Early Emergence and Long-Term Persistence of HIV-Infected T-Cell Clones in Children

Abstract

Little is known about the emergence and persistence of human immunodeficiency virus (HIV)-infected T-cell clones in perinatally infected children. We analyzed peripheral blood mononuclear cells (PBMCs) for clonal expansion in 11 children who initiated antiretroviral therapy (ART) between 1.8 and 17.4 months of age and with viremia suppressed for 6 to 9 years. We obtained 8,662 HIV type 1 (HIV-1) integration sites from pre-ART samples and 1,861 sites from on-ART samples. Expanded clones of infected cells were detected pre-ART in 10/11 children. In 8 children, infected cell clones detected pre-ART persisted for 6 to 9 years on ART. A comparison of integration sites in the samples obtained on ART with healthy donor PBMCs infected ex vivo showed selection for cells with proviruses integrated in BACH2 and STAT5B. Our analyses indicate that, despite marked differences in T-cell composition and dynamics between children and adults, HIV-infected cell clones are established early in children, persist for up to 9 years on ART, and can be driven by proviral integration in proto-oncogenes. IMPORTANCE HIV-1 integrates its genome into the DNA of host cells. Consequently, HIV-1 genomes are copied with the host cell DNA during cellular division. Pediatric immune systems differ significantly from adults, consisting primarily of naive T cells, which have low expression of the HIV-1 coreceptor CCR5. This difference may result in variances in the number or size of infected cell clones that persist in children on ART. Here, we provide the most extensive analysis of the integration landscape of HIV-1 in children. We found that, despite the largely naive cell populations in neonatal immune systems, patterns of HIV-1 integration and the size of infected cell clones are as large and widespread as those in adults. Furthermore, selection for integration events in proto-oncogenes were observed in children despite early ART. If such cell clones persist for the life span of these individuals, there may be long-term consequences that have yet to be realized.

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

“…Previous studies have analyzed integration sites that arose in vivo before the initiation of ART ( 16 , 37 ) and then during ART treatment ( 12–14 , 16 , 37 , 48 , 66 ). Critically, however, the precise interplay among genic integration sites that arise during the initial wave of HIV-1 infection, which was modeled herein using in vitro datasets, with these patient-derived populations is not clearly understood.…”

“…Of the 10 integration site datasets derived from WT transformed and primary cells infected in vitro in this study, the following 8 were published previously: HEK293T #1 ( 20 , 27 ), HEK293T #3 ( 31 ), Jurkat #2 ( 40 ), Jurkat #3 ( 40 ), peripheral blood mononuclear cells (PBMCs) ( 47 , 48 ), monocyte-derived macrophages (MDM) ( 46 ), elite controller (EC) primary CD4+ T cell ( 49 ), and HIV negative primary CD4+ T cell ( 49 ) (see Supplementary Table S2 for numbers of integration sites as well as genomic DNA fragmentation and library construction methodologies). Matched HEK293T #1, HEK293T LKO, HEK293T CKO, and HEK293T double knockout (DKO) datasets were previously described ( 20 , 27 ), as were matched Jurkat #2, LKO Jurkat #1, and LKO Jurkat #2 datasets ( 40 ) ( Supplementary Table S2 ).…”

HIV-1 Persistence in Children during Suppressive ART

“…In perinatally infected children in the CHER cohort, HIV-infected cell clones were detectable before ART initiation and remained detectable up to 9 years on suppressive treatment. In another study, a child who initiated treatment within the first week of life had a potential clone detected 7 hours after birth, suggesting that early ART alone does not interfere with the proliferation of infected cells [105,127]. In adults, clones expand to detectable levels by 4 weeks post-infection (Fiebig stage V) [128].…”

“…Rarely, the site of proviral integration in the host genome, particularly sites in genes responsible for cell growth and survival, may drive the proliferation of infected cell clones or, at least, promote their survival [116,120,124,130,131]. In children, selection for integrations in STAT5B and BACH2 was observed both prior to and during long-term ART [127]. However, antigenic stimulus is likely the greatest contributor to the persistence of infected clones.…”

Insights from Clonal Expansion and HIV Persistence in Perinatal Infections

“…The integration into these genes may also favor certain CD4 T cell subsets, such as T regulatory cells ( 15 ). Bale and Katusiime et al ( 16 ) have shown that these patterns also appear in the setting of early treated perinatal infection, suggesting that integrated provirus in this region also confers an evolutionary advantage even in the context of an immature immune system. The epigenetic landscape of these infected cells is also drastically different in infants ( 17 ), and this may in turn affect integration site and the level of epigenetic repression under ART.…”