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Fan Y, Guo D, Zhao S, Wei Q, Li Y, Lin T. Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy. Front Cell Infect Microbiol 2022; 12:992201. [PMID: 36159639 PMCID: PMC9492876 DOI: 10.3389/fcimb.2022.992201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022] Open
Abstract
Human polyomaviruses (HPyVs) can cause serious and deleterious infections in human. Yet, the molecular mechanism underlying these infections, particularly in polyomavirus nephropathy (PVAN), is not well-defined. In the present study, we aimed to identify human genes with codon usage bias (CUB) similar to that of HPyV genes and explore their potential involvement in the pathogenesis of PVAN. The relative synonymous codon usage (RSCU) values of genes of HPyVs and those of human genes were computed and used for Pearson correlation analysis. The involvement of the identified correlation genes in PVAN was analyzed by validating their differential expression in publicly available transcriptomics data. Functional enrichment was performed to uncover the role of sets of genes. The RSCU analysis indicated that the A- and T-ending codons are preferentially used in HPyV genes. In total, 5400 human genes were correlated to the HPyV genes. The protein-protein interaction (PPI) network indicated strong interactions between these proteins. Gene expression analysis indicated that 229 of these genes were consistently and differentially expressed between normal kidney tissues and kidney tissues from PVAN patients. Functional enrichment analysis indicated that these genes were involved in biological processes related to transcription and in pathways related to protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation and immune system. The identified genes may serve as diagnostic biomarkers and potential therapeutic targets for HPyV associated diseases, especially PVAN.
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Affiliation(s)
- Yu Fan
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Duan Guo
- Department of Palliative Medicine, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu, China
- Palliative Medicine Research Center, West China−Peking Union Medical College, Chen Zhiqian (PUMC C.C). Chen Institute of Health, Sichuan University, Chengdu, China
| | - Shangping Zhao
- Department of Urology, West China School of Nursing and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
| | - Tao Lin
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
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Murray J, Bergeron HC, Jones LP, Reener ZB, Martin DE, Sancilio FD, Tripp RA. Probenecid Inhibits Respiratory Syncytial Virus (RSV) Replication. Viruses 2022; 14:v14050912. [PMID: 35632652 PMCID: PMC9147281 DOI: 10.3390/v14050912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
RNA viruses like SARS-CoV-2, influenza virus, and respiratory syncytial virus (RSV) are dependent on host genes for replication. We investigated if probenecid, an FDA-approved and safe urate-lowering drug that inhibits organic anion transporters (OATs) has prophylactic or therapeutic efficacy to inhibit RSV replication in three epithelial cell lines used in RSV studies, i.e., Vero E6 cells, HEp-2 cells, and in primary normal human bronchoepithelial (NHBE) cells, and in BALB/c mice. The studies showed that nanomolar concentrations of all probenecid regimens prevent RSV strain A and B replication in vitro and RSV strain A in vivo, representing a potential prophylactic and chemotherapeutic for RSV.
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Affiliation(s)
- Jackelyn Murray
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | - Harrison C. Bergeron
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | - Les P. Jones
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | - Zachary Beau Reener
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | | | - Fred D. Sancilio
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL 33431, USA;
| | - Ralph A. Tripp
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
- TrippBio, Inc., Jacksonville, FL 32256, USA;
- Correspondence: ; Tel.: +1-706-542-1557
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Qian Z, Zhang Z, Wang Y. T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection. PeerJ 2019; 7:e7089. [PMID: 31223533 PMCID: PMC6571000 DOI: 10.7717/peerj.7089] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 11/20/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is the main cause of respiratory tract infection, which seriously threatens the health and life of children. This study is conducted to reveal the rehabilitation mechanisms of RSV infection. Methods E-MTAB-5195 dataset was downloaded from EBI ArrayExpress database, including 39 acute phase samples in the acute phase of infection and 21 samples in the recovery period. Using the limma package, differentially expressed RNAs (DE-RNAs) were analyzed. The significant modules were identified using WGCNA package, and the mRNAs in them were conducted with enrichment analysis using DAVID tool. Afterwards, co-expression network for the RNAs involved in the significant modules was built by Cytoscape software. Additionally, RSV-correlated pathways were searched from Comparative Toxicogenomics Database, and then the pathway network was constructed. Results There were 2,489 DE-RNAs between the two groups, including 2,386 DE-mRNAs and 103 DE-lncRNAs. The RNAs in the black, salmon, blue, tan and turquoise modules correlated with stage were taken as RNA set1. Meanwhile, the RNAs in brown, blue, magenta and pink modules related to disease severity were defined as RNA set2. In the pathway networks, CD40LG and RASGRP1 co-expressed with LINC00891/LINC00526/LINC01215 were involved in the T cell receptor signaling pathway, and IL1B, IL1R2, IL18, and IL18R1 co-expressed with BAIAP2-AS1/CRNDE/LINC01503/SMIM25 were implicated in cytokine-cytokine receptor interaction. Conclusion LINC00891/LINC00526/LINC01215 co-expressed with CD40LG and RASGRP1 might affect the rehabilitation process of RSV infection through the T cell receptor signaling pathway. Besides, BAIAP2-AS1/CRNDE/LINC01503/SMIM25 co-expressed with IL1 and IL18 families might function in the clearance process after RSV infection via cytokine-cytokine receptor interaction.
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Affiliation(s)
- Zuanhao Qian
- Department of Pediatrics, Taikang Xianlin Drum Tower Hospital, Nanjing, China
| | - Zhenglei Zhang
- Department of Pediatrics, Taikang Xianlin Drum Tower Hospital, Nanjing, China
| | - Yingying Wang
- Department of Pediatrics, Taikang Xianlin Drum Tower Hospital, Nanjing, China
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Francesconi V, Giovannini L, Santucci M, Cichero E, Costi MP, Naesens L, Giordanetto F, Tonelli M. Synthesis, biological evaluation and molecular modeling of novel azaspiro dihydrotriazines as influenza virus inhibitors targeting the host factor dihydrofolate reductase (DHFR). Eur J Med Chem 2018; 155:229-243. [PMID: 29886325 PMCID: PMC7115377 DOI: 10.1016/j.ejmech.2018.05.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/27/2018] [Accepted: 05/31/2018] [Indexed: 01/08/2023]
Abstract
Recently we identified cycloguanil-like dihydrotriazine derivatives, which provided host-factor directed antiviral activity against influenza viruses and respiratory syncytial virus (RSV), by targeting the human dihydrofolate reductase (hDHFR) enzyme. In this context we deemed interesting to further investigate the structure activity relationship (SAR) of our first series of cycloguanil-like dihydrotriazines, designing two novel azaspiro dihydrotriazine scaffolds. The present study allowed the exploration of the potential chemical space, around these new scaffolds, that are well tolerated for maintaining the antiviral effect by means of interaction with the hDHFR enzyme. The new derivatives confirmed their inhibitory profile against influenza viruses, especially type B. In particular, the two best compounds shared potent antiviral activity (4: EC50 = 0.29 μM; 6: EC50 = 0.19 μM), which was comparable to that of zanamivir (EC50 = 0.14 μM), and better than that of ribavirin (EC50 = 3.2 μM). In addition, these two compounds proved to be also effective against RSV (4: EC50 = 0.40 μM, SI ≥ 250; 6: EC50 = 1.8 μM, SI ≥ 56), surpassing the potency and selectivity index (SI) of ribavirin (EC50 = 5.8 μM, SI > 43). By a perspective of these results, the above adequately substituted azaspiro dihydrotriazines may represent valuable hit compounds worthy of further structural optimization to develop improved host DHFR-directed antiviral agents.
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Affiliation(s)
- Valeria Francesconi
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132, Genoa, Italy
| | - Luca Giovannini
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132, Genoa, Italy
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41100, Modena, Italy
| | - Elena Cichero
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132, Genoa, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41100, Modena, Italy
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Fabrizio Giordanetto
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227, Dortmund, Germany
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132, Genoa, Italy.
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Dapat C, Oshitani H. Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis. Expert Rev Anti Infect Ther 2016; 14:285-97. [PMID: 26760927 PMCID: PMC4819838 DOI: 10.1586/14787210.2016.1141676] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The lack of vaccine and limited antiviral options against respiratory syncytial virus (RSV) highlights the need for novel therapeutic strategies. One alternative is to develop drugs that target host factors required for viral replication. Several microarray and proteomics studies had been published to identify possible host factors that are affected during RSV replication. In order to obtain a comprehensive understanding of RSV-host interaction, we integrated available proteome and transcriptome datasets and used it to construct a virus-host interaction network. Then, we interrogated the network to identify host factors that are targeted by the virus and we searched for drugs from the DrugBank database that interact with these host factors, which may have potential applications in repositioning for future treatment options of RSV infection.
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Affiliation(s)
- Clyde Dapat
- a Department of Virology , Tohoku University Graduate School of Medicine , Sendai , Miyagi Prefecture , Japan
| | - Hitoshi Oshitani
- a Department of Virology , Tohoku University Graduate School of Medicine , Sendai , Miyagi Prefecture , Japan
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Lee Y, Kim YJ, Jung YJ, Kim KH, Kwon YM, Kim SI, Kang SM. Systems biology from virus to humans. J Anal Sci Technol 2015; 6:3. [PMID: 26269748 PMCID: PMC4527316 DOI: 10.1186/s40543-015-0047-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/15/2015] [Indexed: 12/19/2022] Open
Abstract
Natural infection and then recovery are considered to be the most effective means for hosts to build protective immunity. Thus, mimicking natural infection of pathogens, many live attenuated vaccines such as influenza virus, and yellow fever vaccine 17D were developed and have been successfully used to induce protective immunity. However, humans fail to generate long-term protective immunity to some pathogens after natural infection such as influenza virus, respiratory syncytial virus (RSV), and human immunodeficiency virus (HIV) even if they survive initial infections. Many vaccines are suboptimal since much mortality is still occurring, which is exampled by influenza and tuberculosis. It is critically important to increase our understanding on protein components of pathogens and vaccines as well as cellular and host responses to infections and vaccinations. Here, we highlight recent advances in gene transcripts and protein analysis results in the systems biology to enhance our understanding of viral pathogens, vaccines, and host cell responses.
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Affiliation(s)
- Youri Lee
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Yu-Jin Kim
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Yu-Jin Jung
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Ki-Hye Kim
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Young-Man Kwon
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Seung Il Kim
- Division of Life Science, Korea Basic Science Institute, Daejeon, 305-333 South Korea
| | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
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