HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity
Abstract Background Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERIN...
| Main Authors: | , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2023
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| Online Access: | https://hdl.handle.net/1721.1/150334 |
| _version_ | 1811090151720353792 |
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| author | Naicker, Delon Sonela, Nelson Jin, Steven W. Mulaudzi, Takalani Ojwach, Doty Reddy, Tarylee Brockman, Mark A. Brumme, Zabrina L. Ndung’u, Thumbi Mann, Jaclyn K. |
| author2 | Ragon Institute of MGH, MIT and Harvard |
| author_facet | Ragon Institute of MGH, MIT and Harvard Naicker, Delon Sonela, Nelson Jin, Steven W. Mulaudzi, Takalani Ojwach, Doty Reddy, Tarylee Brockman, Mark A. Brumme, Zabrina L. Ndung’u, Thumbi Mann, Jaclyn K. |
| author_sort | Naicker, Delon |
| collection | MIT |
| description | Abstract
Background
Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed.
Results
No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant.
Conclusions
These results suggest that SERINC5 down-regulation is a significant contributor to overall Nef function and identify potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics. |
| first_indexed | 2024-09-23T14:35:18Z |
| format | Article |
| id | mit-1721.1/150334 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:35:18Z |
| publishDate | 2023 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/1503342024-01-22T17:39:06Z HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity Naicker, Delon Sonela, Nelson Jin, Steven W. Mulaudzi, Takalani Ojwach, Doty Reddy, Tarylee Brockman, Mark A. Brumme, Zabrina L. Ndung’u, Thumbi Mann, Jaclyn K. Ragon Institute of MGH, MIT and Harvard Abstract Background Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed. Results No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant. Conclusions These results suggest that SERINC5 down-regulation is a significant contributor to overall Nef function and identify potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics. 2023-04-03T12:13:40Z 2023-04-03T12:13:40Z 2023-03-31 2023-04-03T04:59:08Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/150334 Retrovirology. 2023 Mar 31;20(1):3 PUBLISHER_CC en https://doi.org/10.1186/s12977-023-00618-7 Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s) application/pdf BioMed Central BioMed Central |
| spellingShingle | Naicker, Delon Sonela, Nelson Jin, Steven W. Mulaudzi, Takalani Ojwach, Doty Reddy, Tarylee Brockman, Mark A. Brumme, Zabrina L. Ndung’u, Thumbi Mann, Jaclyn K. HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity |
| title | HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity |
| title_full | HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity |
| title_fullStr | HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity |
| title_full_unstemmed | HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity |
| title_short | HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity |
| title_sort | hiv 1 subtype c nef mediated serinc5 down regulation significantly contributes to overall nef activity |
| url | https://hdl.handle.net/1721.1/150334 |
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