The human immunodeficiency virus (HIV), the virus that causes healthy adults to become immunosuppressed, integrates its viral genetic code into the genome of the immune CD4+ T cells. While antiretroviral therapy (ART) enables people living with HIV to suppress the virus and maintain their immune response, the integrated viral DNA remains hidden, forming what is known as the HIV reservoir. This reservoir is a major barrier to a HIV cure since these cells can continue to grow and expand the HIV reservoir over time. Intriguingly, people who start ART soon after initial infection have less HIV reservoir expansion over time as compared those who start ART treatment later during chronic HIV infection. Several factors may influence this difference including where HIV integration occurs within the genome of the CD4+ T cells. The relationship between HIV integration and gene expression depends on whether the DNA is open and accessible or closed and inaccessible, a feature that also controls if a gene is expressed or silent. Because of this dependency on “open” versus “closed” DNA state for HIV integration, Dr. Paul Edlefsen’s Group at Fred Hutchinson Cancer Center and Dr. Lisa Frenkel’s Lab at Seattle Children’s Research Institute / University of Washington combined their skills to investigate if timing of ART initiation impacts where HIV integrates into the host genome to better understand how this might affect cure strategies aimed at eliminating the HIV reservoir. Their findings, published in the Journal of Clinical Investigation, provide new insights into how timing of ART administration for HIV has secondary consequences of altered HIV site integration.
During early infection, CD4+ T cells that recognize HIV antigens are activated and express antiviral genes to try to clear the virus. Conversely, chronic infection is associated with CD4+ T cell exhaustion. The researchers predicted that these differences of gene expression profiles that alter chromatin accessibility plus the timing of ART administered will affect where HIV integrates into the genome. To explore this, the researchers performed several assays using peripheral blood mononuclear cells (PBMC) from people living with HIV who either received ART less than 1.5 months following HIV infection—during acute infection—or more than 6 months following HIV infection—during chronic infection. The whole cohort of 11 individuals had no or low HIV viral levels for more than 2 years and had high CD4+ T cell counts, two criteria that are consistent with adherence to ART treatment and continued suppression of HIV progeny production. From these studies, Dr. Frenkel shared, “We found that the HIV “reservoir” that persists during antiretroviral [ART] varies in (1) the antigen specificity of the HIV-infected CD4+ T-cells and (2) the genetic pathways in which HIV is integrated, depending on whether treatment is started during acute or chronic infection.” In other words, “if treatment was started during acute infection, then HIV is integrated disproportionately in HIV-specific CD4+ T-cells and is integrated in genes controlling lipid metabolism and HIF-1 –mediated hypoxia,” explained Dr. Frenkel. “Whereas if treatment is started in chronic infection the HIV-infected cells are more likely to target multiple herpesviruses, as well as HIV, and likely other infections, and integration is enriched in genes controlling EZH2 histone methylation.” Integration of HIV into genes associated with lipid metabolism and hypoxia may result in a growth advantage of these cells over other, uninfected CD4+ T cells since these pathways ramp up energy production to meet the needs of these activated, growing immune cells. Therefore, targeting these pathways that drive energy production may be feasible to reduce or eliminate HIV infected cells during acute infection. Integration of HIV into genes that control DNA methylation—a cellular process in which a methyl group is added to DNA to, in some cases, block gene expression—may reverse host-mediated silencing of host genes involved in cell growth or viral genes pertinent for virus production. As a result, therapeutic interventions that silence pro-growth genes or virus genes involved in replication may again tilt the scale in favor of ART successful suppression of virus production and may also reduce expansion of the HIV reservoir.
While ART can keep HIV in a dormant state and increase the abundance of CD4+ T cells and normalize immune function, these findings highlight additional targets specific to acute or chronic HIV infection conditions that may reduce the HIV reservoir and get us one step closer to a cure for HIV. “Our findings bring up several questions: whether (1) our findings are reproducible in additional populations and if so, (2) if differences in antigen specificities and integration sites of HIV-infected cells might be leveraged to develop new strategies to cure HIV infection,” shared Dr. Frenkel. These will be driving questions for future research from the Frenkel and Edlefsen groups. These novel findings and efforts to find a cure for HIV were part of a collaborative effort. “The cancer consortium has provided a wonderfully collaborative environment and enabled an effectively seamless collaboration among Fred Hutch, UW and Seattle Children’s research groups,” concluded Dr. Edlefsen.
The spotlighted research was funded by the US Public Health Services and the National Institutes of Health.
Fred Hutch/University of Washington/Seattle Children's Cancer Consortium members Drs. James I Mullins and Lisa Frenkel contributed to this work.
Joy J, Gervassi AL, Chen L, Kirshenbaum B, Styrchak S, Ko D, McLaughlin S, Shao D, Kosmider E, Edlefsen PT, Maenza J, Collier AC, Mullins JI, Horton H, Frenkel LM. 2024. Antigen specificities and proviral integration sites differ in HIV-infected cells by timing of antiretroviral treatment initiation. J Clin Invest. e159569.
Science spotlight writer Annabel Olson is a postdoctoral research fellow in the Nabet lab at Fred Hutchinson Cancer Center. Her research focuses on studying the mechanisms that drive cancer development for both genetic and virus-associated cancers. A key tool in her research is the use of targeted protein degradation to dissect dysregulated signaling pathways in cancer and double as a relevant therapeutic platform.