Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers

Increasing evidence suggests that durable drug-free control of HIV-1 replication is enabled by effective cellular immune responses that may induce an attenuated viral reservoir configuration with a weaker ability to drive viral rebound. Here, we comprehensively tracked effects of antiviral immune responses on intact and defective proviral sequences from elite controllers (ECs), analyzing both classical escape mutations and HIV-1 chromosomal integration sites as biomarkers of antiviral immune selection pressure. We observed that, within ECs, defective proviruses were commonly located in permissive genic euchromatin positions, which represented an apparent contrast to autologous intact proviruses that were frequently located in heterochromatin regions; this suggests differential immune selection pressure on intact versus defective proviruses in ECs. In comparison to individuals receiving antiretroviral therapy, intact and defective proviruses from ECs showed reduced frequencies of escape mutations in cytotoxic T cell epitopes and antibody contact regions, possibly due to the small and poorly inducible reservoir that may be insufficient to drive effective viral escape in ECs. About 15% of ECs harbored nef deletions in intact proviruses, consistent with increased viral vulnerability to host immunity in the setting of nef dysfunction. Together, these results suggest a distinct signature of immune footprints in proviral sequences from ECs.This work is supported by NIH grants HL134539 (to X.G.Y.), AI155171 (to X.G.Y.), AI116228 (to X.G.Y.), AI078799 (to X.G.Y.), DA047034 (to X.G.Y.), AI150396 (to X.G.Y.), the Bill and Melinda Gates Foundation (INV-002703) (to X.G.Y.), AI114235 (to M.L.), AI117841 (to M.L.), AI120008 (to M.L.), AI130005 (to M.L.), DK120387 (to M.L.), AI152979 (to M.L.), AI135940 (to M.L.), AI155233 (to M.L.), and the American Foundation for AIDS Research (amfAR#110181) (to M.L.). X.G.Y. and M.L. are members of the DARE Collaboratory (UM1AI126611) and the BEAT-HIV Martin Delaney Collaboratory (UM1 AI126620). E.R.-M. was supported by Consejo Superior de Investigaciones Científicas (CSIC) and by grant PI19/01127, Instituto de Salud Carlos III, Fondos FEDER, and Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades Junta de Andalucia (P20_01276). Support was also provided by the Harvard University and University of California at San Francisco (UCSF)/Gladstone Institute for HIV Cure Research Centers for AIDS Research (P30 AI060354 and P30 AI027763, respectively), which are supported by the following institutes and centers co-funded by and participating with the U.S. National Institutes of Health: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, and OAR. Additional support for the SCOPE cohort was provided by the Delaney AIDS Research Enterprise (DARE; AI096109 and A127966) and the amfAR Institute for HIV Cure Research (amfAR 109301). The International HIV Controller Cohort is supported by the Bill and Melinda Gates Foundation (OPP1066973), the Ragon Institute of MGH, MIT and Harvard, the NIH (R37 AI067073 to B.D.W.), and the Mark and Lisa Schwartz Family Foundation. This project has been funded in whole or in part with federal funds from the Frederick National Laboratory for Cancer Research, under contract no. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. government. This research was supported in part by the Intramural Research Program of the NIH, Frederick National Lab, Center for Cancer Research

Transcriptional Changes during Naturally Acquired Zika Virus Infection Render Dendritic Cells Highly Conducive to Viral Replication

Summary: Although dendritic cells are among the human cell population best equipped for cell-intrinsic antiviral immune defense, they seem highly susceptible to infection with the Zika virus (ZIKV). Using highly purified myeloid dendritic cells isolated from individuals with naturally acquired acute infection, we here show that ZIKV induces profound perturbations of transcriptional signatures relative to healthy donors. Interestingly, we noted a remarkable downregulation of antiviral interferon-stimulated genes and innate immune sensors, suggesting that ZIKV can actively suppress interferon-dependent immune responses. In contrast, several host factors known to support ZIKV infection were strongly upregulated during natural ZIKV infection; these transcripts included AXL, the main entry receptor for ZIKV; SOCS3, a negative regulator of ISG expression; and IDO-1, a recognized inducer of regulatory T cell responses. Thus, during in vivo infection, ZIKV can transform the transcriptome of dendritic cells in favor of the virus to render these cells highly conducive to ZIKV infection. : Sun et al. find distinct transcriptional signatures in myeloid dendritic cells isolated from individuals with naturally acquired Zika Virus infection. These data indicate that Zika virus can reprogram dendritic cells to increase their susceptibility to further ZIKV infection. Keywords: Zika virus, flavivirus, interferon stimulated genes, dendritic cells, acute infection, RNA-seq, SOCS3, IDO-1, AX

Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses.

HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently considered transcriptionally silent, but active viral gene expression may occur in some cells, challenging the concept of viral latency. Applying an assay for profiling the transcriptional activity and the chromosomal locations of individual proviruses, we describe a global genomic and epigenetic map of transcriptionally active and silent proviral species and evaluate their longitudinal evolution in persons receiving suppressive ART. Using genome-wide epigenetic reference data, we show that proviral transcriptional activity is associated with activating epigenetic chromatin features in linear proximity of integration sites and in their inter- and intrachromosomal contact regions. Transcriptionally active proviruses were actively selected against during prolonged ART; however, this pattern was violated by large clones of virally infected cells that may outcompete negative selection forces through elevated intrinsic proliferative activity. Our results suggest that transcriptionally active proviruses are dynamically evolving under selection pressure by host factors

Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals

Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals. Here, we show a significant increase of HIV burden in the CD4+ T cells of infected individuals during ATI that was correlated with the level of plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters, including markers of exhaustion and activation, returned to pre-ATI levels 6–12 months after the study participants resumed ART. Of note, the proportions of near full-length, genome-intact and structurally defective HIV proviral DNA sequences were similar prior to ATI and following reinitiation of ART. In addition, there was no evidence of emergence of antiretroviral drug resistance mutations within intact HIV proviral DNA sequences following reinitiation of ART. These data demonstrate that short-term ATI does not necessarily lead to expansion of the persistent HIV reservoir nor irreparable damages to the immune system in the peripheral blood, warranting the inclusion of ATI in future clinical trials evaluating curative strategies

Extensive virologic and immunologic characterization in an HIV-infected individual following allogeneic stem cell transplant and analytic cessation of antiretroviral therapy: A case study.

BackgroundNotwithstanding 1 documented case of HIV-1 cure following allogeneic stem cell transplantation (allo-SCT), several subsequent cases of allo-SCT in HIV-1 positive individuals have failed to cure HIV-1 infection. The aim of our study was to describe changes in the HIV reservoir in a single chronically HIV-infected patient on suppressive antiretroviral therapy who underwent allo-SCT for treatment of acute lymphoblastic leukemia.Methods and findingsWe prospectively collected peripheral blood mononuclear cells (PBMCs) by leukapheresis from a 55-year-old man with chronic HIV infection before and after allo-SCT to measure the size of the HIV-1 reservoir and characterize viral phylogeny and phenotypic changes in immune cells. At day 784 post-transplant, when HIV-1 was undetectable by multiple measures-including PCR measurements of both total and integrated HIV-1 DNA, replication-competent virus measurement by large cell input quantitative viral outgrowth assay, and in situ hybridization of colon tissue-the patient consented to an analytic treatment interruption (ATI) with frequent clinical monitoring. He remained aviremic off antiretroviral therapy until ATI day 288, when a low-level virus rebound of 60 HIV-1 copies/ml occurred, which increased to 1,640 HIV-1 copies/ml 5 days later, prompting reinitiation of ART. Rebounding plasma HIV-1 sequences were phylogenetically distinct from proviral HIV-1 DNA detected in circulating PBMCs before transplantation. The main limitations of this study are the insensitivity of reservoir measurements, and the fact that it describes a single case.Conclusionsallo-SCT led to a significant reduction in the size of the HIV-1 reservoir and a >9-month-long ART-free remission from HIV-1 replication. Phylogenetic analyses suggest that the origin of rebound virus was distinct from the viruses identified pre-transplant in the PBMCs

Impact of ATI and reinitiation of ART on HIV reservoirs.

<p>(<b>A</b>) Longitudinal measurements of plasma viremia (red triangles) and the frequency of CD4⁺ T cells carrying HIV DNA (blue triangles) from study participants are shown. The grey bars indicate duration of ATI. One participant (N04) self-administered antiretroviral drugs for 3 days during the ATI period. (<b>B</b>) Relationship between the level of peak plasma viremia and % increase of the frequency of CD4⁺ T cells carrying HIV DNA during the ATI phase over baseline. The % HIV DNA increase was calculated as follows: ((copy number of HIV DNA/10⁶ CD4⁺ T cells at ATI—copy number of HIV DNA/10⁶ CD4⁺ T cells at baseline)/copy number of HIV DNA/10⁶ CD4⁺ T cells at baseline)*100. (<b>C</b>) Kinetics of HIV DNA burden in CD4⁺ T cells of 10 study participants prior to ATI (Pre-ATI), during ATI (ATI), and after reinitiation of ART (Post-ATI). (<b>D</b>) Dynamics of cell-associated HIV RNA in CD4⁺ T cells of study participants prior to ATI (Pre-ATI) during ATI (ATI) and after reinitiation of ART (Post-ATI). (E) Ratios between the level of cell-associated HIV RNA and DNA. (<b>F</b>) Impact of ATI and reinitiation of ART on the level of CD4⁺ T cells carrying replication-competent HIV in 6 study participants in whom longitudinal leukapheresis was performed. Statistical significance was tested with Wilcoxon’s signed rank test for panels C, D, E, and F. A correlation was determined by the Spearman rank method for panel b. **<i>P</i> < 0.01, ns, not significant.</p

Immunologic parameters monitored for the duration of the trial.

<p>(<b>A</b>) CD4⁺ and (<b>B</b>) CD8⁺ T cell counts and percentages prior to treatment interruption (Pre-ATI), during ATI (ATI), and following reinitiation of ART (Post-ATI) and levels of (<b>C</b>) B cells, (<b>D</b>) NK cells, and (<b>E</b>) CD8⁺ T cells expressing CD38 and HLA-DR prior to treatment interruption (Pre-ATI), during ATI (ATI), and following reinitiation of ART (Post-ATI).</p