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.
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•A multidimensional assay for HIV-1 reservoir cell profiling is presented (PRIP-seq)•Transcriptionally active HIV-1 proviruses are actively selected against during ART•Large transcriptionally active proviral clones resist negative host selection forces•Epigenetic signals in linear and 3D chromatin contacts influence HIV-1 transcription
PRIP-seq is a multidimensional single-cell assay that simultaneously captures the proviral sequence, the corresponding chromosomal integration site, and the expression of HIV-1 RNA in single virally infected cells and allows for the global mapping of transcriptionally active and silent proviruses in patients receiving suppressive antiretroviral therapy.
Sexual and gender minority (SGM) people, including lesbian, gay, bisexual, transgender, and queer individuals, are a diverse population with a wide spectrum of gynecologic needs. Institutionalized ...cisheteronormativity, stigmatization, lack of provider training, and fear of discrimination contribute to health disparities in this patient population. In this article, we review key topics in the gynecologic care of SGM patients and provide strategies to enable gynecologists to provide SGM people with equitable and inclusive full spectrum reproductive health care.
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
deletions in intact proviruses, consistent with increased viral vulnerability to host immunity in the setting of
dysfunction. Together, these results suggest a distinct signature of immune footprints in proviral sequences from ECs.
Infection with Chlamydia trachomatis drives severe mucosal immunopathology; however, the immune responses that are required for mediating pathology vs. protection are not well understood. Here, we ...employed a mouse model to identify immune responses required for C. trachomatis-induced upper genital tract pathology and to determine whether these responses are also required for bacterial clearance. In mice as in humans, immunopathology was characterized by extravasation of leukocytes into the upper genital tract that occluded luminal spaces in the uterus and ovaries. Flow cytometry identified these cells as neutrophils at early time points and CD4⁺ and CD8⁺ T cells at later time points. To determine what draws these cells to C. trachomatis-infected tissue, we measured the expression of 700 inflammation-related genes in the upper genital tract and found an up-regulation of many chemokines, including a node of interaction between CXCL9/10/11 and their common receptor CXCR3. Either depleting neutrophils or reducing T-cell numbers by CXCR3 blockade was sufficient to significantly ameliorate immunopathology but had no effect on bacterial burden, demonstrating that these responses are necessary for mucosal pathology but dispensable for C. trachomatis clearance. Therapies that specifically target these host responses may therefore prove useful in ameliorating C. trachomatis-induced pathology without exacerbating infection or transmission.
HIV-1 establishes a life-long reservoir of virally infected cells which cannot be eliminated by antiretroviral therapy (ART). Here, we demonstrate a markedly altered viral reservoir profile of ...long-term ART-treated individuals, characterized by large clones of intact proviruses preferentially integrated in heterochromatin locations, most prominently in centromeric satellite/micro-satellite DNA. Longitudinal evaluations suggested that this specific reservoir configuration results from selection processes that promote the persistence of intact proviruses in repressive chromatin positions, while proviruses in permissive chromosomal locations are more likely to be eliminated. A bias toward chromosomal integration sites in heterochromatin locations was also observed for intact proviruses in study participants who maintained viral control after discontinuation of antiretroviral therapy. Together, these results raise the possibility that antiviral selection mechanisms during long-term ART may induce an HIV-1 reservoir structure with features of deep latency and, possibly, more limited abilities to drive rebound viremia upon treatment interruptions.
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•After LT-ART, intact HIV proviruses are predominantly integrated in heterochromatin•These distinct integration sites result from longitudinal selection mechanisms•No similar selection processes are observed for defective proviruses•Intact proviruses are mainly integrated in heterochromatin in post-treatment controllers
Lian et al. show that following two decades of continuous antiretroviral therapy, the integration site profile of intact HIV-1 proviruses is heavily biased toward heterochromatin locations, likely as a result of immune selection mechanisms; such proviruses are less transcriptionally active and, possibly, less rebound competent.
An effective vaccine against
is urgently needed as infection rates continue to rise and
causes reproductive morbidity. An obligate intracellular pathogen,
employs a type 3 secretion system (T3SS) for ...host cell entry. The tip of the injectosome is composed of the protein CT584, which represents a potential target for neutralization with vaccine-induced antibody. Here, we investigate the immunogenicity and efficacy of a vaccine made of CT584 epitopes coupled to a bacteriophage virus-like particle (VLP), a novel platform for
vaccines modeled on the success of HPV vaccines. Female mice were immunized intramuscularly, challenged transcervically with
and assessed for systemic and local antibody responses and bacterial burden in the upper genital tract. Immunization resulted in a 3-log increase in epitope-specific IgG in serum and uterine homogenates and in the detection of epitope-specific IgG in uterine lavage at low levels. By contrast, sera from women infected with
and virgin controls had similarly low titers to CT584 epitopes, suggesting these epitopes are not systemically immunogenic during natural infection but can be rendered immunogenic by the VLP platform.
burden in the upper genital tract of mice varied after active immunization, yet passive protection was achieved when immune sera were pre-incubated with
prior to inoculation into the genital tract. These data demonstrate the potential for antibody against the T3SS to contribute to protection against
and the value of VLPs as a novel platform for
vaccines.
CD4
T cells are central to long-term immunity against viruses through the functions of T helper 1 (T
1) and T follicular helper (T
) cell subsets. To better understand the role of these subsets in ...coronavirus disease 2019 (COVID-19) immunity, we conducted a longitudinal study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific CD4
T cell and antibody responses in convalescent individuals who seroconverted during the first wave of the pandemic in Boston, MA, USA, across a range of COVID-19 disease severities. Analyses of spike (S) and nucleocapsid (N) epitope-specific CD4
T cells using peptide and major histocompatibility complex class II (pMHCII) tetramers demonstrated expanded populations of T cells recognizing the different SARS-CoV-2 epitopes in most individuals compared with prepandemic controls. Individuals who experienced a milder disease course not requiring hospitalization had a greater percentage of circulating T
(cT
) and T
1 cells among SARS-CoV-2-specific cells. Analysis of SARS-CoV-2-specific CD4
T cells responses in a subset of individuals with sustained anti-S antibody responses after viral clearance also revealed an increased proportion of memory cT
cells. Our findings indicate that efficient early disease control also predicts favorable long-term adaptive immunity.
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