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Fries CN, Chen JL, Dennis ML, Votaw NL, Eudailey J, Watts BE, Hainline KM, Cain DW, Barfield R, Chan C, Moody MA, Haynes BF, Saunders KO, Permar SR, Fouda GG, Collier JH. HIV envelope antigen valency on peptide nanofibers modulates antibody magnitude and binding breadth. Sci Rep 2021; 11:14494. [PMID: 34262096 PMCID: PMC8280189 DOI: 10.1038/s41598-021-93702-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023] Open
Abstract
A major challenge in developing an effective vaccine against HIV-1 is the genetic diversity of its viral envelope. Because of the broad range of sequences exhibited by HIV-1 strains, protective antibodies must be able to bind and neutralize a widely mutated viral envelope protein. No vaccine has yet been designed which induces broadly neutralizing or protective immune responses against HIV in humans. Nanomaterial-based vaccines have shown the ability to generate antibody and cellular immune responses of increased breadth and neutralization potency. Thus, we have developed supramolecular nanofiber-based immunogens bearing the HIV gp120 envelope glycoprotein. These immunogens generated antibody responses that had increased magnitude and binding breadth compared to soluble gp120. By varying gp120 density on nanofibers, we determined that increased antigen valency was associated with increased antibody magnitude and germinal center responses. This study presents a proof-of-concept for a nanofiber vaccine platform generating broad, high binding antibody responses against the HIV-1 envelope glycoprotein.
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Affiliation(s)
- Chelsea N Fries
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA
| | - Jui-Lin Chen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Maria L Dennis
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Nicole L Votaw
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA
| | - Joshua Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Brian E Watts
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kelly M Hainline
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Richard Barfield
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Box 103020, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin O Saunders
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sallie R Permar
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Box 103020, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pediatrics, New York-Presbyterian/Weill Cornell Medicine, New York, NY, 10065, USA
| | - Genevieve G Fouda
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Box 103020, Durham, NC, 27710, USA.
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA.
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA.
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Mangan RJ, Stamper L, Ohashi T, Eudailey JA, Go EP, Jaeger FH, Itell HL, Watts BE, Fouda GG, Erickson HP, Alam SM, Desaire H, Permar SR. Determinants of Tenascin-C and HIV-1 envelope binding and neutralization. Mucosal Immunol 2019; 12:1004-1012. [PMID: 30976088 PMCID: PMC6599478 DOI: 10.1038/s41385-019-0164-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/04/2023]
Abstract
Interactions between innate antiviral factors at mucosal surfaces and HIV-1 virions contribute to the natural inefficiency of HIV-1 transmission and are a platform to inform the development of vaccine and nonvaccine strategies to block mucosal HIV-1 transmission. Tenascin-C (TNC) is a large, hexameric extracellular matrix glycoprotein identified in breast milk and genital fluids that broadly neutralizes HIV-1 via interaction with the HIV-1 Envelope (Env) variable 3 (V3) loop. In this report, we characterize the specific determinants of the interaction between TNC and the HIV-1 Env. We observed that TNC binding and neutralization of HIV-1 is dependent on the TNC fibrinogen-like globe (fbg) and fibronectin-type III (fn) domains, oligomerization, and its newly-mapped glycan structure. Moreover, we observed that TNC-mediated neutralization is also dependent on Env V3 residues 321/322 and 326/327, which surround the IGDIR motif of the V3 loop, as well the N332 glycan, which is critical to the broadly neutralizing activity of glycan-dependent V3-specific antibodies such as PGT128. Our results demonstrate a striking parallel between innate and adaptive immune mechanisms of broad HIV neutralization and provide further insight into the host protein-virus interactions responsible for the natural inefficiency of mucosal HIV-1 transmission.
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Affiliation(s)
- Riley J. Mangan
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Lisa Stamper
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tomoo Ohashi
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Frederick H. Jaeger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hannah L. Itell
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Brian E. Watts
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA;,Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA;,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA,Address correspondence to Sallie R. Permar, MD., Ph.D.,
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Enam SF, Krieger JR, Saxena T, Watts BE, Olingy CE, Botchwey EA, Bellamkonda RV. Enrichment of endogenous fractalkine and anti-inflammatory cells via aptamer-functionalized hydrogels. Biomaterials 2017; 142:52-61. [PMID: 28727998 DOI: 10.1016/j.biomaterials.2017.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/27/2017] [Accepted: 07/09/2017] [Indexed: 12/27/2022]
Abstract
Early recruitment of non-classical monocytes and their macrophage derivatives is associated with augmented tissue repair and improved integration of biomaterial constructs. A promising therapeutic approach to recruit these subpopulations is by elevating local concentrations of chemoattractants such as fractalkine (FKN, CX3CL1). However, delivering recombinant or purified proteins is not ideal due to their short half-lives, suboptimal efficacy, immunogenic potential, batch variabilities, and cost. Here we report an approach to enrich endogenous FKN, obviating the need for delivery of exogenous proteins. In this study, modified FKN-binding-aptamers are integrated with poly(ethylene glycol) diacrylate to form aptamer-functionalized hydrogels ("aptagels") that localize, dramatically enrich and passively release FKN in vitro for at least one week. Implantation in a mouse model of excisional skin injury demonstrates that aptagels enrich endogenous FKN and stimulate significant local increases in Ly6CloCX3CR1hi non-classical monocytes and CD206+ M2-like macrophages. The results demonstrate that orchestrators of inflammation can be manipulated without delivery of foreign proteins or cells and FKN-aptamer functionalized biomaterials may be a promising approach to recruit anti-inflammatory subpopulations to sites of injury. Aptagels are readily synthesized, highly customizable and could combine different aptamers to treat complex diseases in which regulation or enrichment of multiple proteins may be therapeutic.
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Affiliation(s)
- Syed Faaiz Enam
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Jack R Krieger
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Tarun Saxena
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Brian E Watts
- Duke Human Vaccine Institute, Duke University, Durham, NC 27708, USA
| | - Claire E Olingy
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Edward A Botchwey
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Ravi V Bellamkonda
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
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Makarova AV, Nick McElhinny SA, Watts BE, Kunkel TA, Burgers PM. Ribonucleotide incorporation by yeast DNA polymerase ζ. DNA Repair (Amst) 2014; 18:63-7. [PMID: 24674899 DOI: 10.1016/j.dnarep.2014.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 02/26/2014] [Indexed: 12/01/2022]
Abstract
During replication in yeast, the three B family DNA replicases frequently incorporate ribonucleotides (rNMPs) into DNA, and their presence in the nuclear genome can affect genome stability. This prompted us to examine ribonucleotide incorporation by the fourth B family member, Pol ζ, the enzyme responsible for the majority of damage-induced mutagenesis in eukaryotes. We first show that Pol ζ inserts rNMPs into DNA and can extend primer termini containing 3'-ribonucleotides. We then measure rNMP incorporation by Pol ζ in the presence of its cofactors, RPA, RFC and PCNA and at normal cellular dNTP and rNTP concentrations that exist under unstressed conditions. Under these conditions, Pol ζ stably incorporates one rNMP for every 200-300 dNMPs incorporated, a frequency that is slightly higher than for the high fidelity replicative DNA polymerases. Under damage-induced conditions wherein cellular dNTP concentrations are elevated 5-fold, Pol ζ only incorporates one rNMP per 1300 dNMPs. Functional interaction of Pol ζ with the mutasome assembly factor Rev1 gives comparable rNMP incorporation frequencies. These results suggest that ribonucleotide incorporation into DNA during Pol ζ-mediated mutagenesis in vivo may be rare.
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Affiliation(s)
- Alena V Makarova
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie A Nick McElhinny
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Brian E Watts
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Nick McElhinny SA, Kumar D, Clark AB, Watt DL, Watts BE, Lundström EB, Johansson E, Chabes A, Kunkel TA. Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol 2010; 6:774-81. [PMID: 20729855 PMCID: PMC2942972 DOI: 10.1038/nchembio.424] [Citation(s) in RCA: 304] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 07/15/2010] [Indexed: 11/16/2022]
Abstract
Maintaining the chemical identity of DNA depends on ribonucleotide exclusion by DNA polymerases. However, ribonucleotide exclusion during DNA synthesis in vitro is imperfect. To determine if ribonucleotides are incorporated during DNA replication in vivo, we substituted leucine or glycine for an active site methionine in yeast DNA polymerase ε (Pol ε). Compared to wild type Pol ε, ribonucleotide incorporation in vitro was 3-fold lower for M644L and 11-fold higher for M644G Pol ε. This hierarchy was re-capitulated in vivo in yeast strains lacking RNase H2. Moreover, the pol2-M644G rnh201Δ strain progressed more slowly through S-phase, had elevated dNTP pools and generated 2–5 base pair deletions in repetitive sequences at a high rate and gene orientation-dependent manner. The data indicate that ribonucleotides are incorporated during replication in vivo, that they are removed by RNase H2-dependent repair, and that defective repair results in replicative stress and genome instability via DNA strand misalignment.
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Affiliation(s)
- Stephanie A Nick McElhinny
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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