Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells
ABSTRACT Integration site landscapes, clonal dynamics, and latency reversal with or without vpr were compared in HIV-1-infected Jurkat cell populations, and the properties of individual clones were defined. Clones differed in fractions of long terminal repeat (LTR)-active daughter cells, with some c...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-04-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.03748-21 |
| _version_ | 1828351586256027648 |
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| author | Edmond Atindaana Abena Kissi-Twum Sarah Emery Cleo Burnett Jake Pitcher Myra Visser Jeffrey M. Kidd Alice Telesnitsky |
| author_facet | Edmond Atindaana Abena Kissi-Twum Sarah Emery Cleo Burnett Jake Pitcher Myra Visser Jeffrey M. Kidd Alice Telesnitsky |
| author_sort | Edmond Atindaana |
| collection | DOAJ |
| description | ABSTRACT Integration site landscapes, clonal dynamics, and latency reversal with or without vpr were compared in HIV-1-infected Jurkat cell populations, and the properties of individual clones were defined. Clones differed in fractions of long terminal repeat (LTR)-active daughter cells, with some clones containing few to no LTR-active cells, while almost all cells were LTR active for others. Clones varied over 4 orders of magnitude in virus release per active cell. Proviruses in largely LTR-active clones were closer to preexisting enhancers and promoters than low-LTR-active clones. Unsurprisingly, major vpr+ clones contained fewer LTR-active cells than vpr− clones, and predominant vpr+ proviruses were farther from enhancers and promoters than those in vpr− pools. Distances to these marks among intact proviruses previously reported for antiretroviral therapy (ART)-suppressed patients revealed that patient integration sites were more similar to those in the vpr+ pool than to vpr− integrants. Complementing vpr-defective proviruses with vpr led to the rapid loss of highly LTR-active clones, indicating that the effect of Vpr on proviral populations occurred after integration. However, major clones in the complemented pool and its vpr− parent population did not differ in burst sizes. When the latency reactivation agents prostratin and JQ1 were applied separately or in combination, vpr+ and vpr− population-wide trends were similar, with dual-treatment enhancement being due in part to reactivated clones that did not respond to either drug applied separately. However, the expression signatures of individual clones differed between populations. These observations highlight how Vpr, exerting selective pressure on proviral epigenetic variation, can shape integration site landscapes, proviral expression patterns, and reactivation properties. IMPORTANCE A bedrock assumption in HIV-1 population modeling is that all active cells release the same amount of virus. However, the findings here revealed that when HIV-infected cells expand into clones, each clone differs in virus production. Reasoning that this variation in expression patterns constituted a population of clones from which differing subsets would prevail under differing environmental conditions, the cytotoxic HIV-1 protein Vpr was introduced, and population dynamics and expression properties were compared in the presence and absence of Vpr. The results showed that whereas most clones produced fairly continuous levels of virus in the absence of Vpr, its presence selected for a distinct subset of clones with properties reminiscent of persistent populations in patients, suggesting the possibility that the interclonal variation in expression patterns observed in culture may contribute to proviral persistence in vivo. |
| first_indexed | 2024-04-14T01:41:18Z |
| format | Article |
| id | doaj.art-4b5520f5fe5940bc85035a35cf73229e |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-04-14T01:41:18Z |
| publishDate | 2022-04-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-4b5520f5fe5940bc85035a35cf73229e2022-12-22T02:19:44ZengAmerican Society for MicrobiologymBio2150-75112022-04-0113210.1128/mbio.03748-21Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat CellsEdmond Atindaana0Abena Kissi-Twum1Sarah Emery2Cleo Burnett3Jake Pitcher4Myra Visser5Jeffrey M. Kidd6Alice Telesnitsky7Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USAWest African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Greater Accra Region, GhanaHuman Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USADepartment of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USADepartment of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USADepartment of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USAHuman Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USADepartment of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USAABSTRACT Integration site landscapes, clonal dynamics, and latency reversal with or without vpr were compared in HIV-1-infected Jurkat cell populations, and the properties of individual clones were defined. Clones differed in fractions of long terminal repeat (LTR)-active daughter cells, with some clones containing few to no LTR-active cells, while almost all cells were LTR active for others. Clones varied over 4 orders of magnitude in virus release per active cell. Proviruses in largely LTR-active clones were closer to preexisting enhancers and promoters than low-LTR-active clones. Unsurprisingly, major vpr+ clones contained fewer LTR-active cells than vpr− clones, and predominant vpr+ proviruses were farther from enhancers and promoters than those in vpr− pools. Distances to these marks among intact proviruses previously reported for antiretroviral therapy (ART)-suppressed patients revealed that patient integration sites were more similar to those in the vpr+ pool than to vpr− integrants. Complementing vpr-defective proviruses with vpr led to the rapid loss of highly LTR-active clones, indicating that the effect of Vpr on proviral populations occurred after integration. However, major clones in the complemented pool and its vpr− parent population did not differ in burst sizes. When the latency reactivation agents prostratin and JQ1 were applied separately or in combination, vpr+ and vpr− population-wide trends were similar, with dual-treatment enhancement being due in part to reactivated clones that did not respond to either drug applied separately. However, the expression signatures of individual clones differed between populations. These observations highlight how Vpr, exerting selective pressure on proviral epigenetic variation, can shape integration site landscapes, proviral expression patterns, and reactivation properties. IMPORTANCE A bedrock assumption in HIV-1 population modeling is that all active cells release the same amount of virus. However, the findings here revealed that when HIV-infected cells expand into clones, each clone differs in virus production. Reasoning that this variation in expression patterns constituted a population of clones from which differing subsets would prevail under differing environmental conditions, the cytotoxic HIV-1 protein Vpr was introduced, and population dynamics and expression properties were compared in the presence and absence of Vpr. The results showed that whereas most clones produced fairly continuous levels of virus in the absence of Vpr, its presence selected for a distinct subset of clones with properties reminiscent of persistent populations in patients, suggesting the possibility that the interclonal variation in expression patterns observed in culture may contribute to proviral persistence in vivo.https://journals.asm.org/doi/10.1128/mbio.03748-21HIV-1 expression propertiesHIV-1 persistenceHIV-1 population dynamicsintegration siteslatency reactivationlatency-reversing agents |
| spellingShingle | Edmond Atindaana Abena Kissi-Twum Sarah Emery Cleo Burnett Jake Pitcher Myra Visser Jeffrey M. Kidd Alice Telesnitsky Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells mBio HIV-1 expression properties HIV-1 persistence HIV-1 population dynamics integration sites latency reactivation latency-reversing agents |
| title | Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells |
| title_full | Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells |
| title_fullStr | Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells |
| title_full_unstemmed | Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells |
| title_short | Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells |
| title_sort | bimodal expression patterns and not viral burst sizes predict the effects of vpr on hiv 1 proviral populations in jurkat cells |
| topic | HIV-1 expression properties HIV-1 persistence HIV-1 population dynamics integration sites latency reactivation latency-reversing agents |
| url | https://journals.asm.org/doi/10.1128/mbio.03748-21 |
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