IFITM1 targets HIV-1 latently infected cells for antibody-dependent cytolysis

Single-Cell Profiling of Latently SIV-Infected CD4+ T Cells Directly Ex Vivo to Reveal Host Factors Supporting Reservoir Persistence

HIV-1 cure strategies aiming to eliminate persistent infected cell reservoirs are hampered by a poor understanding of cells harboring viral DNA in vivo. We describe a novel method to identify, enumerate, and characterize in detail individual cells infected in vivo using a combination of single-cell multiplexed assays for integrated proviral DNA, quantitative viral and host gene expression, and quantitative surface protein expression without any in vitro manipulation. Latently infected CD4+ T cells, defined as harboring integrated provirus in the absence of spliced viral mRNA, were identified from macaque lymph nodes during acute, chronic, and combination antiretroviral therapy (cART)-suppressed simian immunodeficiency virus (SIV) infection. Latently infected CD4+ T cells were most abundant during acute SIV (~8% of memory CD4+ T cells) and persisted in chronic and cART-suppressed infection. Productively infected cells actively transcribing viral mRNA, by contrast, were much more labile and declined substantially between acute and chronic or cART-suppressed infection. Expression of most surface proteins and host genes was similar between latently infected cells and uninfected cells. Elevated FLIP mRNA and surface CD3 expression among latently infected cells suggest increased survival potential and capacity to respond to T cell receptor stimulation. These findings point to a large pool of latently infected CD4+ T cells established very early in acute infection and upregulated host factors that may facilitate their persistence in vivo, both of which pose potential challenges to eliminating HIV-1 reservoirs. IMPORTANCE Effective combination antiretroviral therapy controls HIV-1 infection but fails to eliminate latent viral reservoirs that give rise to viremia upon treatment interruption. Strategies to eradicate latently infected cells require a better understanding of their biology and distinguishing features to promote their elimination. Tools for studying these cells from patients are currently limited. Here, we developed a single-cell method to identify cells latently infected in vivo and to characterize these cells for expression of surface proteins and host genes without in vitro manipulation, capturing their in vivo state from SIV-infected macaques. Host factors involved in cell survival and proliferation were upregulated in latently infected cells, which were abundant in the earliest stages of acute infection. These studies provide insight into the basic biology of latently infected cells as well as potential mechanisms underlying the persistence of HIV-1/SIV reservoirs to inform development of novel HIV-1 cure strategies.

Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

A detailed understanding of the mechanisms that establish or maintain the latent reservoir of HIV will guide approaches to eliminate persistent infection. We used a cell line and primary cell models of HIV latency to investigate viral RNA (vRNA) expression and the role of the host transcriptome using single-cell approaches. Single-cell vRNA quantitation identified distinct populations of cells expressing various levels of vRNA, including completely silent populations. Strikingly, single-cell RNA-seq of latently infected primary cells demonstrated that HIV downregulation occurred in diverse transcriptomic environments but was significantly associated with expression of a specific set of cellular genes. In particular, latency was more frequent in cells expressing a transcriptional signature that included markers of naive and central memory T cells. These data reveal that expression of HIV proviruses within the latent reservoir are influenced by the host cell transcriptional program. Therapeutic modulation of these programs may reverse or enforce HIV latency.

Markers of the HIV-1 reservoir: facts and controversies

PURPOSE OF REVIEW

The HIV-1 reservoir is composed of infected cells poised to replicate and spread the virus upon treatment interruption. It constitutes the main obstacle toward an HIV-1 cure. Whether marker(s) may allow the detection of cells that form the reservoir is an outstanding question. Here, we present and discuss recent advances and controversies in the identification and characterization of markers of the HIV-1 reservoir.

RECENT FINDINGS

Latently infected T cells that persist under successful therapy do not express viral antigens, making their identification challenging. HIV is not equally distributed across T cells subsets. For instance, central memory, Th17, and T follicular helper cells largely contribute to viral persistence. Recently, novel markers of the reservoir have been identified. Using various strategies, different teams have reported that surface molecules such as immune checkpoints inhibitors, CD30, or CD32a may be enriched in latently infected cells or in cells harboring viral RNA.

SUMMARY

Understanding the mechanisms underlying the presence of markers of HIV-1 infected cells will provide new insights into the formation and maintenance of the viral reservoir. These markers should also facilitate the detection of persistently infected cells in patients' samples and in animal models, and represent potential targets for elimination of these cells.

IFITM1 expression is crucial to gammaherpesvirus infection, in vivo

The oncogenic gammaherpesviruses, Epstein–Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV), are etiologically associated with a variety of human cancers, including Burkitt’s lymphoma (BL), Hodgkin lymphoma (HL), Kaposi’s sarcoma (KS), and primary effusion lymphoma (PEL). Recently, we demonstrated KSHV infection of B- and endothelial cells to significantly upregulate the expression of interferon induced transmembrane protein 1 (IFITM1) which in turn enhances virus entry. This is an extension of the above study. In here, we determined EBV infection of cells to trigger IFITM1 expression, in vitro. Silencing IFITM1 expression using siRNA specifically lowered gammaherpesvirus infection of cells at a post binding stage of entry. A natural model system to explore the effect of IFITM1 on gammaherpesvirus infection in vivo is infection of BALB/c mice with murine gammaherpesvirus 68 (MHV-68). Priming mice with siRNA specific to IFITM1 significantly lowered MHV-68 titers in the lung specimens compared to priming with (NS)siRNA or PBS. MHV-68 titers were monitored by plaque assay and qPCR. Taken together, for the first time, this study provides insight into the critical role of IFITM1 to promoting in vivo gammaherpesvirus infections.

Human interleukin-34-derived macrophages have increased resistance to HIV-1 infection

The establishment of latent HIV-1 reservoirs in terminally differentiated cells represents a major impediment to the success of antiretroviral therapies. Notably, macrophages (Mϕs) are susceptible to HIV-1 infection and recent evidence suggests that they may be involved in long-term HIV-1 persistence. While the extensive functional heterogeneity seen across the Mϕ cell lineage parallels the spectrum of HIV-1 susceptibility reported across these cell subsets, the facets of Mϕ HIV-1 resistance and susceptibility remain to be fully defined. Notably, the differentiation of most Mϕ subsets depends on signaling through the macrophage colony-stimulating factor receptor (M-CSFR), which in addition to M-CSF, is now known to bind the unrelated interleukin-34 (IL-34) cytokine. The biological need for two M-CSFR ligands awaits full elucidation. Here, we report that Mϕs differentiated from human peripheral blood monocytes with IL-34 are substantially more resistant to HIV-1 infection than M-CSF-derived Mϕs. Moreover, while both Mϕ subsets express comparable surface protein levels of the HIV-1 receptor and co-receptor, CD4 and CCR5 respectively, the IL-34-Mϕs express significantly greater levels of pertinent restriction factor genes, potentially accounting for their greater resistance to HIV-1 infection than that observed in M-CSF-Mϕs. Together, our findings underline previously unexplored differentiation pathways resulting in HIV-1-susceptible and resistant Mϕ subsets and pave the way for further research that may overcome one of the last major hurdles in developing more successful antiretroviral therapy.

A flow cytometry based assay that simultaneously measures cytotoxicity and monocyte mediated antibody dependent effector activity

Antibody effector functions such as antibody dependent cellular cytotoxicity (ADCC) and antibody dependent cellular phagocytosis (ADCP) are considered important immunologic parameters following results from the RV144 clinical trial where a reduced risk of infection was associated with non-neutralizing antibody against the V1/V2 region of HIV envelope. The rapid and fluorometric ADCC (RFADCC) assay has been widely used to measure ADCC, however, the mechanism behind the activity measured remains unclear. Here, we demonstrate that monocytes acquire the PKH26 dye used in the RFADCC assay and that the commonly used RFADCC readout correlates with phagocytosis. The RFADCC assay was combined with an amine reactive dye staining to confirm target cell killing. Interestingly, the majority of RFADCC and amine indices were mutually exclusive. In fact, the amine reactive assay results correlated with results from another assays that directly measure NK cell antibody effector functions not associated with phagocytosis. Together, this combined assay offers the opportunity to discriminate monocytes and NK cell antibody effector functions simultaneously.

SERPING1 mRNA overexpression in monocytes from HIV+ patients

OBJECTIVE

The HIV-1 virus activates the complement system, an essential element of the immune system. SERPING1 is a protease inhibitor that disables C1r/C1s in the C1 complex of the classical complement pathway.

METHODS

In this paper, we performed an analysis of several microarrays deposited in GEO dataset to demonstrate that SERPING1 mRNA is modulated in CD14⁺ monocytes from HIV-1-infected individuals. In addition, data were validated on monocytes isolated from seronegative healthy volunteers, treated with IFNs.

RESULTS

Our analysis shows that SERPING1 mRNA is overexpressed in monocytes from HIV-1+ patients and the expression levels correlate positively with viral load and negatively with the CD4⁺ T-cell count. Of note, anti-retroviral therapy is able to reduce the levels of SERPING1 mRNA, ex vivo. In addition, we found that 30% of the SERPING1 genes network is upregulated in monocytes from HIV-1+ patients. Noteworthy, the expression levels of IFITM1-an antiviral molecule belonging to the genes network-correlate positively with SERPING1 expression. Interestingly, the monocytes treatment with IFN-gamma, IFN-beta and IFN-alpha significantly upregulates the SERPING1 mRNA expression levels.

CONCLUSIONS

From the outcome of our investigation, it is possible to conclude that SERPING1 and its network serve as important components of the innate immune system to restrict HIV-1 infection.