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Jeffy J, Parthasarathy D, Ahmed S, Cervera-Benet H, Xiong U, Harris M, Mazurov D, Pickthorn S, Herschhorn A. Alternative substitutions of N332 in HIV-1 AD8 gp120 differentially affect envelope glycoprotein function and viral sensitivity to broadly neutralizing antibodies targeting the V3-glycan. mBio 2024; 15:e0268623. [PMID: 38470051 PMCID: PMC11005340 DOI: 10.1128/mbio.02686-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The envelope glycoprotein (Env) trimer on the surface of human immunodeficiency virus type I (HIV-1) mediates viral entry into host CD4+ T cells and is the sole target of neutralizing antibodies. Broadly neutralizing antibodies (bnAbs) that target gp120 V3-glycan of HIV-1 Env trimer are potent and block the entry of diverse HIV-1 strains. Most V3-glycan bnAbs interact, to a different extent, with a glycan attached to N332, but Asn at this position is not absolutely conserved or required for HIV-1 entry based on the prevalence of N332 in different circulating HIV-1 strains from diverse clades. Here, we studied the effects of amino acid changes at position 332 of HIV-1AD8 Envs on HIV-1 sensitivity to antibodies, cold exposure, and soluble CD4. We further investigated how these changes affect Env function and HIV-1 infectivity in vitro. Our results suggest robust tolerability of HIV-1AD8 Env N332 to changes, with specific changes that resulted in extended exposure of gp120 V3 loop, which is typically concealed in most primary HIV-1 isolates. Viral evolution leading to Asn at position 332 of HIVAD8 Envs is supported by the selection advantage of high levels of cell-cell fusion, transmission, and infectivity with high levels of cell surface expression and slightly higher gp120 shedding than most N332 variants. Thus, tolerance of HIV-1AD8 Envs to different amino acids at position 332 provides increased flexibility to respond to changing conditions/environments and evade the immune system. Modeling studies of the distance between N332 glycan and specific bnAbs were in agreement with N332 glycan dependency on bnAb neutralization. Overall, our studies provide insights into the contribution of specific amino acids at position 332 to Env antigenicity, stability on ice, and conformational states. IMPORTANCE Glycan attached to amino acid asparagine at position 332 of HIV-1 envelope glycoproteins is a main target of a subset of broadly neutralizing antibodies that block HIV-1 infection. Here, we defined the contribution of different amino acids at this position to Env antigenicity, stability on ice, and conformational states.
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Affiliation(s)
- Jeffy Jeffy
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Durgadevi Parthasarathy
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Shamim Ahmed
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Héctor Cervera-Benet
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ulahn Xiong
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Miranda Harris
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Dmitriy Mazurov
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephanie Pickthorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Engineering in Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- Center of Genomic Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota, USA
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, Minnesota, USA
- Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota, Minneapolis, Minnesota, USA
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Misra M, Jeffy J, Liao C, Pickthorn S, Wagh K, Herschhorn A. HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies. Bioinformatics 2024; 40:btae103. [PMID: 38426331 PMCID: PMC10919947 DOI: 10.1093/bioinformatics/btae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/14/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
MOTIVATION Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. RESULTS Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs. AVAILABILITY AND IMPLEMENTATION HIResist is freely available at https://hiresist.ahc.umn.edu/.
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Affiliation(s)
- Milind Misra
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jeffy Jeffy
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Charis Liao
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Stephanie Pickthorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kshitij Wagh
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
- Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455, United States
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States
- Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States
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Liu H, Tan S, Han S, Liu X, Li Z, Wang N, Wu Z, Ma J, Shi K, Wang W, Sha Z. Effects of miR-722 on gene expression and alternative splicing in the liver of half-smooth tongue sole after infection with Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109275. [PMID: 38081443 DOI: 10.1016/j.fsi.2023.109275] [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: 10/12/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/31/2023]
Abstract
MicroRNAs play crucial roles in various biological processes, including but not limited to differentiation, development, disease, and immunity. However, their immunoregulatory roles in half-smooth tongue sole are lacking. Our previous studies indicated that miR-722 could target C5aR1 to modulate the complement pathway to alleviate inflammatory response and even affect the mortality after the bacterial infection with Vibrio anguillarum. Driven by the purpose of revealing the underlying mechanisms, in this study, we investigated the effects of miR-722 on the gene expression and alternative splicing (AS) in the liver of half-smooth tongue sole after Vibrio anguillarum infection, with the approach of miR-722 overexpression/silencing and subsequent RNA-seq. Among the different comparisons, the I group (miR-722 inhibitor and V. anguillarum) versus blank control (PBS) exhibited the highest number of differentially expressed genes (DEGs), suggesting that the immune response was overactivated after inhibiting the miR-722. In addition, enrichment analyses were performed to reveal the functions of DEGs and differential AS (DAS) genes, reflecting the enrichment of RNA splicing and immune-related pathways including NF-κB and T cell receptor signaling pathway. Comparing the M group (miR-722 mimic and V. anguillarum) with the negative control (random sequence and V. anguillarum), two immune-related genes, cd48 and mapk8, were differentially expressed, of which mapk8 was also differentially spliced, indicating their importance in the immune response. Furthermore, representative gene analysis was performed, suggesting their corresponding functional changes due to AS. To verify the RNA-seq data, quantitative real-time PCR was employed with twenty pairs of primers for DEGs and DAS events. Overall, our results demonstrated that miR-722 could mediate the transcriptome-wide changes of gene expression and AS in half-smooth tongue sole, and provided insights into the regulatory role of miR-722 in immune responses, laying the foundation for further functional analyses and practical applications in aquaculture.
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Affiliation(s)
- Hongning Liu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Suxu Tan
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Sen Han
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xinbao Liu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhujun Li
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Ningning Wang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China; College of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Zhendong Wu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Jie Ma
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Kunpeng Shi
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Wenwen Wang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhenxia Sha
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Liu H, Tan S, Chen Y, Chen X, Liu X, Li Z, Wang N, Han S, Wu Z, Ma J, Shi K, Wang W, Sha Z. Regulatory mechanism of miR-722 on C5aR1 and its functions against bacterial inflammation in half-smooth tongue sole (Cynoglossus semilaevis). Int J Biol Macromol 2023; 252:126445. [PMID: 37611685 DOI: 10.1016/j.ijbiomac.2023.126445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in various biological processes, including immunity. Previously, we investigated the miRNAs of half-smooth tongue sole (Cynoglossus semilaevis) and found that miR-722 (designated Cse-miR-722) was significantly differentially expressed after infection with Vibrio anguillarum, reflecting its importance in immune response. Our preliminary bioinformatic analysis suggested that Cse-miR-722 could target C5aR1 (designated CsC5aR1), which was known to play crucial roles in complement activation and inflammatory response, as a receptor of C5a. However, the underlying mechanisms of their interactions and specific functions in inflammatory and immune response are still enigmas. In this study, we successfully cloned the precursor sequence of Cse-miR-722 (94 bp) and the full length of CsC5aR1 (1541 bp, protein molecular weight 39 kDa). The target gene of Cse-miR-722 was verified as CsC5aR1 by a dual luciferase reporter assay, and Cse-miR-722 was confirmed to regulate CsC5aR1 at the protein level using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. The expression of CsC5aR1 and Cse-miR-722 in liver cells and four immune tissues of half-smooth tongue sole changed significantly after LPS stimulation and infection with V. anguillarum. To explore the functional role of Cse-miR-722 in half-smooth tongue sole, we performed both in vitro and in vivo experiments. Cse-miR-722 was observed to affect phagocytosis and respiratory burst activity of macrophages by regulating CsC5aR1 in half-smooth tongue sole. Furthermore, we found that Cse-miR-722 regulated the expression of CsC5aR1, CsC5a, and the inflammatory factors CsIL1-β, CsIL6, CsIL8, and CsTNF-α both in vitro and in vivo. In addition, Cse-miR-722 reduced mortality and pathological damage. This study clarified the regulatory mechanism of Cse-miR-722 on CsC5aR1 and provided insight into the regulatory roles of Cse-miR-722 in immune responses, laying a theoretical foundation for the feasibility of using miR-722 to prevent and control bacterial diseases in teleost.
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Affiliation(s)
- Hongning Liu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Suxu Tan
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Yadong Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xuejie Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xinbao Liu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Zhujun Li
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Ningning Wang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China; College of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Sen Han
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Zhendong Wu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Jie Ma
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Kunpeng Shi
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Wenwen Wang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Zhenxia Sha
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China.
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Bauer AN, Majumdar N, Williams F, Rajput S, Pokhrel LR, Cook PP, Akula SM. MicroRNAs: Small but Key Players in Viral Infections and Immune Responses to Viral Pathogens. BIOLOGY 2023; 12:1334. [PMID: 37887044 PMCID: PMC10604607 DOI: 10.3390/biology12101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Since the discovery of microRNAs (miRNAs) in C. elegans in 1993, the field of miRNA research has grown steeply. These single-stranded non-coding RNA molecules canonically work at the post-transcriptional phase to regulate protein expression. miRNAs are known to regulate viral infection and the ensuing host immune response. Evolving research suggests miRNAs are assets in the discovery and investigation of therapeutics and diagnostics. In this review, we succinctly summarize the latest findings in (i) mechanisms underpinning miRNA regulation of viral infection, (ii) miRNA regulation of host immune response to viral pathogens, (iii) miRNA-based diagnostics and therapeutics targeting viral pathogens and challenges, and (iv) miRNA patents and the market landscape. Our findings show the differential expression of miRNA may serve as a prognostic biomarker for viral infections in regard to predicting the severity or adverse health effects associated with viral diseases. While there is huge market potential for miRNA technology, the novel approach of using miRNA mimics to enhance antiviral activity or antagonists to inhibit pro-viral miRNAs has been an ongoing research endeavor. Significant hurdles remain in terms of miRNA delivery, stability, efficacy, safety/tolerability, and specificity. Addressing these challenges may pave a path for harnessing the full potential of miRNAs in modern medicine.
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Affiliation(s)
- Anais N. Bauer
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
| | - Niska Majumdar
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
| | - Frank Williams
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
| | - Smit Rajput
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
| | - Lok R. Pokhrel
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
| | - Paul P. Cook
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
| | - Shaw M. Akula
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
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Liu S, Guo T, Hu J, Huang W, She P, Wu Y. HIV-1-related factors interact with p53 to influence cellular processes. AIDS Res Ther 2023; 20:66. [PMID: 37691100 PMCID: PMC10493029 DOI: 10.1186/s12981-023-00563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is the primary epidemic strain in China. Its genome contains two regulatory genes (tat and rev), three structural genes (gag, pol, and env), and four accessory genes (nef, vpr, vpu, and vif). Long terminal repeats (LTRs) in thegenome regulate integration, duplication, and expression of viral gene. The permissibility of HIV-1 infection hinges on the host cell cycle status. HIV-1 replicates by exploiting various cellular processes via upregulation or downregulation of specific cellular proteins that also control viral pathogenesis. For example, HIV-1 regulates the life cycle of p53, which in turn contributes significantly to HIV-1 pathogenesis. In this article, we review the interaction between HIV-1-associated factors and p53, providing information on their regulatory and molecular mechanisms, hinting possible directions for further research.
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Affiliation(s)
- Shanling Liu
- Department of Laboratory Medicine, The First Hospital of Changsha, 311 Yingpan Road, Changsha, 410005, Hunan, China
| | - Ting Guo
- Department of Laboratory Medicine, The First Hospital of Changsha, 311 Yingpan Road, Changsha, 410005, Hunan, China
| | - Jinwei Hu
- Department of Laboratory Medicine, The First Hospital of Changsha, 311 Yingpan Road, Changsha, 410005, Hunan, China
| | - Weiliang Huang
- Department of Laboratory Medicine, The First Hospital of Changsha, 311 Yingpan Road, Changsha, 410005, Hunan, China
| | - Pengfei She
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Yong Wu
- Department of Laboratory Medicine, The First Hospital of Changsha, 311 Yingpan Road, Changsha, 410005, Hunan, China.
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