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Rezapour M, Niazi MKK, Lu H, Narayanan A, Gurcan MN. Machine learning-based analysis of Ebola virus' impact on gene expression in nonhuman primates. Front Artif Intell 2024; 7:1405332. [PMID: 39282474 PMCID: PMC11392916 DOI: 10.3389/frai.2024.1405332] [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: 03/22/2024] [Accepted: 08/12/2024] [Indexed: 09/19/2024] Open
Abstract
Introduction This study introduces the Supervised Magnitude-Altitude Scoring (SMAS) methodology, a novel machine learning-based approach for analyzing gene expression data from non-human primates (NHPs) infected with Ebola virus (EBOV). By focusing on host-pathogen interactions, this research aims to enhance the understanding and identification of critical biomarkers for Ebola infection. Methods We utilized a comprehensive dataset of NanoString gene expression profiles from Ebola-infected NHPs. The SMAS system combines gene selection based on both statistical significance and expression changes. Employing linear classifiers such as logistic regression, the method facilitates precise differentiation between RT-qPCR positive and negative NHP samples. Results The application of SMAS led to the identification of IFI6 and IFI27 as key biomarkers, which demonstrated perfect predictive performance with 100% accuracy and optimal Area Under the Curve (AUC) metrics in classifying various stages of Ebola infection. Additionally, genes including MX1, OAS1, and ISG15 were significantly upregulated, underscoring their vital roles in the immune response to EBOV. Discussion Gene Ontology (GO) analysis further elucidated the involvement of these genes in critical biological processes and immune response pathways, reinforcing their significance in Ebola pathogenesis. Our findings highlight the efficacy of the SMAS methodology in revealing complex genetic interactions and response mechanisms, which are essential for advancing the development of diagnostic tools and therapeutic strategies. Conclusion This study provides valuable insights into EBOV pathogenesis, demonstrating the potential of SMAS to enhance the precision of diagnostics and interventions for Ebola and other viral infections.
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Affiliation(s)
- Mostafa Rezapour
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Muhammad Khalid Khan Niazi
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Hao Lu
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Aarthi Narayanan
- Department of Biology, George Mason University, Fairfax, VA, United States
| | - Metin Nafi Gurcan
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, United States
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Żychowska J, Ćmil M, Skórka P, Olejnik-Wojciechowska J, Plewa P, Bakinowska E, Kiełbowski K, Pawlik A. The Role of Epigenetic Mechanisms in the Pathogenesis of Hepatitis C Infection. Biomolecules 2024; 14:986. [PMID: 39199374 PMCID: PMC11352264 DOI: 10.3390/biom14080986] [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: 07/11/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
Hepatitis C virus (HCV) is a hepatotropic virus that can be transmitted through unsafe medical procedures, such as injections, transfusions, and dental treatment. The infection may be self-limiting or manifest as a chronic form that induces liver fibrosis, cirrhosis, or progression into hepatocellular carcinoma (HCC). Epigenetic mechanisms are major regulators of gene expression. These mechanisms involve DNA methylation, histone modifications, and the activity of non-coding RNAs, which can enhance or suppress gene expression. Abnormal activity or the dysregulated expression of epigenetic molecules plays an important role in the pathogenesis of various pathological disorders, including inflammatory diseases and malignancies. In this review, we summarise the current evidence on epigenetic mechanisms involved in HCV infection and progression to HCC.
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Affiliation(s)
- Justyna Żychowska
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Maciej Ćmil
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Patryk Skórka
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | | | - Paulina Plewa
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland;
| | - Estera Bakinowska
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Kajetan Kiełbowski
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
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Yu X, Tian J, Wang Y, Su N, Luo J, Duan M, Shi N. The pseudogene GBP1P1 suppresses influenza A virus replication by acting as a protein decoy for DHX9. J Virol 2024; 98:e0073824. [PMID: 38940585 PMCID: PMC11264600 DOI: 10.1128/jvi.00738-24] [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: 04/25/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Recently, substantial evidence has demonstrated that pseudogene-derived long noncoding RNAs (lncRNAs) as regulatory RNAs have been implicated in basic physiological processes and disease development through multiple modes of functional interaction with DNA, RNA, and proteins. Here, we report an important role for GBP1P1, the pseudogene of guanylate-binding protein 1, in regulating influenza A virus (IAV) replication in A549 cells. GBP1P1 was dramatically upregulated after IAV infection, which is controlled by JAK/STAT signaling. Functionally, ectopic expression of GBP1P1 in A549 cells resulted in significant suppression of IAV replication. Conversely, silencing GBP1P1 facilitated IAV replication and virus production, suggesting that GBP1P1 is one of the interferon-inducible antiviral effectors. Mechanistically, GBP1P1 is localized in the cytoplasm and functions as a sponge to trap DHX9 (DExH-box helicase 9), which subsequently restricts IAV replication. Together, these studies demonstrate that GBP1P1 plays an important role in antagonizing IAV replication.IMPORTANCELong noncoding RNAs (lncRNAs) are extensively expressed in mammalian cells and play a crucial role as regulators in various biological processes. A growing body of evidence suggests that host-encoded lncRNAs are important regulators involved in host-virus interactions. Here, we define a novel function of GBP1P1 as a decoy to compete with viral mRNAs for DHX9 binding. We demonstrate that GBP1P1 induction by IAV is mediated by JAK/STAT activation. In addition, GBP1P1 has the ability to inhibit IAV replication. Importantly, we reveal that GBP1P1 acts as a decoy to bind and titrate DHX9 away from viral mRNAs, thereby attenuating virus production. This study provides new insight into the role of a previously uncharacterized GBP1P1, a pseudogene-derived lncRNA, in the host antiviral process and a further understanding of the complex GBP network.
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Affiliation(s)
- Xiaohang Yu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Jiaxin Tian
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun, Jilin Province, China
| | - Yihe Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Ning Su
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Jinna Luo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Ming Duan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Ning Shi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
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Li Y, Mao X, Shi P, Wan Z, Yang D, Ma T, Wang B, Wang J, Wang J, Zhu R. Microbiome-host interactions in the pathogenesis of acute exacerbation of chronic obstructive pulmonary disease. Front Cell Infect Microbiol 2024; 14:1386201. [PMID: 39091676 PMCID: PMC11291260 DOI: 10.3389/fcimb.2024.1386201] [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: 02/14/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Objective To explore the underlying mechanisms the airway microbiome contributes to Acute Exacerbation of Chronic Obstructive Pulmonary Disease(AECOPD). Methods We enrolled 31 AECOPD patients and 26 stable COPD patients, their sputum samples were collected for metagenomic and RNA sequencing, and then subjected to bioinformatic analyses. The expression of host genes was validated by Quantitative Real-time PCR(qPCR) using the same batch of specimens. Results Our results indicated a higher expression of Rothia mucilaginosa(p=0.015) in the AECOPD group and Haemophilus influenzae(p=0.005) in the COPD group. The Different expressed genes(DEGs) detected were significantly enriched in "type I interferon signaling pathway"(p<0.001, q=0.001) in gene function annotation, and "Cytosolic DNA-sensing pathway"(p=0.002, q=0.024), "Toll-like receptor signaling pathway"(p=0.006, q=0.045), and "TNF signaling pathway"(p=0.006, q=0.045) in KEGG enrichment analysis. qPCR amplification experiment verified that the expression of OASL and IL6 increased significantly in the AECOPD group. Conclusion Pulmonary bacteria dysbiosis may regulate the pathogenesis of AECOPD through innate immune system pathways like type I interferon signaling pathway and Toll-like receptor signaling pathway.
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Affiliation(s)
- Yao Li
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian, China
| | - Xiaoyan Mao
- Department of Intensive Care Unit, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Pengfei Shi
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian, China
| | - Zongren Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Dan Yang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Ting Ma
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Baolan Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Jipeng Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Jingjing Wang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rong Zhu
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian, China
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Reid VA, Ramos EI, Veerapandian R, Carmona A, Gadad SS, Dhandayuthapani S. Differential Expression of lncRNAs in HIV Patients with TB and HIV-TB with Anti-Retroviral Treatment. Noncoding RNA 2024; 10:40. [PMID: 39051374 PMCID: PMC11270221 DOI: 10.3390/ncrna10040040] [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: 05/21/2024] [Revised: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Tuberculosis (TB) is the leading cause of death among people with HIV-1 infection. To improve the diagnosis and treatment of HIV-TB patients, it is important to understand the mechanisms underlying these conditions. Here, we used an integrated genomics approach to analyze and determine the lncRNAs that are dysregulated in HIV-TB patients and HIV-TB patients undergoing anti-retroviral therapy (ART) using a dataset available in the public domain. The analyses focused on the portion of the genome transcribed into non-coding transcripts, which historically have been poorly studied and received less focus. This revealed that Mtb infection in HIV prominently up-regulates the expression of long non-coding RNA (lncRNA) genes DAAM2-AS1, COL4A2-AS1, LINC00599, AC008592.1, and CLRN1-AS1 and down-regulates the expression of lncRNAs AC111000.4, AC100803.3, AC016168.2, AC245100.7, and LINC02073. It also revealed that ART down-regulates the expression of some lncRNA genes (COL4A2-AS1, AC079210.1, MFA-AS1, and LINC01993) that are highly up-regulated in HIV-TB patients. Furthermore, the interrogation of the genomic regions that are associated with regulated lncRNAs showed enrichment for biological processes linked to immune pathways in TB-infected conditions. However, intriguingly, TB patients treated with ART showed completely opposite and non-overlapping pathways. Our findings suggest that lncRNAs could be used to identify critical diagnostic, prognostic, and treatment targets for HIV-TB patients.
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Affiliation(s)
- Victoria A. Reid
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
| | - Enrique I. Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Raja Veerapandian
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
| | - Areanna Carmona
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
| | - Shrikanth S. Gadad
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
| | - Subramanian Dhandayuthapani
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA; (V.A.R.); (R.V.); (A.C.)
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA;
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
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Qin Y, Ren J, Yu H, He X, Cheng S, Chen W, Yang Z, Sun F, Wang C, Yuan S, Chen P, Wu D, Ren F, Huang A, Chen J. HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306810. [PMID: 38647380 PMCID: PMC11200093 DOI: 10.1002/advs.202306810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.
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Affiliation(s)
- YiPing Qin
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing400030China
| | - JiHua Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - HaiBo Yu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Xin He
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - ShengTao Cheng
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - WeiXian Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Zhen Yang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - FengMing Sun
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)College of Laboratory MedicineChongqing Medical UniversityChongqing400016China
| | - ChunDuo Wang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - SiYu Yuan
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Peng Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - DaiQing Wu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Fang Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - AiLong Huang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Juan Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- State Key Laboratory of Ultrasound in Medicine and EngineeringCollege of Biomedical EngineeringChongqing Medical UniversityChongqing400016China
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Forabosco P, Pala M, Crobu F, Diana MA, Marongiu M, Cusano R, Angius A, Steri M, Orrù V, Schlessinger D, Fiorillo E, Devoto M, Cucca F. Transcriptome organization of white blood cells through gene co-expression network analysis in a large RNA-seq dataset. Front Immunol 2024; 15:1350111. [PMID: 38629067 PMCID: PMC11018966 DOI: 10.3389/fimmu.2024.1350111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Gene co-expression network analysis enables identification of biologically meaningful clusters of co-regulated genes (modules) in an unsupervised manner. We present here the largest study conducted thus far of co-expression networks in white blood cells (WBC) based on RNA-seq data from 624 individuals. We identify 41 modules, 13 of them related to specific immune-related functions and cell types (e.g. neutrophils, B and T cells, NK cells, and plasmacytoid dendritic cells); we highlight biologically relevant lncRNAs for each annotated module of co-expressed genes. We further characterize with unprecedented resolution the modules in T cell sub-types, through the availability of 95 immune phenotypes obtained by flow cytometry in the same individuals. This study provides novel insights into the transcriptional architecture of human leukocytes, showing how network analysis can advance our understanding of coding and non-coding gene interactions in immune system cells.
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Affiliation(s)
- Paola Forabosco
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Francesca Crobu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Maria Antonietta Diana
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Mara Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Roberto Cusano
- CRS4-Next Generation Sequencing (NGS) Core, Parco POLARIS, Cagliari, Italy
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health (NIH), Baltimore, MA, United States
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Marcella Devoto
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Medicina Traslazionale e di Precisione, Università Sapienza, Roma, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
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Bartosh UI, Dome AS, Zhukova NV, Karitskaya PE, Stepanov GA. CRISPR/Cas9 as a New Antiviral Strategy for Treating Hepatitis Viral Infections. Int J Mol Sci 2023; 25:334. [PMID: 38203503 PMCID: PMC10779197 DOI: 10.3390/ijms25010334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatitis is an inflammatory liver disease primarily caused by hepatitis A (HAV), B (HBV), C (HCV), D (HDV), and E (HEV) viruses. The chronic forms of hepatitis resulting from HBV and HCV infections can progress to cirrhosis or hepatocellular carcinoma (HCC), while acute hepatitis can lead to acute liver failure, sometimes resulting in fatality. Viral hepatitis was responsible for over 1 million reported deaths annually. The treatment of hepatitis caused by viral infections currently involves the use of interferon-α (IFN-α), nucleoside inhibitors, and reverse transcriptase inhibitors (for HBV). However, these methods do not always lead to a complete cure for viral infections, and chronic forms of the disease pose significant treatment challenges. These facts underscore the urgent need to explore novel drug developments for the treatment of viral hepatitis. The discovery of the CRISPR/Cas9 system and the subsequent development of various modifications of this system have represented a groundbreaking advance in the quest for innovative strategies in the treatment of viral infections. This technology enables the targeted disruption of specific regions of the genome of infectious agents or the direct manipulation of cellular factors involved in viral replication by introducing a double-strand DNA break, which is targeted by guide RNA (spacer). This review provides a comprehensive summary of our current knowledge regarding the application of the CRISPR/Cas system in the regulation of viral infections caused by HAV, HBV, and HCV. It also highlights new strategies for drug development aimed at addressing both acute and chronic forms of viral hepatitis.
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Affiliation(s)
| | | | | | | | - Grigory A. Stepanov
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; (U.I.B.); (A.S.D.); (N.V.Z.); (P.E.K.)
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Ramos EI, Veerapandian R, Das K, Chacon JA, Gadad SS, Dhandayuthapani S. Pathogenic mycoplasmas of humans regulate the long noncoding RNAs in epithelial cells. Noncoding RNA Res 2023; 8:282-293. [PMID: 36970372 PMCID: PMC10031284 DOI: 10.1016/j.ncrna.2023.03.002] [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: 11/10/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs), specifically long ncRNAs (lncRNAs), regulate cellular processes by affecting gene expression at the transcriptional, post-transcriptional, and epigenetic levels. Emerging evidence indicates that pathogenic microbes dysregulate the expression of host lncRNAs to suppress cellular defense mechanisms and promote survival. To understand whether the pathogenic human mycoplasmas dysregulate host lncRNAs, we infected HeLa cells with Mycoplasma genitalium (Mg) and Mycoplasma penumoniae (Mp) and assessed the expression of lncRNAs by directional RNA-seq analysis. HeLa cells infected with these species showed up-and-down regulation of lncRNAs expression, indicating that both species can modulate host lncRNAs. However, the number of upregulated (200 for Mg and 112 for Mp) and downregulated lncRNAs (30 for Mg and 62 for Mp) differ widely between these two species. GREAT analysis of the noncoding regions associated with differentially expressed lncRNAs showed that Mg and Mp regulate a discrete set of lncRNA plausibly related to transcription, metabolism, and inflammation. Further, signaling network analysis of the differentially regulated lncRNAs exhibited diverse pathways such as neurodegeneration, NOD-like receptor signaling, MAPK signaling, p53 signaling, and PI3K signaling, suggesting that both species primarily target signaling mechanisms. Overall, the study's results suggest that Mg and Mp modulate lncRNAs to promote their survival within the host but in distinct manners.
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Affiliation(s)
- Enrique I. Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Raja Veerapandian
- Center of Emphasis in Infectious Diseases, Paul L. Foster School of Medicine, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Kishore Das
- Center of Emphasis in Infectious Diseases, Paul L. Foster School of Medicine, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Jessica A. Chacon
- Department of Medical Education, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Shrikanth S. Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, Texas, 79905, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson Cancer Center, San Antonio, TX, 78229, USA
| | - Subramanian Dhandayuthapani
- Center of Emphasis in Infectious Diseases, Paul L. Foster School of Medicine, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, Texas, 79905, USA
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10
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Qin L, Fan W, Zheng F, Chen H, Qian P, Li X. Swine IFI6 confers antiviral effects against Japanese encephalitis virus in vitro and in vivo. J Gen Virol 2023; 104. [PMID: 37097881 DOI: 10.1099/jgv.0.001847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Swine are considered to be an important intermediate host in the cycle of Japanese encephalitis virus (JEV) infection. Most existing antiviral studies of JEV mainly focus on the host factor of the dead-end hosts. However, little research has addressed this in swine. Here, we found that swine interferon alpha-inducible protein 6 (sIFI6) possessed antiviral activity against JEV. In vitro studies showed that overexpression of sIFI6 inhibited the infection of JEV, while sIFI6 knockdown enhanced the infection of JEV in PK-15 cells. In addition, we also found that the structural integrity of sIFI6 was required by anti-JEV activity and that sIFI6 interacted with JEV nonstructural protein 4A (NS4A), an integral membrane protein with a pivotal function in replication complex during JEV replication. The interaction domain was mapped to the fourth transmembrane domain (TMD), also known as the 2K peptide of NS4A. The antiviral activity of sIFI6 was regulated by endoplasmic reticulum (ER) stress-related protein, Bip. In vivo studies revealed that sIFI6 alleviated symptoms of JEV infection in C57BL/6 mice. In addition, the antiviral spectrum of sIFI6 showed that sIFI6 specifically inhibited JEV infection. In conclusion, this study identified sIFI6 as a host factor against JEV infection for the first time. Our findings provide a potential drug target against JEV infection.
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Affiliation(s)
- Liuxing Qin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wenchun Fan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Feiteng Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, PR China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, PR China
| | - Ping Qian
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, PR China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, PR China
| | - Xiangmin Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, PR China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, PR China
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11
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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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12
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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13
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Role of Genetic and Epigenetic Modifications in the Progression of Hepatocellular Carcinoma in Chronic HCV Patients. LIVERS 2023. [DOI: 10.3390/livers3010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Globally, hepatocellular carcinoma (HCC) is a significant cause of mortality and morbidity among chronically infected HCV patients. It is established that HCV is a primary risk factor for HCC progression. The treatment of HCV infection has been transformed by the introduction of DAAs with high rates of virological clearance. The reduction in cirrhosis-related consequences, particularly HCC, is the long-term objective of DAAs therapy for HCV. Although the risk of developing HCC is decreased in HCV patients who achieve a disease-sustaining virological response, these patients are nevertheless at risk, especially those with severe fibrosis and cirrhosis. Previous studies have shown that HCV induce several mechanisms of hepatocarcinogenesis in the host’s hepatic micro- and macro-environment, which leads to HCC progression. In an HCV-altered environment, compensatory liver regeneration favors chromosomal instability and irreversible alterations, which encourage hepatocyte neoplastic transformation and the development of malignant clones. These mechanisms involve a series of genetic and epigenetic modifications including host genetic factors, dysregulation of several signaling pathways, histone, and DNA modifications including methylation and acetylation. This review highlights the genetic and epigenetic factors that lead to the development of HCC in chronic HCV-infected individuals and can be targeted for earlier HCC diagnosis and prevention.
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14
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Zhu L, Zhang XP, Xu S, Hu MG, Zhao ZM, Zhao GD, Xiao ZH, Liu R. Identification of a CD4+ conventional T cells-related lncRNAs signature associated with hepatocellular carcinoma prognosis, therapy, and tumor microenvironment. Front Immunol 2023; 13:1111246. [PMID: 36700197 PMCID: PMC9868629 DOI: 10.3389/fimmu.2022.1111246] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide, and CD4+ T lymphocytes can inhibit hepatocarcinogenesis and mediate tumor regression. However, few studies have focused on the prognostic power of CD4+ Tconv-related lncRNAs in HCC patients. Method We obtained data from TCGA and GEO databases and identified CD4+Tconv-related lncRNAs in HCC. The risk score was constructed using lasso regression and the model was validated using two validation cohorts. The RS was also assessed in different clinical subgroups, and a nomogram was established to further predict the patients' outcomes. Furthermore, we estimated the immune cell infiltration and cancer-associated fibroblasts (CAFs) through TIMER databases and assessed the role of RS in immune checkpoint inhibitors response. Results We constructed a CD4+ Tconv-related lncRNAs risk score, including six lncRNAs (AC012073.1, AL031985.3, LINC01060, MKLN1-AS, MSC-AS1, and TMCC1-AS1), and the RS had good predictive ability in validation cohorts and most clinical subgroups. The RS and the T stage were included in the nomogram with optimum prediction and the model had comparable OS prediction power compared to the AJCC. Patients in the high-risk group had a poor immune response phenotype, with high infiltrations of macrophages, CAFs, and low infiltrations of NK cells. Immunotherapy and chemotherapy response analysis indicated that low-risk group patients had good reactions to immune checkpoint inhibitors. Conclusion We constructed and validated a novel CD4+ Tconv-related lncRNAs RS, with the potential predictive value of HCC patients' survival and immunotherapy response.
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Affiliation(s)
- Lin Zhu
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China,The First Clinical Medical School, Lanzhou University, Lanzhou, China
| | - Xiu-Ping Zhang
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Shuai Xu
- Department of Liver Transplantation and Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ming-Gen Hu
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Zhi-Ming Zhao
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Guo-Dong Zhao
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Zhao-Hui Xiao
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Rong Liu
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China,The First Clinical Medical School, Lanzhou University, Lanzhou, China,*Correspondence: Rong Liu,
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15
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Yin Y, Zhao Y, Chen Q, Chen Y, Mao L. Dual roles and potential applications of exosomes in HCV infections. Front Microbiol 2022; 13:1044832. [PMID: 36578571 PMCID: PMC9791051 DOI: 10.3389/fmicb.2022.1044832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
The hepatitis C virus (HCV) causes severe liver diseases, including hepatitis, liver cirrhosis, and hepatocellular carcinoma, which have high morbidity and mortality. Antibody targeting receptor-mediated HCV infections have limited therapeutic benefits, suggesting that the transmission of HCV infections is possibly mediated via receptor-independent mechanisms. Exosomes are membrane-enclosed vesicles with a diameter of 30-200 nm, which originate from the fusion of endosomal multivesicular bodies with the plasma membrane. Accumulating evidence suggests that exosomes have a pivotal role in HCV infections. Exosomes can transfer viral and cellular bioactive substances, including nucleic acids and proteins, to uninfected cells, thus spreading the infection by masking these materials from immunological recognition. In addition, exosomes originating from some cells can deliver antiviral molecules or prompt the immune response to inhibit HCV infection. Exosomes can be used for the diagnosis of HCV-related diseases, and are being presently evaluated as therapeutic tools for anti-HCV drug delivery. This review summarizes the current knowledge on the dual roles and potential clinical applications of exosomes in HCV infections.
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16
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Tripathi SK, Pal A, Ghosh S, Goel A, Aggarwal R, Banerjee S, Das S. LncRNA NEAT1 regulates HCV-induced Hepatocellular carcinoma by modulating the miR-9-BGH3 axis. J Gen Virol 2022; 103. [PMID: 36748628 DOI: 10.1099/jgv.0.001809] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection is a leading cause of end-stage liver diseases, such as fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Several cellular entities, including paraspeckles and their related components, are involved in viral pathogenesis and cancer progression. NEAT1 lncRNA is a major component of paraspeckles that has been linked to several malignancies. In this study, analysis of the Cancer Genome Atlas (TCGA) database and validation in HCV-induced HCC tissue and serum samples showed significantly high expression of NEAT1 in patients with liver cancer. Moreover, we found that NEAT1 levels increased upon HCV infection. To further understand the mechanism of NEAT1-induced HCC progression, we selected one of its targets, miR-9-5 p, which regulates BGH3 mRNA levels. Interestingly, miR-9-5 p levels were downregulated upon HCV infection, whereas BGH3 levels were upregulated. Additionally, partial NEAT1 knockdown increased miR-9-5 p levels and decreased BGH3 levels, corroborating our initial results. BGH3 levels were also upregulated in HCV-induced HCC and TCGA tissue samples, which could be directly correlated with NEAT1 levels. As a known oncogene, BGH3 is directly linked to HCC progression mediated by NEAT1. We also found that NEAT1 levels remained upregulated in serum samples from patients treated with direct-acting antivirals (DAA), indicating that NEAT1 might be a molecular trigger that promotes HCC development. Collectively, these findings provide molecular insights into HCV-induced HCC progression via the NEAT1-miR-9-BGH3 axis.
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Affiliation(s)
| | - Apala Pal
- Indian Institute of Science, Bangalore, India
| | - Suchandrima Ghosh
- Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Amit Goel
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Rakesh Aggarwal
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Soma Banerjee
- Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Saumitra Das
- Indian Institute of Science, Bangalore, India.,National Institute of Biomedical Genomics, Kalyani, India
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17
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Min J, Liu W, Li J. Emerging Role of Interferon-Induced Noncoding RNA in Innate Antiviral Immunity. Viruses 2022; 14:2607. [PMID: 36560611 PMCID: PMC9780829 DOI: 10.3390/v14122607] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Thousands of unique noncoding RNAs (ncRNAs) exist within the genomes of higher eukaryotes. Upon virus infection, the host generates interferons (IFNs), which initiate the expression of hundreds of interferon-stimulated genes (ISGs) through IFN receptors on the cell surface, establishing a barrier as the host's antiviral innate immunity. With the development of novel RNA-sequencing technology, many IFN-induced ncRNAs have been identified, and increasing attention has been given to their functions as regulators involved in the antiviral innate immune response. IFN-induced ncRNAs regulate the expression of viral proteins, IFNs, and ISGs, as well as host genes that are critical for viral replication, cytokine and chemokine production, and signaling pathway activation. This review summarizes the complex regulatory role of IFN-induced ncRNAs in antiviral innate immunity from the above aspects, aiming to improve understanding of ncRNAs and provide reference for the basic research of antiviral innate immunity.
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Affiliation(s)
- Jie Min
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Hong Y, Zhang Y, Zhao H, Chen H, Yu QQ, Cui H. The roles of lncRNA functions and regulatory mechanisms in the diagnosis and treatment of hepatocellular carcinoma. Front Cell Dev Biol 2022; 10:1051306. [PMID: 36467404 PMCID: PMC9716033 DOI: 10.3389/fcell.2022.1051306] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 10/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent and deadly type of liver cancer. While the underlying molecular mechanisms are poorly understood, it is documented that lncRNAs may play key roles. Many HCC-associated lncRNAs have been linked to HBV and HCV infection, mediating gene expression, cell growth, development, and death. Studying the regulatory mechanisms and biological functions of HCC-related lncRNAs will assist our understanding of HCC pathogenesis as well as its diagnosis and management. Here, we address the potential of dysregulated lncRNAs in HCC as diagnostic and therapeutic biomarkers, and we evaluate the oncogenic or tumor-suppressive properties of these lncRNAs.
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Affiliation(s)
- Yuling Hong
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Yunxing Zhang
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Haibo Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Hailing Chen
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Qing-Qing Yu
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Hongxia Cui
- Jining First People’s Hospital, Jining Medical College, Jining, China
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19
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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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20
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Sun Y, Teng Y, Wang L, Zhang Z, Chen C, Wang Y, Zhang X, Xiang P, Song X, Lu J, Li N, Gao L, Liang X, Xia Y, Wu Z, Ma C. LINC01431 Promotes Histone H4R3 Methylation to Impede HBV Covalently Closed Circular DNA Transcription by Stabilizing PRMT1. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103135. [PMID: 35398991 PMCID: PMC9165498 DOI: 10.1002/advs.202103135] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Covalently closed circular DNA (cccDNA) is the transcriptional template of hepatitis B virus (HBV), which interacts with both host and viral proteins to form minichromosome in the nucleus and is resistant to antiviral agents. Identification of host factors involved in cccDNA transcriptional regulation is expected to prove a new venue for HBV therapy. Recent evidence suggests the involvement of long noncoding RNAs (lncRNAs) in mediating the interaction of host factors with various viruses, however, lncRNAs that HBV targets and represses cccDNA transcription have not been fully elucidated. Here, the authors identified LINC01431 as a novel host restriction factor for HBV transcription. Mechanically, LINC01431 competitively bound with type I protein arginine methyltransferase (PRMT1) to block the HBx-mediated PRMT1 ubiquitination and degradation. Consequently, LINC01431 increased the occupancy of PRMT1 on cccDNA, leading to enhanced H4R3me2a modification and reduced acetylation of cccDNA-bound histones, thereby repressing cccDNA transcription. In turn, to facilitate viral replication, HBV transcriptionally repressed LINC01431 expression by HBx-mediated repression of transcription factor Zinc fingers and homeoboxes 2 (ZHX2). Collectively, the study demonstrates LINC01431 as a novel epigenetic regulator of cccDNA minichromosome and highlights a feedback loop of HBx-LINC01431-PRMT1 in HBV replication, which provides potential therapeutic targets for HBV treatment.
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Affiliation(s)
- Yang Sun
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Yan Teng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and ImmunologyInstitute of Medical VirologySchool of Basic Medical SciencesWuhan UniversityWuhanHubei430072China
| | - Liyuan Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Zhaoying Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - ChaoJia Chen
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Yingchun Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Xiaodong Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Peng Xiang
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Xiaojia Song
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Jinghui Lu
- Department of Hepatobiliary SurgeryQilu Hospital of Shandong University, JinanShandong250012China
| | - Nailin Li
- Karolinska InstituteDepartment of Medicine‐SolnaClinical Pharmacology GroupStockholm17176Sweden
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and ImmunologyInstitute of Medical VirologySchool of Basic Medical SciencesWuhan UniversityWuhanHubei430072China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of ImmunologySchool of Basic Medical SciencesCheeloo Medical CollegeShandong UniversityJinanShandong250012China
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21
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Zhou H, Li S, Pan W, Wu S, Ma F, Jin P. Interaction of lncRNA-CR33942 with Dif/Dorsal Facilitates Antimicrobial Peptide Transcriptions and Enhances Drosophila Toll Immune Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1978-1988. [PMID: 35379744 DOI: 10.4049/jimmunol.2100658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/02/2022] [Indexed: 01/08/2023]
Abstract
The Drosophila Toll signaling pathway mainly responds to Gram-positive (G+) bacteria or fungal infection, which is highly conserved with mammalian TLR signaling pathway. Although many positive and negative regulators involved in the immune response of the Toll pathway have been identified in Drosophila, the roles of long noncoding RNAs (lncRNAs) in Drosophila Toll immune responses are poorly understood to date. In this study, our results demonstrate that lncRNA-CR33942 is mainly expressed in the nucleus and upregulated after Micrococcus luteus infection. Especially, lncRNA-CR33942 not only modulates differential expressions of multiple antimicrobial peptide genes but also affects the Drosophila survival rate during response to G+ bacterial infection based on the transiently overexpressing and the knockdown lncRNA-CR33942 assays in vivo. Mechanically, lncRNA-CR33942 interacts with the NF-κB transcription factors Dorsal-related immunity factor/Dorsal to promote the transcriptions of antimicrobial peptides drosomycin and metchnikowin, thus enhancing Drosophila Toll immune responses. Taken together, this study identifies lncRNA-CR33942 as a positive regulator of Drosophila innate immune response to G+ bacterial infection to facilitate Toll signaling via interacting with Dorsal-related immunity factor/Dorsal. It would be helpful to reveal the roles of lncRNAs in Toll immune response in Drosophila and provide insights into animal innate immunity.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and.,Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing, People's Republic of China
| | - Wanwan Pan
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
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22
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Li G, Ma L, He S, Luo R, Wang B, Zhang W, Song Y, Liao Z, Ke W, Xiang Q, Feng X, Wu X, Zhang Y, Wang K, Yang C. WTAP-mediated m 6A modification of lncRNA NORAD promotes intervertebral disc degeneration. Nat Commun 2022; 13:1469. [PMID: 35304463 PMCID: PMC8933458 DOI: 10.1038/s41467-022-28990-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent RNA modification at the posttranscriptional level and involved in various diseases and cellular processes. However, the underlying mechanism of m6A regulation in intervertebral disc degeneration (IVDD) remains elusive. Here, we show that methylation of the lncRNA NORAD significantly increases in senescent nucleus pulposus cells (NPCs) by m6A sequencing. Subsequent loss- and gain-of-function experiments reveal WTAP is increased in senescent NPCs due to an epigenetic increase in H3K4me3 of the promoter mediated by KDM5a, and significantly promotes NORAD m6A modification. Furthermore, YTHDF2-mediated decay of NORAD is enhanced in senescent NPCs, and then deficiency of NORAD results in less sequestraion of PUMILIO proteins, contributing to the augmented activity of PUM1/2, thus repressing the expression of target E2F3 mRNAs and promoting the cellular senescence. Here, we show interruption of NORAD m6A modification or the NORAD/PUMILIO/E2F3 axis could serve as a potential therapeutic target to inhibit the senescence of NPCs and development of IVDD. Intervertebral disc degeneration (IVDD) is the leading cause of low back pain and Nucleus pulposus cell senescence contributes a lot to its progression. Here, the authors reveal WTAP-mediated m6A modification of lncRNA NORAD promotes IVDD.
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Affiliation(s)
- Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Liang Ma
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Shujie He
- Department of Cardiology, Union Hospital, and Key Laboratory of Biological Targeted Therapy of the Ministry of Education, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Bingjin Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Zhiwei Liao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Wencan Ke
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Qian Xiang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xiaobo Feng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xinghuo Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yukun Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Kun Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
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23
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The Role of Long Noncoding RNA BST2-2 in the Innate Immune Response to Viral Infection. J Virol 2022; 96:e0020722. [PMID: 35297670 DOI: 10.1128/jvi.00207-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) widely exist in the cells and play important roles in various biological processes. The role of lncRNAs in immunity remains largely unknown. lncRNA BST2-2 (lncBST2-2) was upregulated upon viral infection and dependent on the interferon (IFN)/JAK/STAT signaling pathway. There was no coding potential found in the lncBST2-2 transcript. Overexpression of lncBST2-2 inhibited the replication of hepatitis C virus (HCV), Newcastle disease virus (NDV), vesicular stomatitis virus (VSV), and herpes simplex virus (HSV), while knockdown of lncBST2-2 facilitated viral replication. Further studies showed that lncBST2-2 promoted the phosphorylation, dimerization, and nuclear transport of IRF3, promoting the production of IFNs. Importantly, lncBST2-2 interacted with the DNA-binding domain of IRF3, which augmented TBK1 and IRF3 interaction, thereby inducing robust production of IFNs. Moreover, lncBST2-2 impaired the interaction between IRF3 and PP2A-RACK1 complex, an essential step for the dephosphorylation of IRF3. These data shown that lncBST2-2 promotes the innate immune response to viral infection through targeting IRF3. Our study reveals the lncRNA involved in the activation of IRF3 and provides a new insight into the role of lncRNA in antiviral innate immunity. IMPORTANCE Innate immunity is an important part of the human immune system to resist the invasion of foreign pathogens. IRF3 plays a critical role in the innate immune response to viral infection. In this study, we demonstrated that lncBST2-2 plays an important role in innate immunity. Virus-induced lncBST2-2 positively regulates innate immunity by interacting with IRF3 and blocking the dephosphorylation effect of RACK1-PP2A complex on IRF3, thus inhibiting viral infection. Our study provides a new insight into the role of lncBST2-2 in the regulation of IRF3 signaling activation.
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24
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Li W, Duan X, Zhu C, Liu X, Jeyarajan AJ, Xu M, Tu Z, Sheng Q, Chen D, Zhu C, Shao T, Cheng Z, Salloum S, Schaefer EA, Kruger AJ, Holmes JA, Chung RT, Lin W. Hepatitis B and Hepatitis C Virus Infection Promote Liver Fibrogenesis through a TGF-β1-Induced OCT4/Nanog Pathway. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:672-684. [PMID: 35022275 PMCID: PMC8770612 DOI: 10.4049/jimmunol.2001453] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 11/13/2021] [Indexed: 02/03/2023]
Abstract
Hepatitis B virus (HBV)/hepatitis C virus (HCV) coinfection accelerates liver fibrosis progression compared with HBV or HCV monoinfection. Octamer binding transcription factor 4 (OCT4) and Nanog are direct targets of the profibrogenic TGF-β1 signaling cascade. We leveraged a coculture model to monitor the effects of HBV and HCV coinfection on fibrogenesis in both sodium taurocholate cotransporting polypeptide-transfected Huh7.5.1 hepatoma cells and LX2 hepatic stellate cells (HSCs). We used CRISPR-Cas9 to knock out OCT4 and Nanog to evaluate their effects on HBV-, HCV-, or TGF-β1-induced liver fibrogenesis. HBV/HCV coinfection and HBx, HBV preS2, HCV Core, and HCV NS2/3 overexpression increased TGF-β1 mRNA levels in sodium taurocholate cotransporting polypeptide-Huh7.5.1 cells compared with controls. HBV/HCV coinfection further enhanced profibrogenic gene expression relative to HBV or HCV monoinfection. Coculture of HBV and HCV monoinfected or HBV/HCV coinfected hepatocytes with LX2 cells significantly increased profibrotic gene expression and LX2 cell invasion and migration. OCT4 and Nanog guide RNA independently suppressed HBV-, HCV-, HBV/HCV-, and TGF-β1-induced α-SMA, TIMP-1, and Col1A1 expression and reduced Huh7.5.1, LX2, primary hepatocyte, and primary human HSC migratory capacity. OCT4/Nanog protein expression also correlated positively with fibrosis stage in liver biopsies from patients with chronic HBV or HCV infection. In conclusion, HBV and HCV independently and cooperatively promote liver fibrogenesis through a TGF-β1-induced OCT4/Nanog-dependent pathway.
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Affiliation(s)
- Wenting Li
- Department of Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou 570100, Hainan Province, China,Department of Infectious Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
| | - Chuanlong Zhu
- Department of Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou 570100, Hainan Province, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Xiao Liu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Southwest University, College of Animal Science and Technology, Chongqing 400715, China
| | - Andre J. Jeyarajan
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Min Xu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zeng Tu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Microbiology, College of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China
| | - Qiuju Sheng
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, Shengjing Hospital of China Medical University, Shenyang 110022, Liaoning Province, China
| | - Dong Chen
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chuanwu Zhu
- Department of Hepatology, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou 215007, Jiangsu Province, China
| | - Tuo Shao
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhimeng Cheng
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Shadi Salloum
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Esperance A. Schaefer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Annie J. Kruger
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Gastroenterology, MedStar Georgetown University Hospital, Washington, DC 20007 USA
| | - Jacinta A. Holmes
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Gastroenterology, St Vincent’s Hospital, Fitzroy, VIC 3065, Australia
| | - Raymond T. Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Corresponding authors (Wenyu Lin and Raymond T. Chung), Correspondence address: Gastrointestinal Unit, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Tel.: +1 617 726 2061; 617 724 7562; fax: +1 617 643 0446. (W. Lin),
| | - Wenyu Lin
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Corresponding authors (Wenyu Lin and Raymond T. Chung), Correspondence address: Gastrointestinal Unit, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Tel.: +1 617 726 2061; 617 724 7562; fax: +1 617 643 0446. (W. Lin),
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25
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Abd El Halim HM, Ali A. Long noncoding RNAs: Emerging players regulating innate immune memory in the red flour beetle. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104304. [PMID: 34756931 DOI: 10.1016/j.dci.2021.104304] [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: 06/30/2021] [Revised: 10/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A variety of strategies have been evolved to eradicate invading microbes. Phagocytes have developed in vertebrates and invertebrates to confer a non-specific immune response to pathogens. Besides, vertebrates have evolved lymphocytes to develop memory cells that can quickly respond upon the next exposure to the same pathogen. Although lymphocytes are absent in invertebrates, historical evidence, dating back to the 1920s, indicated the presence of immune memory in invertebrates. However, the concept of long-lasting non-specific defense predominated until recent evidence has been introduced in the first decade of the 21st century. Although more evidence has been introduced later, the molecular mechanism underlying the innate immune memory is largely undefined in invertebrates. Long noncoding RNAs (lncRNAs) have demonstrated a role in regulating various biological processes, including immune response. In this review, we will explore the potential role of lncRNAs in developing innate immune memory in the red flour beetle (Tribolium castaneum).
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Affiliation(s)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742-231, USA; Department of Zoology, Faculty of Science, Benha University, Benha, 13518, Egypt.
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26
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Ebrahimi S, Khanbabaei H, Abbasi S, Fani M, Soltani S, Zandi M, Najafimemar Z. CRISPR-Cas System: A Promising Diagnostic Tool for Covid-19. Avicenna J Med Biotechnol 2022; 14:3-9. [PMID: 35509363 PMCID: PMC9017467 DOI: 10.18502/ajmb.v14i1.8165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
More than a year has passed since the beginning of the 2019 novel coronavirus diseases (COVID-19) pandemic which has created massive problems globally affecting all aspects of people's life. Due to the emergence of new strains of the SARS-CoV-2, pandemic risk still remains, despite the start of vaccination. Therefore, rapid diagnostic tests are essential to control infection, improve clinical care and stop the spread of the disease. Recently CRISPR-based diagnostic tools have facilitated rapid diagnostic. Here, we review the diagnostic applications of CRISPR-Cas system in COVID-19.
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Affiliation(s)
- Saeedeh Ebrahimi
- Department of Medical Microbiology (Bacteriology & Virology), Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hashem Khanbabaei
- Department of Radiologic Technology, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Mona Fani
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Najafimemar
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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27
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Ren G, Xu L, Zhao J, Shao Y, Lu T, Zhang Q. Comparative transcriptome analysis of long non coding RNA (lncRNA) in RTG-2 cells infected by infectious hematopoietic necrosis virus. FISH & SHELLFISH IMMUNOLOGY 2022; 120:314-324. [PMID: 34890776 DOI: 10.1016/j.fsi.2021.12.001] [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: 08/23/2021] [Revised: 11/09/2021] [Accepted: 12/05/2021] [Indexed: 06/13/2023]
Abstract
Infectious hematopoietic necrosis virus (IHNV) is the vital pathogen that has caused the great economic loss in salmonid fisheries. To date, there is limited information concerning the changes of lncRNAs in RTG-2 cells infected by IHNV. In this study, a comparative transcriptome analysis of lncRNAs was performed in RTG-2 cells with and without IHNV infection to determine their changes and the effects on IHNV infection. The results showed that IHNV infection significantly changed the expression levels of lncRNAs and mRNAs, including 3693 differentially expressed lncRNAs (DE-lncRNAs) and 3503 differentially expressed mRNAs (DE-mRNAs) respectively. These DE-lncRNAs and DE-mRNAs induced by IHNV were mostly associated with immune response, RNA processing, and viral diseases related pathways. Further analysis found that some DE-lncRNAs might participate in the regulation of extracellular matrix metabolism, apoptosis, lipid synthesis, autophagy, and immune responses referring to the functions of their target genes. Afterwards, 349 co-expression relationships were constructed by 223 DE-lncRNAs and 271 DE-mRNAs, of which LTCONS_00146935 was the pivotal node in the interaction networks, and was together with its target genes modulated the immune responses under the IHNV infection. RT-qPCR results showed that the changes of the selected immune-related DEGs were in consistent with the RNA-seq data, suggesting that the sequencing data was relatively reliable. In summary, this is the first study to determine the changes and interactions of lncRNA-mRNA in RTG-2 cells under the IHNV infection. The results provided the valuable information concerning the lncRNAs in salmonid fish, which will benefit for future study on uncovering the roles of lncRNAs-mRNAs during the viral infection.
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Affiliation(s)
- Guangming Ren
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Liming Xu
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Jingzhuang Zhao
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Yizhi Shao
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Tongyan Lu
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Qiya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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28
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Niu B, Yao L, Zhang Y, Xia X, Su H. LncRNA KCNQ1OT1 promoted hepatitis C virus-induced pyroptosis of β-cell through mediating the miR-223-3p/NLRP3 axis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1387. [PMID: 34733939 PMCID: PMC8506540 DOI: 10.21037/atm-21-3862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/12/2021] [Indexed: 01/10/2023]
Abstract
Background Type 2 diabetes is a well described extra-hepatic manifestation of hepatitis C virus (HCV) infection. This study aimed to explore the potential mechanism of KCNQ1 overlapping transcript 1 (KCNQ1OT1) in type 2 diabetes mellitus (T2DM) caused by HCV infection. Methods Min6 cells were infected with HCV to establish a vitro model, and the HCV copy number was detected by real-time quantitative PCR (RT-qPCR). The mRNA and protein expressions of IL-1β, IL-18, NLRP3, caspase-1, and GSDMD were analyzed by RT-qPCR and Western blot. Flow cytometry and TUNEL assay were used to evaluate the pyroptosis of cells and enzyme-linked immunosorbent assay (ELISA) detected the secretion of insulin. A dual luciferase reporter gene assay then verified the targeting relationship of KCNQ1OT1, miRNA-223-3p, and NLRP3. Results KCNQ1OT1 was highly expressed in HCV-infected T2DM patients and HCV-infected β-cells. Silencing KCNQ1OT1 inhibited β-cell pyroptosis by regulating miR-223-3p/NLRP3, and inhibition of miR-223-3p or overexpression of NLRP3 reversed the pyroptosis by silencing KCNQ1OT1. Conclusions Our findings indicate KCNQ1OT1 promotes HCV-infected β-cell pyroptosis through the miRNA-223-3p/NLRP3 axis, effecting the production of insulin and accelerating the occurrence and development of T2DM.Regulating KCNQ1OT1 and its target genes will help to better understand the pathogenesis of T2DM induced by HCV infection and provide new theoretical foundations and therapeutic targets.
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Affiliation(s)
- Ben Niu
- Department of Endocrinology and Metabolism, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Lixuan Yao
- Department of Endocrinology and Metabolism, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Yating Zhang
- Department of Endocrinology and Metabolism, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Heng Su
- Department of Endocrinology and Metabolism, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
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Zhao H, Li Z, Gao Y, Li J, Zhao X, Yue W. Single-Cell RNA-Sequencing Portraying Functional Diversity and Clinical Implications of IFI6 in Ovarian Cancer. Front Cell Dev Biol 2021; 9:677697. [PMID: 34513825 PMCID: PMC8425592 DOI: 10.3389/fcell.2021.677697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer (OC) is one of the most lethal gynecologic malignancies. Most patients die of metastasis due to a lack of other treatments aimed at improving the prognosis of OC patients. In the present study, we use multiple methods to identify prognostic S1 as the dominant subtype in OC, possessing the most ligand-receptor pairs with other cell types. Based on markers of S1, the consensus clustering algorithm is used to explore the clinical treatment subtype in OC. As a result, we identify two clusters associated with distinct survival and drug response. Notably, IFI6 contributes to the cluster classification and seems to be a vital gene in OC carcinogenesis. Functional enrichment analysis demonstrates that its functions involve G2M and cisplatin resistance, and downregulation of IFI6 suppresses proliferation capabilities and significantly potentiates cisplatin-induced apoptosis of OC cells in vitro. To explore possible mechanisms of IFI6 influencing OC proliferation and cisplatin resistance, GSEA is conducted and shows that IFI6 is positively correlated with the NF-κB pathway, which is validated by RT-qPCR. Significantly, we develop a prognostic model including IFI6, RiskScore, which is an independent prognostic factor and presents encouraging prognostic values. Our findings provide novel insights into elucidating the biology of OC based on single-cell RNA-sequencing. Moreover, this approach is potentially helpful for personalized anti-cancer strategies and predicting outcomes in the setting of OC.
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Affiliation(s)
- Hongyu Zhao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Zhefeng Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yan Gao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Jie Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Xiaoting Zhao
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Wentao Yue
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
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Khatun M, Zhang J, Ray R, Ray RB. Hepatitis C Virus Evades Interferon Signaling by Suppressing Long Noncoding RNA Linc-Pint Involving C/EBP-β. J Virol 2021; 95:e0095221. [PMID: 34160260 PMCID: PMC8354323 DOI: 10.1128/jvi.00952-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 02/01/2023] Open
Abstract
Hepatitis C virus (HCV) regulates many cellular genes in modulating the host immune system for benefit of viral replication and long-term persistence in a host for chronic infection. Long noncoding RNAs (lncRNAs) play an important role in the regulation of many important cellular processes, including immune responses. We recently reported that HCV infection downregulates lncRNA Linc-Pint (long intergenic non-protein-coding RNA p53-induced transcript) expression, although the mechanism of repression and functional consequences are not well understood. In this study, we demonstrate that HCV infection of hepatocytes transcriptionally reduces Linc-Pint expression through CCAAT/enhancer binding protein β (C/EBP-β). Subsequently, we observed that the overexpression of Linc-Pint significantly upregulates interferon alpha (IFN-α) and IFN-β expression in HCV-replicating hepatocytes. Using unbiased proteomics, we identified that Linc-Pint associates with DDX24, which enables RIP1 to interact with IFN-regulatory factor 7 (IRF7) of the IFN signaling pathway. We furthermore observed that IFN-α14 promoter activity was enhanced in the presence of Linc-Pint. Together, these results demonstrated that Linc-Pint acts as a positive regulator of host innate immune responses, especially IFN signaling. HCV-mediated downregulation of Linc-Pint expression appears to be one of the mechanisms by which HCV may evade innate immunity for long-term persistence and chronicity. IMPORTANCE The mechanism by which lncRNA regulates the host immune response during HCV infection is poorly understood. We observed that Linc-Pint was transcriptionally downregulated by HCV. Using a chromatin immunoprecipitation (ChIP) assay, we showed inhibition of transcription factor C/EBP-β binding to the Linc-Pint promoter in the presence of HCV infection. We further identified that Linc-Pint associates with DDX24 for immunomodulatory function. The overexpression of Linc-Pint reduces DDX24 expression, which in turn results in the disruption of DDX24-RIP1 complex formation and the activation of IRF7. The induction of IFN-α14 promoter activity in the presence of Linc-Pint further confirms our observation. Together, our results suggest that Linc-Pint acts as a positive regulator of host innate immune responses. Downregulation of Linc-Pint expression by HCV helps in escaping the innate immune system for the development of chronicity.
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Affiliation(s)
- Mousumi Khatun
- Department of Pathology, Saint Louis University, Saint Louis, Missouri, USA
| | - Jinsong Zhang
- Department of Pharmacology and Physiology, Saint Louis University, Saint Louis, Missouri, USA
| | - Ranjit Ray
- Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, USA
| | - Ratna B. Ray
- Department of Pathology, Saint Louis University, Saint Louis, Missouri, USA
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31
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Zhao P, Malik S, Xing S. Epigenetic Mechanisms Involved in HCV-Induced Hepatocellular Carcinoma (HCC). Front Oncol 2021; 11:677926. [PMID: 34336665 PMCID: PMC8320331 DOI: 10.3389/fonc.2021.677926] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC), is the third leading cause of cancer-related deaths, which is largely caused by virus infection. About 80% of the virus-infected people develop a chronic infection that eventually leads to liver cirrhosis and hepatocellular carcinoma (HCC). With approximately 71 million HCV chronic infected patients worldwide, they still have a high risk of HCC in the near future. However, the mechanisms of carcinogenesis in chronic HCV infection have not been still fully understood, which involve a complex epigenetic regulation and cellular signaling pathways. Here, we summarize 18 specific gene targets and different signaling pathways involved in recent findings. With these epigenetic alterations requiring histone modifications and DNA hyper or hypo-methylation of these specific genes, the dysregulation of gene expression is also associated with different signaling pathways for the HCV life cycle and HCC. These findings provide a novel insight into a correlation between HCV infection and HCC tumorigenesis, as well as potentially preventable approaches. Hepatitis C virus (HCV) infection largely causes hepatocellular carcinoma (HCC) worldwide with 3 to 4 million newly infected cases diagnosed each year. It is urgent to explore its underlying molecular mechanisms for therapeutic treatment and biomarker discovery. However, the mechanisms of carcinogenesis in chronic HCV infection have not been still fully understood, which involve a complex epigenetic regulation and cellular signaling pathways. Here, we summarize 18 specific gene targets and different signaling pathways involved in recent findings. With these epigenetic alterations requiring histone modifications and DNA hyper or hypo-methylation of these specific genes, the dysregulation of gene expression is also associated with different signaling pathways for the HCV life cycle and HCC. These findings provide a novel insight into a correlation between HCV infection and HCC tumorigenesis, as well as potentially preventable approaches.
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Affiliation(s)
- Pin Zhao
- Guandong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Samiullah Malik
- Department of Pathogen Biology, Shenzhen University Health Science Center, Shenzhen, China
| | - Shaojun Xing
- Department of Pathogen Biology, Shenzhen University Health Science Center, Shenzhen, China
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Koskinas J, Armakolas A. Ariadne's Thread in the Network of Hepatocellular Carcinoma Immunobiology. J Clin Transl Hepatol 2021; 9:279-280. [PMID: 34221912 PMCID: PMC8237150 DOI: 10.14218/jcth.2021.00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/05/2021] [Accepted: 05/21/2021] [Indexed: 12/04/2022] Open
Affiliation(s)
- John Koskinas
- 2 Academic Department of Medicine, National and Kapodistrian University of Athens, Medical School Hippokration General Hospital, Athens, Greece
| | - Athanasios Armakolas
- 2 Academic Department of Medicine, National and Kapodistrian University of Athens, Medical School Hippokration General Hospital, Athens, Greece
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33
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Transcriptome Analyses Implicate Endogenous Retroviruses Involved in the Host Antiviral Immune System through the Interferon Pathway. Virol Sin 2021; 36:1315-1326. [PMID: 34009516 PMCID: PMC8131884 DOI: 10.1007/s12250-021-00370-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are the remains of ancient retroviruses that invaded our ancestors' germline cell and were integrated into the genome. The expression of HERVs has always been a cause for concern because of its association with various cancers and diseases. However, few previous studies have focused on specific activation of HERVs by viral infections. Our previous study has shown that dengue virus type 2 (DENV-2) infection induces the transcription of a large number of abnormal HERVs loci; therefore, the purpose of this study was to explore the relationship between exogenous viral infection and HERV activation further. In this study, we retrieved and reanalyzed published data on 21 transcriptomes of human cells infected with various viruses. We found that infection with different viruses could induce transcriptional activation of HERV loci. Through the comparative analysis of all viral datasets, we identified 43 key HERV loci that were up-regulated by DENV-2, influenza A virus, influenza B virus, Zika virus, measles virus, and West Nile virus infections. Furthermore, the neighboring genes of these HERVs were simultaneously up-regulated, and almost all such neighboring genes were interferon-stimulated genes (ISGs), which are enriched in the host's antiviral immune response pathways. Our data supported the hypothesis that activation of HERVs, probably via an interferon-mediated mechanism, plays an important role in innate immunity against viral infections.
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34
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LncRNA: A Potential Research Direction in Intestinal Barrier Function. Dig Dis Sci 2021; 66:1400-1408. [PMID: 32591966 DOI: 10.1007/s10620-020-06417-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/14/2020] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides and play important roles in a variety of diseases. LncRNAs are involved in many biologic processes including cell differentiation, development, and apoptosis. The intestinal barrier is considered one of the most important protective barriers in humans. Severe damage or dysfunction of the intestinal barrier may be associated with the occurrence and development of many diseases, such as inflammatory bowel disease and ulcerative colitis. LncRNAs have been found to be associated with intestinal barrier function in some studies, which are at an early stage. In this review, we introduce the roles of LncRNAs in the intestinal barrier and investigate the possibility of lncRNAs as a research field in the intestinal barrier.
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35
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Liang X, Peng J, Chen D, Tang L, Liu A, Fu Z, Shi L, Wang K, Shao C. Identification of novel hub genes and lncRNAs related to the prognosis and progression of pancreatic cancer by microarray and integrated bioinformatics analysis. Gland Surg 2021; 10:1104-1117. [PMID: 33842254 PMCID: PMC8033078 DOI: 10.21037/gs-21-151] [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: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND Pancreatic cancer (PC) is one of the most invasive and metastatic neoplasms among the fatal malignancies of the digestive system. Abnormal expression of genes and long non-coding RNAs (lncRNAs) are reportedly linked to multiple cancers. However, the lncRNA-mRNA expression profiles and their molecular mechanisms in PC progression are poorly known. This study aimed to map the hub genes and lncRNAs which might play core roles in the development of PC. METHODS This study used microarray expression analysis to screen for both differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between PC and matched adjacent non-tumor (AN) tissues. In order to clarify the functional classification of DEGs, we conducted GO and KEGG pathway enrichment analyses via the Enrichr database. LncRNA-mRNA co-expressed networks were also constructed to explore the probable core regulating DEGs and DElncRNAs. Subsequently, the hub genes and lncRNAs were validated via the ONCOMINE and GEPIA databases and the co-expressed networks. RESULTS By analyzing an mRNA-lncRNA microarray, we identified 943 mRNAs and 1,138 lncRNAs differentially expressed in PC tumors compared with the matched AN tissues. GO analysis confirmed that both up-regulated and down-regulated DEGs were enriched in multiple terms. The KEGG pathways enrichment analyses revealed that DEGs were mostly enriched in the focal adhesion and glutathione metabolism pathways, amongst others. Co-expressed networks were established to reveal the differential interactions between DEGs and DElncRNAs, and to indicate the core regulatory factors located at the core nodes of the co-expressed networks. The expression levels of potential core-regulating DEGs were validated by the GEPIA and ONCOMINE databases, and the relationship between overall survival and tumor stage and the potential core-regulating DEGs was analyzed using the GEPIA database. As a result, five genes and sixteen lncRNAs were finally considered as the hub transcripts in PC. CONCLUSIONS This study identified DEGs and DElncRNAs between PC tumors and matched AN tissues, and these transcripts were connected with malignant phenotypes in PC through different BPs and signaling pathways. Furthermore, five hub genes and sixteen lncRNAs were identified, which are expected to represent candidate diagnostic biomarkers or potential therapeutic targets for PC.
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Affiliation(s)
- Xing Liang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Junfeng Peng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Danlei Chen
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liang Tang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anan Liu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhiping Fu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ligang Shi
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Keqi Wang
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chenghao Shao
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
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Chen J, Li X, Yang L, Zhang J. Long Non-coding RNA LINC01969 Promotes Ovarian Cancer by Regulating the miR-144-5p/LARP1 Axis as a Competing Endogenous RNA. Front Cell Dev Biol 2021; 8:625730. [PMID: 33614632 PMCID: PMC7889973 DOI: 10.3389/fcell.2020.625730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
Accumulating evidence has shown that long non-coding RNAs (lncRNAs) can be used as biological markers and treatment targets in cancer and play various roles in cancer-related biological processes. However, the lncRNA expression profiles and their roles and action mechanisms in ovarian cancer (OC) are largely unknown. Here, we assessed the lncRNA expression profiles in OC tissues from The Cancer Genome Atlas (TCGA) database, and one upregulated lncRNA, LINC01969, was selected for further study. LINC01969 expression levels in 41 patients were verified using quantitative real-time polymerase chain reaction (qRT-PCR). The in vitro effects of LINC01969 on OC cell migration, invasion, and proliferation were determined by the CCK-8, ethynyl-2-deoxyuridine (EdU), wound healing, and Transwell assays. Epithelial–mesenchymal transition (EMT) was evaluated using qRT-PCR and Western blotting. The molecular mechanisms of LINC01969 in OC were assessed through bioinformatics analysis, RNA-binding protein immunoprecipitation (RIP), dual luciferase reporter gene assays, and a rescue experiment. Finally, in vivo experiments were conducted to evaluate the functions of LINC01969. The results of the current study showed that LINC01969 was dramatically upregulated in OC, and patients with lower LINC01969 expression levels tended to have better overall survival. Further experiments demonstrated that LINC01969 promoted the migration, invasion, and proliferation of OC cells in vitro and sped up tumor growth in vivo. Additionally, LINC01969, which primarily exists in the cytoplasm, boosted LARP1 expression by sponging miR-144-5p and promoted the malignant phenotypes of OC cells. In conclusion, the LINC01969/miR-144-5p/LARP1 axis is a newly identified regulatory signaling pathway involved in OC progression.
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Affiliation(s)
- Jinxin Chen
- Department of Gynecology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Xiaocen Li
- Department of Graduate School, Dalian Medical University, Dalian, China
| | - Lu Yang
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Jingru Zhang
- Department of Gynecology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
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Affiliation(s)
- Lucy Ginn
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
| | - Manuela La Montagna
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
| | - Qinghua Wu
- College of Life Science Yangtze University Jingzhou Hubei China
- Department of Chemistry Faculty of Science University of Hradec Kralove Hradec Kralove East Bohemia Czech Republic
| | - Lei Shi
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
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38
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Xie C, Li SY, Fang JH, Zhu Y, Yang JE. Functional long non-coding RNAs in hepatocellular carcinoma. Cancer Lett 2020; 500:281-291. [PMID: 33129957 DOI: 10.1016/j.canlet.2020.10.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/21/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a prevalent human malignancy with high morbidity worldwide. Hepatocarcinogenesis is a complex multistep process, and its underlying molecular mechanisms remain largely unknown. Recently, long non-coding RNAs (lncRNAs), a class of newly discovered molecules, have been revealed as essential regulators in the development of HCC. HCC-associated lncRNAs affect multiple malignant phenotypes by modulating gene expression or protein activity. Moreover, the dysregulation of lncRNAs in the liver is also associated with diseases predisposing to HCC, such as chronic viral infection, nonalcoholic steatohepatitis, and liver fibrosis/cirrhosis. A deeper understanding of the lncRNA regulatory network in the multistep processes of HCC development will provide new insights into the diagnosis and treatment of HCC. In this review, we introduce the biogenesis and function of lncRNAs and summarize recent knowledge on how lncRNAs regulate the malignant hallmarks of HCC, such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis, and metastasis. We also review emerging insights into the role of lncRNAs in HCC-associated liver diseases. Finally, we discuss the potential applications of lncRNAs as early diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Chen Xie
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Xin Gang Xi Road 135#, Guangzhou 510275, PR China
| | - Song-Yang Li
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Xin Gang Xi Road 135#, Guangzhou 510275, PR China
| | - Jian-Hong Fang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Xin Gang Xi Road 135#, Guangzhou 510275, PR China
| | - Ying Zhu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Xin Gang Xi Road 135#, Guangzhou 510275, PR China
| | - Jin-E Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Xin Gang Xi Road 135#, Guangzhou 510275, PR China.
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39
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Suarez B, Prats-Mari L, Unfried JP, Fortes P. LncRNAs in the Type I Interferon Antiviral Response. Int J Mol Sci 2020; 21:E6447. [PMID: 32899429 PMCID: PMC7503479 DOI: 10.3390/ijms21176447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
The proper functioning of the immune system requires a robust control over a delicate equilibrium between an ineffective response and immune overactivation. Poor responses to viral insults may lead to chronic or overwhelming infection, whereas unrestrained activation can cause autoimmune diseases and cancer. Control over the magnitude and duration of the antiviral immune response is exerted by a finely tuned positive or negative regulation at the DNA, RNA, and protein level of members of the type I interferon (IFN) signaling pathways and on the expression and activity of antiviral and proinflammatory factors. As summarized in this review, committed research during the last decade has shown that several of these processes are exquisitely regulated by long non-coding RNAs (lncRNAs), transcripts with poor coding capacity, but highly versatile functions. After infection, viruses, and the antiviral response they trigger, deregulate the expression of a subset of specific lncRNAs that function to promote or repress viral replication by inactivating or potentiating the antiviral response, respectively. These IFN-related lncRNAs are also highly tissue- and cell-type-specific, rendering them as promising biomarkers or therapeutic candidates to modulate specific stages of the antiviral immune response with fewer adverse effects.
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Affiliation(s)
- Beatriz Suarez
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
| | - Laura Prats-Mari
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
| | - Juan P. Unfried
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
| | - Puri Fortes
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
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Mohammadzadeh I, Qujeq D, Yousefi T, Ferns GA, Maniati M, Vaghari-Tabari M. CRISPR/Cas9 gene editing: A new therapeutic approach in the treatment of infection and autoimmunity. IUBMB Life 2020; 72:1603-1621. [PMID: 32344465 DOI: 10.1002/iub.2296] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein9) may be viewed as an adaptive bacterial immune system. When a virus infects a bacterium, a fragment of the virus genome is inserted into the CRISPR sequence of the bacterial genome as a memory. When the bacterium becomes infected again with the same virus, an RNA molecule that is a transcript of the memory sequence, directs Cas9, an endonuclease, to the complementary region of the virus genome, and Cas9 disables the virus by a double-strand break. In recent years, studies have shown that by designing synthetic RNA molecules and delivering them along with Cas9 into eukaryotic cells, different regions of the cell's genome can be targeted and manipulated. These findings have drawn much attention to this new technology and it has been shown that CRISPR/Cas9 gene editing can be used to treat some human diseases. These include infectious diseases and autoimmune diseases. In this review article, in addition to a brief overview of the biology of the CRISPR/Cas9 system, we collected the most recent findings on the applications of CRISPR/Cas9 technology for better investigation of the pathogenesis and treatment of viral infections (human immunodeficiency virus infection, hepatitis virus infections, and onco-virus infections), non-viral infections (parasitic, fungal, and bacterial infections), and autoimmune diseases.
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Affiliation(s)
- Iraj Mohammadzadeh
- Non-Communicable Pediatric Diseases Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Tooba Yousefi
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Gordon A Ferns
- Department of Medical Education, Brighton & Sussex Medical School, Brighton, UK
| | - Mahmood Maniati
- English Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mostafa Vaghari-Tabari
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Abstract
Hepatocellular carcinoma (HCC) is the most frequent subtype of primary liver cancer and one of the leading causes of cancer-related death worldwide. However, the molecular mechanisms underlying HCC pathogenesis have not been fully understood. Emerging evidences have recently suggested the crucial role of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of HCC. Various HCC-related lncRNAs have been shown to possess aberrant expression and participate in cancerous phenotypes (e.g. persistent proliferation, evading apoptosis, accelerated vessel formation and gain of invasive capability) through their binding with DNA, RNA or proteins, or encoding small peptides. Thus, a deeper understanding of lncRNA dysregulation would provide new insights into HCC pathogenesis and novel tools for the early diagnosis and treatment of HCC. In this review, we summarize the dysregulation of lncRNAs expression in HCC and their tumor suppressive or oncogenic roles during HCC tumorigenesis. Moreover, we discuss the diagnostic and therapeutic potentials of lncRNAs in HCC.
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Interferon Response in Hepatitis C Virus-Infected Hepatocytes: Issues to Consider in the Era of Direct-Acting Antivirals. Int J Mol Sci 2020; 21:ijms21072583. [PMID: 32276399 PMCID: PMC7177520 DOI: 10.3390/ijms21072583] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
When interferons (IFNs) bind to their receptors, they upregulate numerous IFN-stimulated genes (ISGs) with antiviral and immune regulatory activities. Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus that affects over 71 million people in the global population. Hepatocytes infected with HCV produce types I and III IFNs. These endogenous IFNs upregulate a set of ISGs that negatively impact the outcome of pegylated IFN-α and ribavirin treatments, which were previously used to treat HCV. In addition, the IFNL4 genotype was the primary polymorphism responsible for a suboptimal treatment response to pegylated IFN-α and ribavirin. However, recently developed direct-acting antivirals have demonstrated a high rate of sustained virological response without pegylated IFN-α. Herein, we review recent studies on types I and III IFN responses to in HCV-infected hepatocytes. In particular, we focused on open issues related to IFN responses in the direct-acting antiviral era.
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Unfried JP, Fortes P. LncRNAs in HCV Infection and HCV-Related Liver Disease. Int J Mol Sci 2020; 21:ijms21062255. [PMID: 32214045 PMCID: PMC7139329 DOI: 10.3390/ijms21062255] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts with poor coding capacity that may interact with proteins, DNA, or other RNAs to perform structural and regulatory functions. The lncRNA transcriptome changes significantly in most diseases, including cancer and viral infections. In this review, we summarize the functional implications of lncRNA-deregulation after infection with hepatitis C virus (HCV). HCV leads to chronic infection in many patients that may progress to liver cirrhosis and hepatocellular carcinoma (HCC). Most lncRNAs deregulated in infected cells that have been described function to potentiate or block the antiviral response and, therefore, they have a great impact on HCV viral replication. In addition, several lncRNAs upregulated by the infection contribute to viral release. Finally, many lncRNAs have been described as deregulated in HCV-related HCC that function to enhance cell survival, proliferation, and tumor progression by different mechanisms. Interestingly, some HCV-related HCC lncRNAs can be detected in bodily fluids, and there is great hope that they could be used as biomarkers to predict cancer initiation, progression, tumor burden, response to treatment, resistance to therapy, or tumor recurrence. Finally, there is high confidence that lncRNAs could also be used to improve the suboptimal long-term outcomes of current HCC treatment options.
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Affiliation(s)
| | - P. Fortes
- Correspondence: ; Tel.: +34-948194700
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Cho WK, Kim HI, Kim SY, Seo HH, Song J, Kim J, Shin DS, Jo Y, Choi H, Lee JH, Moh SH. Anti-Aging Effects of Leontopodium alpinum (Edelweiss) Callus Culture Extract Through Transcriptome Profiling. Genes (Basel) 2020; 11:E230. [PMID: 32098197 PMCID: PMC7074254 DOI: 10.3390/genes11020230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/14/2022] Open
Abstract
Edelweiss (Leontopodium Alpinum) in the family Asteraceae is a wildflower that grows in rocky limestone places. Here, we investigated the efficacy of edelweiss callus culture extract (Leontopodium Alpinum callus culture extract; LACCE) using multiple assays from in vitro to in vivo as well as transcriptome profiling. Several in vitro assay results showed the strong antioxidant activity of LACCE in response to UVB treatment. Moreover, LACCE suppressed inflammation and wrinkling; however, moisturizing activity was increased by LACCE. The clinical test in vivo demonstrated that constant application of LACCE on the face and skin tissues improved anti-periorbital wrinkles, skin elasticity, dermal density, and skin thickness compared with the placebo. The RNA-Sequencing results showed at least 16.56% of human genes were expressed in keratinocyte cells. LACCE up-regulated genes encoding several KRT proteins; DDIT4, BNIP3, and IGFBP3 were involved in the positive regulation of the developmental process, programmed cell death, keratinization, and cornification forming skin barriers, which provide many advantages in the human skin. By contrast, down-regulated genes were stress-responsive genes, including metal, oxidation, wounding, hypoxia, and virus infection, suggesting LACCE did not cause any harmful stress on the skin. Our comprehensive study demonstrated LACCE is a promising agent for anti-aging cosmetics.
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Affiliation(s)
- Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea (Y.J.)
| | - Hye-In Kim
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Soo-Yun Kim
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Hyo Hyun Seo
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Jihyeok Song
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Jiyeon Kim
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Dong Sun Shin
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea (Y.J.)
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | - Jeong Hun Lee
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
| | - Sang Hyun Moh
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (H.-I.K.); (S.-Y.K.); (H.H.S.); (J.S.); (J.K.); (D.S.S.); (J.H.L.)
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Zhang T, Hu H, Yan G, Wu T, Liu S, Chen W, Ning Y, Lu Z. Long Non-Coding RNA and Breast Cancer. Technol Cancer Res Treat 2020; 18:1533033819843889. [PMID: 30983509 PMCID: PMC6466467 DOI: 10.1177/1533033819843889] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Breast cancer, one of the most common diseases among women, is regarded as a
heterogeneous and complicated disease that remains a major public health concern.
Recently, owing to the development of next-generation sequencing technologies, long
non-coding RNAs have received extensive attention. Numerous studies reveal that long
non-coding RNAs are playing important roles in tumor development. Although the biological
function and molecular mechanisms of long non-coding RNAs remain enigmatic, recent
researchers have demonstrated that an array of long non-coding RNAs express abnormally in
cancers, including breast cancer. Herein, we summarized the latest literature about long
non-coding RNAs in breast cancer, with a particular focus on the multiple molecular roles
of regulatory long non-coding RNAs that regulate cell proliferation, invasion, metastasis,
and apoptosis.
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Affiliation(s)
- Tianzhu Zhang
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Hui Hu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ge Yan
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Tangwei Wu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiyi Liu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiqun Chen
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,4 Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Ning
- 2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhongxin Lu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,4 Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Pan Q, Zhao Z, Liao Y, Chiu SH, Wang S, Chen B, Chen N, Chen Y, Chen JL. Identification of an Interferon-Stimulated Long Noncoding RNA (LncRNA ISR) Involved in Regulation of Influenza A Virus Replication. Int J Mol Sci 2019; 20:ijms20205118. [PMID: 31623059 PMCID: PMC6829313 DOI: 10.3390/ijms20205118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 01/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in a diversity of biological processes. It is known that differential expression of thousands of lncRNAs occurs in host during influenza A virus (IAV) infection. However, only few of them have been well characterized. Here, we identified a lncRNA, named as interferon (IFN)-stimulated lncRNA (ISR), which can be significantly upregulated in response to IAV infection in a mouse model. A sequence alignment revealed that lncRNA ISR is present in mice and human beings, and indeed, we found that it was expressed in several human and mouse cell lines and tissues. Silencing lncRNA ISR in A549 cells resulted in a significant increase in IAV replication, whereas ectopic expression of lncRNA ISR reduced the viral replication. Interestingly, interferon-β (IFN-β) treatment was able to induce lncRNA ISR expression, and induction of lncRNA ISR by viral infection was nearly abolished in host deficient of IFNAR1, a type I IFN receptor. Furthermore, the level of IAV-induced lncRNA ISR expression was decreased either in retinoic acid-inducible gene I (RIG-I) knockout A549 cells and mice or by nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) inhibitor treatment. Together, these data elucidate that lncRNA ISR is regulated by RIG-I-dependent signaling that governs IFN-β production during IAV infection, and has an inhibitory capacity in viral replication.
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Affiliation(s)
- Qidong Pan
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhonghui Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yuan Liao
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shih-Hsin Chiu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Song Wang
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Biao Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Na Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Insights into the Functions of LncRNAs in Drosophila. Int J Mol Sci 2019; 20:ijms20184646. [PMID: 31546813 PMCID: PMC6770079 DOI: 10.3390/ijms20184646] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs longer than 200 nucleotides (nt). LncRNAs have high spatiotemporal specificity, and secondary structures have been preserved throughout evolution. They have been implicated in a range of biological processes and diseases and are emerging as key regulators of gene expression at the epigenetic, transcriptional, and post-transcriptional levels. Comparative analyses of lncRNA functions among multiple organisms have suggested that some of their mechanisms seem to be conserved. Transcriptome studies have found that some Drosophila lncRNAs have highly specific expression patterns in embryos, nerves, and gonads. In vivo studies of lncRNAs have revealed that dysregulated expression of lncRNAs in Drosophila may result in impaired embryo development, impaired neurological and gonadal functions, and poor stress resistance. In this review, we summarize the epigenetic, transcriptional, and post-transcriptional mechanisms of lncRNAs and mainly focus on recent insights into the transcriptome studies and biological functions of lncRNAs in Drosophila.
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48
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Agliano F, Rathinam VA, Medvedev AE, Vanaja SK, Vella AT. Long Noncoding RNAs in Host-Pathogen Interactions. Trends Immunol 2019; 40:492-510. [PMID: 31053495 DOI: 10.1016/j.it.2019.04.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 02/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are key molecules that regulate gene expression in a variety of organisms. LncRNAs can drive different transcriptional and post-transcriptional events that impact cellular functions. Recent studies have identified many lncRNAs associated with immune cell development and activation; however, an understanding of their functional role in host immunity to infection is just emerging. Here, we provide a detailed and updated review of the functional roles of lncRNAs in regulating mammalian immune responses during host-pathogen interactions, because these functions may be either beneficial or detrimental to the host. With increased mechanistic insight into the roles of lncRNAs, it may be possible to design and/or improve lncRNA-based therapies to treat a variety of infectious and inflammatory diseases.
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Affiliation(s)
- Federica Agliano
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Vijay A Rathinam
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Andrei E Medvedev
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Sivapriya Kailasan Vanaja
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
| | - Anthony T Vella
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
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49
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Duan X, Liu X, Li W, Holmes JA, Kruger AJ, Yang C, Li Y, Xu M, Ye H, Li S, Liao X, Sheng Q, Chen D, Shao T, Cheng Z, Kaj B, Schaefer EA, Li S, Chen L, Lin W, Chung RT. Microrna-130a Downregulates HCV Replication through an atg5-Dependent Autophagy Pathway. Cells 2019; 8:E338. [PMID: 30974864 PMCID: PMC6523735 DOI: 10.3390/cells8040338] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022] Open
Abstract
We previously identified that miR-130a downregulates HCV replication through two independent pathways: restoration of host immune responses and regulation of pyruvate metabolism. In this study, we further sought to explore host antiviral target genes regulated by miR-130a. We performed a RT² Profiler™ PCR array to identify the host antiviral genes regulated by miR-130a. The putative binding sites between miR-130a and its downregulated genes were predicted by miRanda. miR-130a and predicted target genes were over-expressed or knocked down by siRNA or CRISPR/Cas9 gRNA. Selected gene mRNAs and their proteins, together with HCV replication in JFH1 HCV-infected Huh7.5.1 cells were monitored by qRT-PCR and Western blot. We identified 32 genes that were significantly differentially expressed more than 1.5-fold following miR-130a overexpression, 28 of which were upregulated and 4 downregulated. We found that ATG5, a target gene for miR-130a, significantly upregulated HCV replication and downregulated interferon stimulated gene expression. miR-130a downregulated ATG5 expression and its conjugation complex with ATG12. ATG5 and ATG5-ATG12 complex affected interferon stimulated gene (ISG) such as MX1 and OAS3 expression and subsequently HCV replication. We concluded that miR-130a regulates host antiviral response and HCV replication through targeting ATG5 via the ATG5-dependent autophagy pathway.
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Affiliation(s)
- Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Xiao Liu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Wenting Li
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
- Department of Infectious Disease, Anhui Provincial Hospital, Anhui Medical University, Hefei 230000, China.
| | - Jacinta A Holmes
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
- Department of Gastroenterology, St Vincent's Hospital, Fitzroy, VIC 3065, Australia.
| | - Annie J Kruger
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Chunhui Yang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Yujia Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Min Xu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Haiyan Ye
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Shuang Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Xinzhong Liao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Qiuju Sheng
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Dong Chen
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Tuo Shao
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Zhimeng Cheng
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Batul Kaj
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Esperance A Schaefer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Shilin Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Limin Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Wenyu Lin
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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50
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Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by Enterovirus 71 Using RNA-Seq. Viruses 2018; 10:v10100556. [PMID: 30314355 PMCID: PMC6213062 DOI: 10.3390/v10100556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
Enterovirus 71 (EV71) is the main pathogen of severe hand-foot-mouth disease (HFMD). Long non-coding RNAs (lncRNAs) are recognized as pivotal factors during the pathogenesis of viral infection. However, the critical functions of lncRNAs in EV71–host interactions have not been characterized. Here, for the first time, we performed global transcriptome analysis of lncRNA and mRNA expression profiles in EV71-infected human rhabdomyosarcoma (RD) cells and skeletal muscle of mice using second-generation sequencing. In our study, a total of 3801 novel lncRNAs were identified. In addition, 23 lncRNAs and 372 mRNAs exhibited remarkable differences in expression levels between infected and uninfected RD cells, while 104 lncRNAs and 2647 mRNAs were differentially expressed in infected skeletal muscle from neonatal mice. Comprehensive bioinformatics analysis included target gene prediction, lncRNA-mRNA co-expression network construction, as well as gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis mainly focused on differentially-expressed genes (DEGs). Our results suggest that lncRNAs may participate in EV71 infection-induced pathogenesis through regulating immune responses, protein binding, cellular component biogenesis and metabolism. The present study provides novel insights into the functions of lncRNAs and the possible pathogenic mechanism following EV71 infection.
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