Heterogeneity of HIV-1 Latent Reservoirs
Human immunodeficiency virus-1 (HIV-1) remains a global health challenge despite significant advancements in antiretroviral therapy (ART). While ART effectively suppresses viral replication, it does not eliminate the virus due to the existence of a stable viral latent reservoir. This reservoir consists of cells harboring replication-competent proviruses that can rekindle infection upon ART interruption. Understanding the heterogeneity of these latent reservoirs is crucial for developing effective strategies to achieve a functional cure for HIV-1. This article delves into the different cell types, mechanisms, and challenges associated with HIV-1 latent reservoirs, providing a comprehensive overview of the current state of research.
Introduction
HIV-1 integrates its viral genome into the host genome of infected cells, a critical step in the retroviral life cycle. A small fraction of these infected cells can survive in a resting state, avoiding immune clearance and cytotoxic effects. These latently infected cells, collectively known as the HIV-1 latent reservoir, can produce infectious viruses and reignite infection if ART is interrupted. Clinical data and mathematical modeling suggest that it could take more than 73 years for these reservoirs to decay to zero under continuous ART. The stability of these reservoirs makes them the primary barrier to viral elimination and the focal point of AIDS cure research.
The successful cases of the “Berlin Patient” and “London Patient,” who achieved functional cure through bone marrow transplantation, have ignited global enthusiasm for finding a cure for HIV-1. However, no significant reduction in the HIV-1 latent reservoir has been observed in other clinical trials. The heterogeneity of these reservoirs poses a significant challenge, necessitating a comprehensive understanding of their characteristics to develop effective therapeutic strategies.
Distribution of HIV-1 Latent Reservoirs in Various Cell Types and Subpopulations
HIV-1 can infect various cell types, including CD4+ T cells, macrophages, and dendritic cells. However, resting memory CD4+ T cells are the most studied and widely regarded as the primary latent reservoirs due to their unique physiological states and dynamic transition processes. Naive T cells (TN), the earliest differentiation state of mature CD4+ T cells, have the greatest proliferative potential and long half-life. Upon antigen exposure, TN cells differentiate into central memory T (TCM), transitional memory T (TTM), effector memory T (TEM), and terminally differentiated T (TTD) cells, identified by specific cell surface markers.
TCM cells are considered the primary component of the HIV-1 latent reservoir due to their abundance and long lifespan. TEM cells, with their shorter lifespan but higher proliferation rates, also harbor a significant portion of latent HIV-1. TTD cells, although a small proportion of the CD4+ T cell reservoir, can also carry integrated HIV-1 DNA. Resident memory T cells (TRM), distributed in tissues, have recently been identified as potential targets of HIV-1 infection and sites of viral persistence.
Besides memory T cell subsets, TN cells can differentiate into functional subsets, including Th1, Th2, Th17, follicular helper T (TFH), and regulatory T (Treg) cells, which also harbor replication-competent HIV-1. Th1/Th17 polarized CD4+ T helper cells are particularly significant as long-term HIV-1 reservoirs during ART. Treg cells, with their high frequency of HIV-1 provirus and role in immune regulation, present a challenge for specific eradication. The QUECEL method, which mimics T cell differentiation and infects them with a reporter pseudovirus, is a powerful tool for studying HIV-1 latency mechanisms.
TFH cells, expressing the C-X-C chemokine receptor type 5 (CXCR5), are major components of the HIV-1 latent reservoirs, more frequently infected by both productive and latent forms of the virus. The ratio of X4-tropic provirus in peripheral T follicular helper (pTFH) cells reflects disease progression and treatment outcomes during ART.
Non-T cell reservoirs, such as macrophages, also play a role in HIV-1 latency. Macrophages, key members of the innate immune system, can carry replication-competent HIV-1 provirus under ART in various tissues, including gut-associated lymphoid tissue, lymph node, brain, lung, urethra, and liver. Although infectious HIV-1 can be recovered from these macrophages, whether these viruses are in a low-level replicative state or truly latent remains unclear. Macrophages’ long lifespan, resistance to cytopathic effects, and tissue distribution make them an important barrier to HIV-1 reservoir elimination.
Astrocytes and microglia, macrophage-like cells in the central nervous system (CNS), are potential viral reservoirs in the brain. They can be infected by cell-to-cell contact with virus-carrying lymphocytes or by up-regulating CD4 and co-receptor expression. The blood-brain barrier makes them challenging to eliminate. The low frequency of latently infected cells in patients under suppressive ART, limited tissue sample availability, and lack of specific detection methods complicate the study of HIV-1 latent reservoir distribution.
Multifactorial Mechanisms Underlying HIV-1 Latency and Its Reversal
The transcriptionally silent state of HIV-1 provirus in ART-suppressed individuals is maintained through various mechanisms. Key initiation factors for HIV-1 transcription, such as nuclear factor kB (NF-kB) and nuclear factor of activated T cells (NFAT), are sequestered in the cytoplasm. The positive transcription elongation factor b (P-TEFb), critical for HIV-1 transcriptional elongation, is restricted in an inactive complex. Epigenetic modifications, including histone deacetylases (HDACs), histone methylases (HMTs), and DNA methyltransferases, also maintain proviral latency.
The “Shock and Kill” strategy is a promising approach for achieving a potential HIV-1 cure. “Shock” involves reactivating latently infected cells to express viral mRNA and produce viral proteins using latency reversal agents (LRAs). “Kill” involves eliminating these reactivated cells through enhanced cytotoxic effects and immune clearance. Various LRAs, including HDAC inhibitors (HDACi), histone methyltransferases inhibitors (HMTi), DNA methyltransferases inhibitors (DNMTi), protein kinase C (PKC) agonists, and P-TEFb activators, have been developed and tested in clinical trials.
HDAC inhibitors, such as vorinostat (SAHA) and panobinostat, increase acetylation of promoter regions, including HIV-1 LTR, to activate transcription. HMT inhibitors like BIX01294 and DNMT inhibitors like decitabine can activate viral gene expression, especially in combination with other LRAs. PKC agonists, such as prostratin and bryostatin-1, activate NF-kB by releasing it from its inhibitor IkB. P-TEFb activators like JQ-1 release the active form of P-TEFb, promoting viral transcriptional elongation.
Despite robust activities in vitro or ex vivo, no significant reduction in the latent reservoir has been reported in clinical trials. The unspecific global T cell activator phytohemagglutinin (PHA) was insufficient to reactivate all proviruses after a single dose, indicating that other factors may control viral latency and reactivation.
Diverse HIV-1 Integration Sites Add to the Heterogeneity of Latent Reservoir
HIV-1 integration sites significantly contribute to the heterogeneity of the latent reservoir. The pre-integration complex (PIC), containing viral integrase and HIV-1 DNA, interacts with the host chromatin-binding protein LEDGF/p75 to target the host genome. Integration is not entirely random, with a preference for active genes. However, latent and replication-competent proviruses can also be found in regions with low transcription levels.
Integration sites are distributed in both euchromatin and heterochromatin, with varying chromatin accessibility. Provirus integration in actively transcribed sites promotes efficient viral protein transcription, while integration in low transcription sites results in latency. The orientation of the provirus relative to the host gene also affects viral transcription, with parallel orientations increasing expression and antiparallel orientations reducing it.
Studies have identified numerous integration sites in latently infected cells from patients under long-term ART, with approximately 70% of locations targeted more than once related to cell growth or mitosis. Many identical integration sites exist in multiple cells within each patient, indicating clonal expansion of latently infected cells. Integration site-dependent clonal expansion is likely driven by increased transcription of pro-proliferation genes or loss of tumor suppressor gene function.
Potential Mechanisms Contributing to the Clonal Expansion of HIV-1 Latent Reservoirs
Clonal expansion of HIV-1 latent reservoirs is a significant mechanism maintaining their long-term stability. Three potential mechanisms drive this expansion: antigen-driven proliferation, homeostatic proliferation mediated by cytokines, and integration site-dependent proliferation. Antigen-driven proliferation, induced by tumor antigens or co-infected viral antigens, results in fluctuating expanded clones. Homeostatic proliferation, driven by cytokines like IL-7 and IL-15, is steady and evades immune surveillance. Integration site-dependent proliferation, driven by integration into pro-proliferation genes or loss of tumor suppressor gene function, increases over time.
Conclusion and Perspective
The heterogeneity of HIV-1 latent reservoirs presents significant challenges to achieving a functional cure for AIDS. Understanding the various cell types, mechanisms, and integration sites contributing to this heterogeneity is crucial for developing effective strategies. Future research should focus on targeting the diverse characteristics of latently infected cells, exploring the mechanisms of integration and clonal expansion, and developing interventions that reach different tissues and anatomical compartments.
doi.org/10.1097/CM9.0000000000001085
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