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.

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

10.1101/2020.09.15.298406 ◽

2020 ◽

Author(s):

Michael J. Bale ◽

Mary Grace Katusiime ◽

Daria Wells ◽

Xiaolin Wu ◽

Jonathan Spindler ◽

...

Keyword(s):

T Cell ◽

Infected Cell ◽

Mononuclear Cells ◽

Ex Vivo ◽

Peripheral Blood Mononuclear ◽

T Cell Clones ◽

Cell Clones ◽

Integration Sites ◽

Infected Cells

AbstractLittle is known about the emergence and persistence of HIV-infected T cell clones in perinatally-infected children. We analyzed peripheral blood mononuclear cells for clonal expansion in 11 children who initiated antiretroviral therapy (ART) between 1.8-17.4 months of age and with viremia suppressed for 6-9 years. We obtained 8,662 HIV-1 integration sites from pre-ART and 1,861 sites on ART. Expanded clones of infected cells were detected pre-ART in 10/11 children. In 8 children, infected cell clones detected pre-ART persisted for 6-9 years on ART. A comparison of integration sites in the samples obtained on ART with healthy donor PBMC 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.

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Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence

Journal of Experimental Medicine ◽

10.1084/jem.20211427 ◽

2021 ◽

Vol 218 (12) ◽

Author(s):

Amy S. Huang ◽

Victor Ramos ◽

Thiago Y. Oliveira ◽

Christian Gaebler ◽

Mila Jankovic ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Cd4 T Cells ◽

Cd4 T Cell ◽

Small Subset ◽

Major Barrier ◽

T Cell Clones ◽

Cell Clones ◽

Hiv 1

Latent intact HIV-1 proviruses persist in a small subset of long-lived CD4+ T cells that can undergo clonal expansion in vivo. Expanded clones of CD4+ T cells dominate latent reservoirs in individuals on long-term antiretroviral therapy (ART) and represent a major barrier to HIV-1 cure. To determine how integration landscape might contribute to latency, we analyzed integration sites of near full length HIV-1 genomes from individuals on long-term ART, focusing on individuals whose reservoirs are highly clonal. We find that intact proviruses in expanded CD4+ T cell clones are preferentially integrated within Krüppel-associated box (KRAB) domain–containing zinc finger (ZNF) genes. ZNF genes are associated with heterochromatin in memory CD4+ T cells; nevertheless, they are expressed in these cells under steady-state conditions. In contrast to genes carrying unique integrations, ZNF genes carrying clonal intact integrations are down-regulated upon cellular activation. Together, the data suggest selected genomic sites, including ZNF genes, can be especially permissive for maintaining HIV-1 latency during memory CD4+ T cell expansion.

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Self-sparing of long-term in vitro-cloned or uncloned cytotoxic T lymphocytes.

Journal of Experimental Medicine ◽

10.1084/jem.164.3.962 ◽

1986 ◽

Vol 164 (3) ◽

pp. 962-967 ◽

Cited By ~ 19

Author(s):

M F Luciani ◽

J F Brunet ◽

M Suzan ◽

F Denizot ◽

P Golstein

Keyword(s):

T Cell ◽

T Lymphocytes ◽

Cytotoxic T Lymphocytes ◽

Cytotoxic T Cell ◽

Cell Populations ◽

Con A ◽

T Cell Clones ◽

Cell Clones

At least some long-term in vitro-cultured cytotoxic T cell clones and uncloned cell populations are able, in the presence of Con A, to lyse other cells, to be lysed by other cells, but not to lyse themselves. This as-yet-unexplained result may have implications as to the mechanism of T cell-mediated cytotoxicity.

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Production of lymphokines derived from fusions of the AKR T-cell tumor BW5147 and selected high-producer T-cell clones in long-term culture

Cellular Immunology ◽

10.1016/0008-8749(82)90411-7 ◽

1982 ◽

Vol 70 (2) ◽

pp. 403-404 ◽

Cited By ~ 2

Author(s):

B. Kaltmann ◽

D. Gemsa ◽

L. Hültner ◽

U. Kees ◽

F. Marcucci ◽

...

Keyword(s):

T Cell ◽

Cell Tumor ◽

T Cell Clones ◽

Long Term Culture ◽

Cell Clones

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Establishing T Cell Memory by Adoptive Transfer of T Cell Clones.

Blood ◽

10.1182/blood.v108.11.866.866 ◽

2006 ◽

Vol 108 (11) ◽

pp. 866-866

Author(s):

Carolina Berger ◽

Michael C. Jensen ◽

Stanley R. Riddell

Keyword(s):

T Cells ◽

T Cell ◽

Adoptive Transfer ◽

Annexin V ◽

T Cell Memory ◽

T Cell Clones ◽

Cell Clones

Abstract Adoptive transfer of T cells has been employed to reconstitute T cell immunity to viruses such as cytomegalovirus (CMV) in immunodeficient allogeneic stem cell transplant (SCT) patients and is being investigated to treat malignancies. In the allogeneic SCT setting, the T cells are derived from the donor and need to be isolated as clones or highly pure populations to avoid graft-versus-host disease. CD8+ T cells can be divided into defined subsets including CD62L− effector memory (TEM) and central memory T cells (TCM) expressing the CD62L lymph node homing molecule. Both TCM and TEM can give rise to cytolytic effector T cells (TE) after antigen stimulation and can be expanded in vitro for immunotherapy. However, the potential of T cells derived from either the TEM or TCM subset to persist in vivo has not been investigated. We used a macaque model to determine whether reconstitution of T cell memory to CMV by adoptive transfer of CD8+ T cell clones depended on their origin from either the CD62L+ TCM or CD62L− TEM subset. T cell clones were retrovirally transduced to express the macaque CD19 or CD20 surface marker to allow tracking of T cells in vivo. Clones derived from both TCM and TEM had similar avidity and proliferative capacity in vitro, and had a TE phenotype (CD62L−CCR7−CD28−CD127−, granzyme B+). TCM and TEM-derived T cell clones were transferred to macaques at doses of 3–6×108/kg and were both detected in the blood one day after transfer at 1.2–2.7% (low dose) to 20–25% (high dose) of CD8+ T cells. However, the frequency of TEM-derived T cells was undetectable after 3–5 days, and the cells were not present in lymph node or bone marrow obtained at day 14. By contrast, TCM-derived clones persisted in peripheral blood, migrated to tissue sites, and were detectable long-term at significant levels. A distinguishing feature of TCM-derived cells was their responsiveness to homeostatic cytokines. Only TCM-derived clones were rescued from apoptotic cell death by low-dose IL15 for >30 days in vitro and this correlated with higher levels of IL15Rα, IL2Rβ, and IL2Rγ, and of Bcl-xL and Bcl-2, which promote cell survival. To determine if the inability of TEM-derived clones to survive in vitro correlated with an increased susceptibility of cell death in vivo, we measured the proportion of infused cells that were positive for propidium iodide (PI) and Annexin V during the short period of in vivo persistence. One day after transfer, 41–45% of TEM-derived T cells were Annexin V+/PI+, analyzed directly in the blood or after 24 hours of culture. By contrast, only a minor fraction of an adoptively transferred TCM-derived T cell clone was Annexin V+/PI+ and the infused cells survived in vivo. A subset of the persisting T cells reacquired TCM marker (CD62L+CCR7+CD127+CD28+) in vivo and regained functional properties of TCM (direct lytic activity; rapid proliferation to antigen). These T cells produced IFN-γ and TNF-α after peptide stimulation, and studies are in progress to assess their in vivo response to antigen by delivery of T cells expressing CMV proteins. Our studies in a large animal model show for the first time that CD8+ TE derived from TCM but not TEM can persist long-term, occupy memory T cell niches, and restore TCM subsets of CMV-specific immunity. Thus, taking advantage of the genetic programming of cells that have become TCM might yield T cells with greater therapeutic activity and could be targeted for human studies of T cell therapy for both viral and malignant disease.

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Gene expression changes in long-term culture of T-cell clones: genomic effects of chronic antigenic stress in aging and immunosenescence

Aging Cell ◽

10.1111/j.1474-9726.2007.00269.x ◽

2007 ◽

Vol 6 (2) ◽

pp. 155-163 ◽

Cited By ~ 17

Author(s):

Dawn J. Mazzatti ◽

Andrew White ◽

Rosalyn J. Forsey ◽

Jonathan R. Powell ◽

Graham Pawelec

Keyword(s):

Gene Expression ◽

T Cell ◽

T Cell Clones ◽

Long Term Culture ◽

Cell Clones ◽

Genomic Effects

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Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection

Journal of Virology ◽

10.1128/jvi.03474-14 ◽

2015 ◽

Vol 89 (8) ◽

pp. 4517-4526 ◽

Cited By ~ 71

Author(s):

William S. DeWitt ◽

Ryan O. Emerson ◽

Paul Lindau ◽

Marissa Vignali ◽

Thomas M. Snyder ◽

...

Keyword(s):

Immune Response ◽

T Cell ◽

Viral Infection ◽

High Throughput Sequencing ◽

Cell Receptor ◽

Cell Repertoire ◽

T Cell Clones ◽

Cell Clones ◽

Acute Viral Infection

ABSTRACTA detailed characterization of the dynamics and breadth of the immune response to an acute viral infection, as well as the determinants of recruitment to immunological memory, can greatly contribute to our basic understanding of the mechanics of the human immune system and can ultimately guide the design of effective vaccines. In addition to neutralizing antibodies, T cells have been shown to be critical for the effective resolution of acute viral infections. We report the first in-depth analysis of the dynamics of the CD8+T cell repertoire at the level of individual T cell clonal lineages upon vaccination of human volunteers with a single dose of YF-17D. This live attenuated yellow fever virus vaccine yields sterile, long-term immunity and has been previously used as a model to understand the immune response to a controlled acute viral infection. We identified and enumerated unique CD8+T cell clones specifically induced by this vaccine through a combined experimental and statistical approach that included high-throughput sequencing of the CDR3 variable region of the T cell receptor β-chain and an algorithm that detected significantly expanded T cell clones. This allowed us to establish that (i) on average, ∼2,000 CD8+T cell clones were induced by YF-17D, (ii) 5 to 6% of the responding clones were recruited to long-term memory 3 months postvaccination, (iii) the most highly expanded effector clones were preferentially recruited to the memory compartment, and (iv) a fraction of the YF-17D-induced clones could be identified from peripheral blood lymphocytes solely by measuring clonal expansion.IMPORTANCEThe exhaustive investigation of pathogen-induced effector T cells is essential to accurately quantify the dynamics of the human immune response. The yellow fever vaccine (YFV) has been broadly used as a model to understand how a controlled, self-resolving acute viral infection induces an effective and long-term protective immune response. Here, we extend this previous work by reporting the identity of activated effector T cell clones that expand in response to the YFV 2 weeks postvaccination (as defined by their unique T cell receptor gene sequence) and by tracking clones that enter the memory compartment 3 months postvaccination. This is the first study to use high-throughput sequencing of immune cells to characterize the breadth of the antiviral effector cell response and to determine the contribution of unique virus-induced clones to the long-lived memory T cell repertoire. Thus, this study establishes a benchmark against which future vaccines can be compared to predict their efficacy.

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