infection, demonstrating that circMerTK is regulated by IFN signaling. Furthermore, circMerTK overexpression or silencing accelerated or impeded IAV and Sendai virus replication, respectively. Silencing circMerTK enhanced the production of type I IFNs and interferon-stimulating genes (ISGs), whereas circMerTK overexpression suppressed their expression at both the mRNA and protein levels. Notably, altering circMerTK expression had no effect on the MerTK mRNA level in cells infected or not infected with IAV, and vice versa. In addition, human circMerTK and mouse homologs functioned similarly in antiviral responses. Together, these results identify circMerTK as an enhancer of IAV replication through suppression of antiviral immunity. IMPORTANCE CircRNAs are an important class of noncoding RNAs characterized by a covalently closed circular structure. CircRNAs have been proven to impact numerous cellular processes, where they conduct specialized biological activities. In addition, circRNAs are believed to play a crucial role in regulating immune responses. Nevertheless, the functions of circRNAs in the innate immunity against IAV infection remain obscure. In this study, we employed transcriptomic analysis to investigate the alterations in circRNAs expression following IAV infection in vivo. It was found that expression of 413 circRNAs was significantly altered, of which 171 were upregulated, and 242 were downregulated following the IAV infection. Interestingly, circMerTK was identified as a positive regulator of IAV replication in both human and mouse hosts. CircMerTK was shown to influence IFN-β production and its downstream signaling, enhancing IAV replication. This finding provides new insights into the critical roles of circRNAs in regulating antiviral immunity.
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Affiliation(s)
- Haori Qiu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bincai Yang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhai Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qianwen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Faxin Wen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Min Peng
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoqing Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guijie Guo
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Biao Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Egypt
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Chen X, Sun M, Feng W, Chen J, Ji X, Xie M, Huang W, Chen X, Zhang B, Nie Y, Fan D, Wu K, Xia L. An integrative analysis revealing cuproptosis-related lncRNAs signature as a novel prognostic biomarker in hepatocellular carcinoma. Front Genet 2023; 14:1056000. [PMID: 36845390 PMCID: PMC9950118 DOI: 10.3389/fgene.2023.1056000] [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: 09/28/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
Background: Cuproptosis is a newly defined form of cell death, whether cuproptosis involved in hepatocellular carcinoma (HCC) remains elusive. Method: We obtained patients' RNA expression data and follow-up information from University of California Santa Cruz (UCSC) and The Cancer Genome Atlas (TCGA). We analyzed the mRNA level of Cuproptosis-related genes (CRGs) and performed univariate Cox analysis. Liver hepatocellular carcinoma (LIHC) was chosen for further investigation. Real-Time quantitative PCR (RT-qPCR), Western blotting (WB), Immunohistochemical (IHC), and Transwell assays were used to determine expression patterns and functions of CRGs in LIHC. Next, we identified CRGs-related lncRNAs (CRLs) and differentially expressed CRLs between HCC and normal cases. Univariate Cox analysis, least absolute shrinkage selection operator (LASSO) analysis and Cox regression analysis were used to construct the prognostic model. Univariate and multivariate Cox analysis was used to assess whether the risk model can act as an independent risk factor of overall survival duration. Different risk groups performed immune correlation analysis, tumor mutation burden (TMB), and Gene Set Enrichment Analysis (GSEA) analysis were performed in different risk groups. Finally, we assessed the performance of the predictive model in drug sensitivity. Results: CRGs expression levels have significant differences between tumor and normal tissues. High expression of Dihydrolipoamide S-Acetyltransferase (DLAT) correlated to metastasis of HCC cells and indicated poor prognosis for HCC patients. Our prognostic model consisted of four cuproptosis-related lncRNA (AC011476.3, AC026412.3, NRAV, MKLN1-AS). The prognostic model performed well in predicting survival rates. The results from Cox regression analysis suggested that risk score can serve as an independent prognostic element for survival durations. Survival analysis revealed that low risk patients have extended survival periods compared with those with high risk. The results of the immune analysis indicated that risk score has a positive correlation with B cell and CD4+ T cell Th2, while has a negative relationship with endothelial cell and hematopoietic cells. Besides, immune checkpoint genes have higher expression folds in the high-risk set than in the low-risk set. The high-risk group had higher rates of genetic mutation than the low-risk set while having a shorter survival time. GSEA revealed the signaling pathways enriched in the high-risk group were mostly immune-related, while metabolic-related pathways were enriched in the low-risk group. Drugs sensitivity analysis indicated that our model has the ability to predict the efficacy of clinical treatment. Conclusion: The Cuproptosis-related lncRNAs prognostic formula is a novel predictor of HCC patients' prognosis and drug sensitivity.
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Affiliation(s)
- Xilang Chen
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Mengyu Sun
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Weibo Feng
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jie Chen
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaoyu Ji
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meng Xie
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Chen
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bixiang Zhang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China,*Correspondence: Kaichun Wu, ; Limin Xia,
| | - Limin Xia
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi, China,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China,*Correspondence: Kaichun Wu, ; Limin Xia,
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Innate Immunity in Cardiovascular Diseases-Identification of Novel Molecular Players and Targets. J Clin Med 2023; 12:jcm12010335. [PMID: 36615135 PMCID: PMC9821340 DOI: 10.3390/jcm12010335] [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: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
During the past few years, unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking advantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss the emerging clinical relevance of advanced diagnostics for cardiovascular diseases, including those associated with COVID-19-with a focus on the role of inflammation in cardiomyopathies and arrhythmias. Second, we consider newly identified immunological interactions at organ and system levels which affect cardiovascular pathogenesis. Thus, studies into immune influences arising from the intestinal system are moving towards therapeutic exploitation. Further, powerful new research tools have enabled novel insight into brain-immune system interactions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress-acting through defined brain regions-upon viral and cardiovascular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.
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Haridevamuthu B, Guru A, Velayutham M, Snega Priya P, Arshad A, Arockiaraj J. Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost. REVIEWS IN AQUACULTURE 2023; 15:163-178. [DOI: 10.1111/raq.12709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 10/16/2023]
Abstract
AbstractThe global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.
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Affiliation(s)
- B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Ajay Guru
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Manikandan Velayutham
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - P. Snega Priya
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
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MIR155HG Plays a Bivalent Role in Regulating Innate Antiviral Immunity by Encoding Long Noncoding RNA-155 and microRNA-155-5p. mBio 2022; 13:e0251022. [PMID: 36321836 PMCID: PMC9765511 DOI: 10.1128/mbio.02510-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
MIR155HG encodes a precursor RNA of microRNA-155 (miRNA-155). We previously identified this RNA also as a long noncoding RNA (lncRNA) that we call lncRNA-155. To define the functions of miRNA-155 and lncRNA-155, we generated miRNA-155 knockout (KO) mice lacking only 19 bp of the miRNA-155 core sequence without affecting the expression of lncRNA-155. Surprisingly, compared with the miRNA-155KO mice, previously generated lncRNA-155KO mice were more susceptible to both influenza virus (RNA virus) and pseudorabies virus (DNA virus) infection, as characterized by lower survival rate, higher body weight loss, and higher viral load. We found that miRNA-155-5p enhanced antiviral responses by positively regulating activation of signal transducer and activator of transcription 1 (STAT1), but the STAT1 activity differed greatly in the animals (lncRNA-155KO < miRNA-155KO < wild type). In line with this, expression levels of several critical interferon-stimulated genes (ISGs) were also significantly different (lncRNA-155KO < miRNA-155KO < wild type). We found that lncRNA-155 augmented interferon beta (IFN-β) production during the viral infection, but miRNA-155 had no significant effect on the virus-induced IFN-β expression. Furthermore, we observed that lncRNA-155 loss in mice resulted in dramatic inhibition of virus-induced activation of interferon regulatory factor 3 compared to both miRNA-155KO and wild-type (WT) animals. Moreover, lncRNA-155 still significantly suppressed the viral infection even though the miRNA-155 derived from lncRNA-155 was deleted or blocked. These results reveal that lncRNA-155 and miRNA-155 regulate antiviral responses through distinct mechanisms, indicating a bivalent role for MIR155HG in innate immunity. IMPORTANCE Here, we found that lncRNA-155KO mice lacking most of the lncRNA-155 sequences along with pre-miRNA-155, were more susceptible to influenza virus or pseudorabies virus infection than miRNA-155KO mice lacking only 19 bp of the miRNA-155 core sequence without affecting the expression of lncRNA-155, as evidenced by faster body weight loss, poorer survival, and higher viral load, suggesting an additional role of lncRNA-155 in regulating viral pathogenesis besides via processing miRNA-155. Congruously, miRNA-155-deleted lncRNA-155 significantly attenuated the viral infection. Mechanistically, we demonstrated miRNA-155-5p potentiated antiviral responses by promoting STAT1 activation but could not directly regulate the IFN-β expression. In contrast, lncRNA-155 enhanced virus-induced IFN-β production by regulating the activation of interferon regulatory factor 3. This finding reveals a bivalent role of MIR155HG in regulating antiviral responses through encoding lncRNA-155 and miRNA-155-5p and provides new insights into complicated mechanisms underlying interaction between virus and host innate immunity.
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Liu X, Li Y, Jiang X, Deng Y, Ma C, Yu Q, Gao D. Long non-coding RNA: Multiple effects on the differentiation, maturity and cell function of dendritic cells. Clin Immunol 2022; 245:109167. [DOI: 10.1016/j.clim.2022.109167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/29/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022]
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Chen N, Zhang B, Deng L, Liang B, Ping J. Virus-host interaction networks as new antiviral drug targets for IAV and SARS-CoV-2. Emerg Microbes Infect 2022; 11:1371-1389. [PMID: 35476817 PMCID: PMC9132403 DOI: 10.1080/22221751.2022.2071175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, SARS-CoV-2, especially the Omicron strain, is ravaging the world and even co-infecting human beings with IAV, which is a serious threat to human public health. As of yet, no specific antiviral drug has been discovered for SARS-CoV-2. This requires deeper understandings of the molecular mechanisms of SARS-CoV-2-host interaction, to explore antiviral drug targets and provide theoretical basis for developing anti-SARS-CoV-2 drugs. This article discussed IAV, which has been comprehensively studied and is expected to provide the most important reference value for the SARS-CoV-2 study apart from members of the Coronaviridae family. We wish to establish a theoretical system for the studies on virus-host interaction. Previous studies have shown that host PRRs recognize RNAs of IAV or SARS-CoV-2 and then activate innate immune signaling pathways to induce the expression of host restriction factors, such as ISGs, to ultimately inhibit viral replication. Meanwhile, viruses have also evolved various regulatory mechanisms to antagonize host innate immunity at transcriptional, translational, post-translational modification, and epigenetic levels. Besides, viruses can hijack supportive host factors for their replication. Notably, the race between host antiviral innate immunity and viral antagonism of host innate immunity forms virus-host interaction networks. Additionally, the viral replication cycle is co-regulated by proteins, ncRNAs, sugars, lipids, hormones, and inorganic salts. Given this, we updated the mappings of antiviral drug targets based on virus-host interaction networks and proposed an innovative idea that virus-host interaction networks as new antiviral drug targets for IAV and SARS-CoV-2 from the perspectives of viral immunology and systems biology.
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Affiliation(s)
- Na Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Baoge Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Lulu Deng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bing Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
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Liu Q, Yang H, Zhao L, Huang N, Ping J. A Novel lncRNA SAAL Suppresses IAV Replication by Promoting Innate Responses. Microorganisms 2022; 10:microorganisms10122336. [PMID: 36557591 PMCID: PMC9785332 DOI: 10.3390/microorganisms10122336] [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: 10/31/2022] [Revised: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Influenza A virus (IAV) infection has traditionally been a serious problem in animal husbandry and human public health security. Recently, many studies identified that long noncoding RNAs play an important role in the antiviral immune response after the infection of the influenza virus. However, there are still lots of IAV-related lncRNAs that have not been well-characterized. Using RNA sequencing analysis, we identified a lncRNA, named Serpina3i Activation Associated lncRNA (SAAL), which can be significantly upregulated in mice after IAV infection. In this study, we found that overexpression of SAAL inhibited the replication of A/WSN/33(WSN). SAAL upregulated Serpina3i with or without WSN infection. Overexpression of Serpina3i reduced influenza virus infection. Meanwhile, knockdown of Serpina3i enhanced the replication of WSN. Furthermore, knockdown of Serpina3i abolished the SAAL-mediated decrease in WSN infection. Overexpression of SAAL or Serpina3i positively regulated the transcription of interferon β (IFN-β) and several critical ISGs after WSN infection. In conclusion, we found that the novel lncRNA SAAL is a critical anti-influenza regulator by upregulating the mRNA level of Serpina3i.
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Affiliation(s)
- Qingzheng Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hongjun Yang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Lingcai Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Pelisek J, Reutersberg B, Greber UF, Zimmermann A. Vascular dysfunction in COVID-19 patients: update on SARS-CoV-2 infection of endothelial cells and the role of long non-coding RNAs. Clin Sci (Lond) 2022; 136:1571-1590. [PMID: 36367091 PMCID: PMC9652506 DOI: 10.1042/cs20220235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 08/16/2023]
Abstract
Although COVID-19 is primarily a respiratory disease, it may affect also the cardiovascular system. COVID-19 patients with cardiovascular disorder (CVD) develop a more severe disease course with a significantly higher mortality rate than non-CVD patients. A common denominator of CVD is the dysfunction of endothelial cells (ECs), increased vascular permeability, endothelial-to-mesenchymal transition, coagulation, and inflammation. It has been assumed that clinical complications in COVID-19 patients suffering from CVD are caused by SARS-CoV-2 infection of ECs through the angiotensin-converting enzyme 2 (ACE2) receptor and the cellular transmembrane protease serine 2 (TMPRSS2) and the consequent dysfunction of the infected vascular cells. Meanwhile, other factors associated with SARS-CoV-2 entry into the host cells have been described, including disintegrin and metalloproteinase domain-containing protein 17 (ADAM17), the C-type lectin CD209L or heparan sulfate proteoglycans (HSPG). Here, we discuss the current data about the putative entry of SARS-CoV-2 into endothelial and smooth muscle cells. Furthermore, we highlight the potential role of long non-coding RNAs (lncRNAs) affecting vascular permeability in CVD, a process that might exacerbate disease in COVID-19 patients.
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Affiliation(s)
- Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zürich, Zürich, Switzerland
| | | | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Switzerland
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Liu J, Ji Q, Cheng F, Chen D, Geng T, Huang Y, Zhang J, He Y, Song T. The lncRNAs involved in regulating the RIG-I signaling pathway. Front Cell Infect Microbiol 2022; 12:1041682. [PMID: 36439216 PMCID: PMC9682092 DOI: 10.3389/fcimb.2022.1041682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 09/23/2023] Open
Abstract
Understanding the targets and interactions of long non-coding RNAs (lncRNAs) related to the retinoic acid-inducible gene-I (RIG-I) signaling pathway is essential for developing interventions, which would enable directing the host inflammatory response regulation toward protective immunity. In the RIG-I signaling pathway, lncRNAs are involved in the important processes of ubiquitination, phosphorylation, and glycolysis, thus promoting the transport of the interferon regulatory factors 3 and 7 (IRF3 and IRF7) and the nuclear factor kappa B (NF-κB) into the nucleus, and activating recruitment of type I interferons (IFN-I) and inflammatory factors to the antiviral action site. In addition, the RIG-I signaling pathway has recently been reported to contain the targets of coronavirus disease-19 (COVID-19)-related lncRNAs. The molecules in the RIG-I signaling pathway are directly regulated by the lncRNA-microRNAs (miRNAs)-messenger RNA (mRNA) axis. Therefore, targeting this axis has become a novel strategy for the diagnosis and treatment of cancer. In this paper, the studies on the regulation of the RIG-I signaling pathway by lncRNAs during viral infections and cancer are comprehensively analyzed. The aim is to provide a solid foundation of information for conducting further detailed studies on lncRNAs and RIG-I in the future and also contribute to clinical drug development.
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Affiliation(s)
- Jing Liu
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Qinglu Ji
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Feng Cheng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Dengwang Chen
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Tingting Geng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yueyue Huang
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
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Li R, Jin C, Zhao W, Liang R, Xiong H. Development of a novel immune-related lncRNA prognostic signature for patients with hepatocellular carcinoma. BMC Gastroenterol 2022; 22:450. [PMID: 36344926 PMCID: PMC9639314 DOI: 10.1186/s12876-022-02540-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common neoplasm and the major cause of cancer-associated death worldwide. The high mortality rate of HCC is mainly attributed to its widespread prevalence and the lack of effective treatment. Immunotherapy as a promising, innovative approach has revolutionised the treatment of solid tumours. However, owing to the heterogeneity and complex tumour microenvironment of HCC, an efficient biomarker for immunotherapy has yet to be identified. We investigated the role of immune-related long non-coding RNAs (lncRNAs) as prognostic biomarkers in patients with HCC from The Cancer Genome Atlas (TCGA) database. Spearman correlation, univariate and multivariate Cox, and lasso regression analyses were utilised to screen lncRNAs associated with prognosis. Four lncRNAs were filtered out to develop an immune-associated lncRNA prognostic signature in TCGA training as well as validation cohorts. Patients with HCC were then categorised into low- and high-risk groups according to the median value of the risk scores to evaluate the ability of the prognostic model between training and validation cohorts. A nomogram (based on risk score and stage) was constructed to appraise the general overall survival (OS) of patients with HCC. Differences in immune cell infiltration, immune checkpoint inhibitor (ICI) treatment response, gene mutation, and drug sensitivity were observed between the two groups. Thus, the lncRNA prognostic signature can serve as a sensitive prognostic biomarker with potential in individualised immunotherapy for HCC patients.
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Affiliation(s)
- Rui Li
- grid.33199.310000 0004 0368 7223Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Chen Jin
- grid.268099.c0000 0001 0348 3990Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang China
| | - Weiheng Zhao
- grid.33199.310000 0004 0368 7223Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Rui Liang
- grid.190737.b0000 0001 0154 0904Biological Engineering Academy, Chongqing University, Chongqing, China
| | - Huihua Xiong
- grid.33199.310000 0004 0368 7223Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei China
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Forst CV, Chung M, Hockman M, Lashua L, Adney E, Hickey A, Carlock M, Ross T, Ghedin E, Gresham D. Vaccination History, Body Mass Index, Age, and Baseline Gene Expression Predict Influenza Vaccination Outcomes. Viruses 2022; 14:2446. [PMID: 36366544 PMCID: PMC9697051 DOI: 10.3390/v14112446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Seasonal influenza is a primary public health burden in the USA and globally. Annual vaccination programs are designed on the basis of circulating influenza viral strains. However, the effectiveness of the seasonal influenza vaccine is highly variable between seasons and among individuals. A number of factors are known to influence vaccination effectiveness including age, sex, and comorbidities. Here, we sought to determine whether whole blood gene expression profiling prior to vaccination is informative about pre-existing immunological status and the immunological response to vaccine. We performed whole transcriptome analysis using RNA sequencing (RNAseq) of whole blood samples obtained prior to vaccination from 275 participants enrolled in an annual influenza vaccine trial. Serological status prior to vaccination and 28 days following vaccination was assessed using the hemagglutination inhibition assay (HAI) to define baseline immune status and the response to vaccination. We find evidence that genes with immunological functions are increased in expression in individuals with higher pre-existing immunity and in those individuals who mount a greater response to vaccination. Using a random forest model, we find that this set of genes can be used to predict vaccine response with a performance similar to a model that incorporates physiological and prior vaccination status alone. A model using both gene expression and physiological factors has the greatest predictive power demonstrating the potential utility of molecular profiling for enhancing prediction of vaccine response. Moreover, expression of genes that are associated with enhanced vaccination response may point to additional biological pathways that contribute to mounting a robust immunological response to the seasonal influenza vaccine.
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Affiliation(s)
- Christian V. Forst
- Department of Genetics and Genomic Sciences, Department of Microbiology, Icahn School of Medicine at Mt Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574, USA
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20894, USA
| | - Megan Hockman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Lauren Lashua
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Emily Adney
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Angela Hickey
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Michael Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Ted Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20894, USA
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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