Functional anomaly of CD8 T cells at earlier differentiation stages during HIV infection as established by analysis of synaptic interface and degranulation pattern

It is thought that HIV infection could lead to a global defect in CD8+ T cell function. However, the effect of the infection on CD8+ T cells at various stages of differentiation has not been well studied. To evaluate the functional activity of CD8+ T cells from HIV infected people at various differentiation stages, we assessed their ability to form synaptic interfaces using planar lipid bilayers containing anti-CD3 antibody and soluble ICAM-1 ligand. We analyzed the dynamics of the T cell/bilayer interface formation, size of adhesion area, and kinetics of T-cell degranulation, parameters that are linked to the efficiency of CD8+ T cell functional activity. Unexpectedly, we observed that purified naïve CD8+ T cells (TN) and transitional memory (TTM) from HIV-infected individuals developed mature synapses whereas the same subsets from HIV uninfected individuals did not. While the kinetics of degranulation of naïve T cells was slower, both TN and TTM cells reached a similar extent of degranulation. The fraction and kinetics of CD27-CD45RO+ T cell degranulation were similar to that observed for TTM cells. Treatment with ART led to increase in the fraction of degranulating CD27-CD45RO+ T cells. As opposed to memory cells from healthy donors, a sizable fraction of CD27-CD45RO+ T cells from infected individuals develop lamellopodia and a larger adhesion area after synapse formation. These data suggest that less differentiated CD8+ T cells from HIV-infected people revealed functional anomaly that is likely mediated by aberrant functions of integrins and cytoskeleton causing changes in T-cell plasticity as a result of continuous inflammation during chronic HIV infection.

The Transcription Factor T-bet Resolves Memory B Cell Subsets with Distinct Tissue Distributions and Antibody Specificities in Mice and Humans

B cell subsets expressing the transcription factor T-bet are associated with humoral immune responses and autoimmunity. Here, we examined the anatomic distribution, clonal relationships, and functional properties of T-bet⁺ and T-bet^- memory B cells (MBCs) in the context of the influenza-specific immune response. In mice, both T-bet^- and T-bet⁺ hemagglutinin (HA)-specific B cells arose in germinal centers, acquired memory B cell markers, and persisted indefinitely. Lineage tracing and IgH repertoire analyses revealed minimal interconversion between T-bet^- and T-bet⁺ MBCs, and parabionts showed differential tissue residency and recirculation properties. T-bet⁺ MBCs could be subdivided into recirculating T-bet^lo MBCs and spleen-resident T-bet^hi MBCs. Human MBCs displayed similar features. Conditional gene deletion studies revealed that T-bet expression in B cells was required for nearly all HA stalk-specific IgG2c antibodies and for durable neutralizing titers to influenza. Thus, T-bet expression distinguishes MBC subsets that have profoundly different homing, residency, and functional properties, and mediate distinct aspects of humoral immune memory.

Identifying and targeting pathogenic PI3K/AKT/mTOR signaling in IL-6-blockade-refractory idiopathic multicentric Castleman disease

BACKGROUND

Idiopathic multicentric Castleman disease (iMCD) is a hematologic illness involving cytokine-induced lymphoproliferation, systemic inflammation, cytopenias, and life-threatening multi-organ dysfunction. The molecular underpinnings of interleukin-6(IL-6)-blockade refractory patients remain unknown; no targeted therapies exist. In this study, we searched for therapeutic targets in IL-6-blockade refractory iMCD patients with the thrombocytopenia, anasarca, fever/elevated C-reactive protein, reticulin myelofibrosis, renal dysfunction, organomegaly (TAFRO) clinical subtype.

METHODS

We analyzed tissues and blood samples from three IL-6-blockade refractory iMCD-TAFRO patients. Cytokine panels, quantitative serum proteomics, flow cytometry of PBMCs, and pathway analyses were employed to identify novel therapeutic targets. To confirm elevated mTOR signaling, a candidate therapeutic target from the above assays, immunohistochemistry was performed for phosphorylated S6, a read-out of mTOR activation, in three iMCD lymph node tissue samples and controls. Proteomic, immunophenotypic, and clinical response assessments were performed to quantify the effects of administration of the mTOR inhibitor, sirolimus.

RESULTS

Studies of three IL-6-blockade refractory iMCD cases revealed increased CD8+ T cell activation, VEGF-A, and PI3K/Akt/mTOR pathway activity. Administration of sirolimus significantly attenuated CD8+ T cell activation and decreased VEGF-A levels. Sirolimus induced clinical benefit responses in all three patients with durable and ongoing remissions of 66, 19, and 19 months.

CONCLUSION

This precision medicine approach identifies PI3K/Akt/mTOR signaling as the first pharmacologically-targetable pathogenic process in IL-6-blockade refractory iMCD. Prospective evaluation of sirolimus in treatment-refractory iMCD is planned (NCT03933904).

FUNDING

Castleman's Awareness & Research Effort/Castleman Disease Collaborative Network, Penn Center for Precision Medicine, University Research Foundation, Intramural NIH funding, and National Heart Lung and Blood Institute.

T follicular helper cells in human efferent lymph retain lymphoid characteristics

T follicular helper cells (Tfh), a subset of CD4+ T cells, provide requisite help to B cells in the germinal centers (GC) of lymphoid tissue. GC Tfh are identified by high expression of the chemokine receptor CXCR5 and the inhibitory molecule PD-1. Although more accessible, blood contains lower frequencies of CXCR5+ and PD-1+ cells that have been termed circulating Tfh (cTfh). However, it remains unclear whether GC Tfh exit lymphoid tissues and populate this cTfh pool. To examine exiting cells, we assessed the phenotype of Tfh present within the major conduit of efferent lymph from lymphoid tissues into blood, the human thoracic duct. Unlike what was found in blood, we consistently identified a CXCR5-bright PD-1-bright (CXCR5BrPD-1Br) Tfh population in thoracic duct lymph (TDL). These CXCR5BrPD-1Br TDL Tfh shared phenotypic and transcriptional similarities with GC Tfh. Moreover, components of the epigenetic profile of GC Tfh could be detected in CXCR5BrPD-1Br TDL Tfh and the transcriptional imprint of this epigenetic signature was enriched in an activated cTfh subset known to contain vaccine-responding cells. Together with data showing shared TCR sequences between the CXCR5BrPD-1Br TDL Tfh and cTfh, these studies identify a population in TDL as a circulatory intermediate connecting the biology of Tfh in blood to Tfh in lymphoid tissue.

T follicular regulatory cells (Tfr) reduce proliferation and downregulate induction of costimulatory molecules on human Tfh and B cells

Recently defined specialized subset of Treg expressing CXCR5+PD1+FoxP3+ termed as T follicular regulatory (Tfr) cells regulates T follicular helper (Tfh) mediated B cell high-affinity and isotype-switched antibody production. To date, much of our understanding of the suppression mechanism of Tfr cells has been obtained from animal studies. The mechanism of Tfr regulation of humoral immunity in humans is still understudied. Here, we used cells from human mesenteric lymph nodes to study how Tfr affect Tfh and B cells and what specific Tfr-induced changes occur on Tfh and B cells in vitro. We report that Tfr suppress both Tfh and B cell function and proliferation in a dose dependent manner. We find that Tfr downregulate CD40, CD80/CD86 and CD38 on B cells and CD28, OX40, ICOS and CD38 on Tfh cells. We also show that blocking immune checkpoint receptors inhibits Tfr suppression of Tfh and B cells and partially restores the Tfh mediated B cell antibody production. These findings reveal that Tfr regulate activation of Tfh and B cells by downregulating key costimulatory receptors and ligands that help induce activation in both Tfh and B cells. These changes ultimately lead to decreased proliferation of both B cells and Tfh and reduced production of immunoglobulin by B cells.

This research was supported in part by NIH R01 and VA.

Identity of recirculating T cells i humans

Memory T cells are widely considered to continually recirculate between tissues and blood via lymph to maintain immunosurveillance. While much effort has been dedicated to understand which memory T cells that are present in tissues, less is known about peripheral blood memory T cell subsets that recirculate through and egress from tissues during steady-state. Here we directly identify the tissue egressing (recirculating) immune system by sampling thoracic duct lymph (TDL), blood and peripheral tissues in humans and primates. We find that 70% of all immune cells egressing from tissues are T cells. Through transcriptional, functional, clonotypic, and epigenetic profiling, we find that cytolytic memory CD8+ T cell subsets are almost entirely confined to blood, while their phenotypic counterparts in TDL and many tissues represent non-cytolytic cells with higher regenerative capacity. Cytolytic T cells in blood possess a distinct clonotype distribution compared to TDL CCR7- T cells and are retained in blood after treatment with the tissue egress inhibitor fingolimod. We additionally find that HIV-specific CD8+ T cells can be readily found in TDL but again lack a cytolytic phenotype. We propose that cytolytic molecule expression is confined to a blood-resident memory T cell population in steady-state and that the intermediate differentiation status of HIV-specific CD8+ T cells is a fingerprint of their systemic recirculation capacity, rather than dysfunction, in humans.

High Throughput pMHC-I Multimer Library Production Using Chaperone-Mediated Peptide Exchange

The development of pMHC-multimer technologies has been indispensable for the characterisation of T cell responses to individual viral and tumor peptide antigens. Given the large variety of T cell receptors expressed in polyclonal repertoires, peptide exchange technologies are becoming increasingly important in providing a high throughput means of generating pMHC-multimer libraries, containing a wide range of antigens to probe such repertoires. Here we present a simple method for the isolation of empty MHC-I molecules which can be readily used for high throughput multimer library preparation. We utilise the chaperone TAPBPR, which binds MHC-I molecules and stabilises them in a peptide-receptive conformation, to isolate empty MHC-I molecules through the combination of placeholder peptides and small molecule competitors. We demonstrate that empty H-2Dd:TAPBPR and HLA-A*02:01:TAPBPR complexes can be stored long term and subsequently loaded with peptides of choice in a high throughput fashion to afford pMHC-multimer libraries. The resulting pMHC-multimers show equivalent flow cytometric properties to multimers made from MHC-I molecules refolded in vitro with synthetic peptides and are significantly improved relative to multimers prepared using peptide exchange of conditional ligands. Using this simple system to generate a library of oligonucleotide-labeled pMHC-multimers, combined with our recently described multi-modal cellular indexing technology (ECCITE-seq), we can identify distinct T cell receptor sequences present in polyclonal repertoires, together with their antigen specificities.

Limited recirculation of cytotoxic NK cells during normal homeostasis in humans

Natural killer (NK) cells are well known for their cytolytic functions to directly kill virus-infected and malignant cells. Two major NK cell populations exist in humans: Cytotoxic CD56dim and immunoregulatory CD56bright NK cells. Although NK cells are distributed throughout the human body, little is known about which NK cell populations that traffic tissues and egress from tissues to recirculate back to blood. Here, we set outto determine the recirculation patterns of human NK cell subsets during normal homeostasis through access to multiple types of tissues, blood, and thoracic duct lymph (TDL). Whereas cytotoxic NK cells were dominant in peripheral blood, non-lymphoid tissues (liver, uterus, duodenum, adipose tissue) were enriched for immunoregulatory NK cells expressing markers of tissue-residency. Similarly, few cytotoxic NK cells were present in secondary lymphoid organs and efferent lymph (TDL). Instead, afferent and efferent venous blood of human liver was similar in NK cell subset composition as peripheral blood, suggesting that cytotoxic NK cells are retained in vasculature during steady-state. Ongoing mechanistic efforts include assessment of NK cell subsets in patients before and after blocking cellular egress from tissues with FTY-720 (S1PR agonist) treatment. These results offer a revised model for NK cell subset trafficking behavior and suggests that cytotoxic NK cells have limited access to peripheral tissues during normal homeostasis.

Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue

Current paradigms of CD8⁺ T cell-mediated protection in HIV infection center almost exclusively on studies of peripheral blood, which is thought to provide a window into immune activity at the predominant sites of viral replication in lymphoid tissues (LTs). Through extensive comparison of blood, thoracic duct lymph (TDL), and LTs in different species, we show that many LT memory CD8⁺ T cells bear phenotypic, transcriptional, and epigenetic signatures of resident memory T cells (T_RMs). Unlike their circulating counterparts in blood or TDL, most of the total and follicular HIV-specific CD8⁺ T cells in LTs also resemble T_RMs Moreover, high frequencies of HIV-specific CD8⁺ T_RMs with skewed clonotypic profiles relative to matched blood samples are present in LTs of individuals who spontaneously control HIV replication in the absence of antiretroviral therapy (elite controllers). Single-cell RNA sequencing analysis confirmed that HIV-specific T_RMs are enriched for effector-related immune genes and signatures compared with HIV-specific non-T_RMs in elite controllers. Together, these data indicate that previous studies in blood have largely failed to capture the major component of HIV-specific CD8⁺ T cell responses resident within LTs.

Susceptibility to SIV Infection After Adenoviral Vaccination in a Low Dose Rhesus Macaque Challenge Model

Background:

Vaccination with the Merck human adenovirus serotype-5 (HAdV-5) vectored HIV-1 subtype B gag/pol/nef vaccine was unexpectedly associated with enhanced susceptibility to HIV-1 infection in uncircumcised HAdV-5 seropositive men. It has been hypothesized that vaccination may have resulted in activated CD4+ T lymphocytes trafficking to mucosal sites thereby increasing targets for HIV infection. We have previously shown that AdV-vector vacci-nation in rhesus macaques resulted in an increase in the frequency of activated mucosal CD4+ T cells. However, whether this increase in activation is sufficient to increase susceptibility to HIV/SIV infection is unclear.

Methods:

To examine this scenario, we developed a preliminary, proof-of-concept vaccination-challenge model in order to examine vaccine-induced SIV susceptibility in rhesus macaques. Rhesus macaques (n = 10/group) were vaccinated with a simian AdV-7 (SAdV-7)-vector encoding an irrelevant insert (SARS spike) and challenged 5 weeks post-prime in an escalating dosing regimen starting with sub-infectious doses (1:10,000 or 2TCID₅₀) of SIVmac251.

Results:

In contrast to our previous study, the SAdV-7 vaccine regimen did not induce detectable mucosal CD4+ T cell activation at the time points assessed in animals obtained from a different vendor and housed in a different facility. Within the power of the study, we did not observe significantly increased SIV acquisition in SAdV-7-vaccinated (5/10) versus placebo-vaccinated (3/10) macaques after repeated low-dose intra-rectal SIVmac251 challenge (P < 0.2).

Conclusions:

These results lay groundwork for future experiments to assess vaccine-induced SIV susceptibility in rhesus macaques. Further larger-scale studies are necessary to confirm the AdV-vector vaccination associated trend towards increased SIV/HIV acquisition and clarify associated mechanisms.

The receptor repertoire and functional profile of follicular T cells in HIV-infected lymph nodes

Follicular helper CD4⁺ T cells (T_FH) play an integral role in promoting B cell differentiation and affinity maturation. Whereas T_FH cell frequencies are increased in lymph nodes (LNs) from individuals infected with HIV, humoral immunity remains impaired during chronic HIV infection. Whether HIV inhibits T_FH responses in LNs remains unclear. Advances in this area have been limited by the difficulty of accessing human lymphoid tissues. Here, we combined high-dimensional mass cytometry with T cell receptor repertoire sequencing to interrogate the composition of T_FH cells in primary human LNs. We found evidence for intact antigen-driven clonal expansion of T_FH cells and selective utilization of specific complementarity-determining region 3 (CDR3) motifs during chronic HIV infection, but the resulting T_FH cells acquired an activation-related T_FH cell signature characterized by interleukin-21 (IL-21) dominance. These IL-21⁺ T_FH cells contained an oligoclonal HIV-reactive population that preferentially accumulated in patients with severe HIV infection and was associated with aberrant B cell distribution in the same LN. These data indicate that T_FH cells remain capable of responding to HIV antigens during chronic HIV infection but become functionally skewed and oligoclonally restricted under persistent antigen stimulation.

AAV8 Gene Therapy for Crigler-Najjar Syndrome in Macaques Elicited Transgene T Cell Responses That Are Resident to the Liver

Systemic delivery of adeno-associated viral (AAV) vectors has been evaluated for the treatment of several liver diseases, including homozygous familial hypercholesterolemia, ornithine transcarbamylase deficiency, and hemophilia. Here, we evaluated this approach for the treatment of Crigler-Najjar syndrome. We administered wild-type rhesus macaques with 1.0 × 10¹³ or 2.5 × 10¹³ genome copies/kg of an AAV serotype 8 vector expressing a codon-optimized version of human uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1) from a liver-specific promoter. We extensively studied vector biodistribution, transgene expression, and immune responses following vector administration. All rhesus macaques survived until their scheduled necropsy at day 56 and showed no clinical abnormalities during the course of the study. Macaques administered with either vector dose developed a T cell response to the AAV capsid and/or transgene. We mapped the immunodominant epitope in the human UGT1A1 sequence, and we found no correlation between peripheral and tissue-resident lymphocyte responses. Upon further investigation, we characterized CD107a⁺, granzyme B⁺, CD4⁺, and CD8⁺ transgene-specific cellular responses that were restricted to tissue-resident T cells. This study highlights the importance of studying immune responses at the vector transduction site and the limited usefulness of blood as a surrogate to evaluate tissue-restricted T cell responses.

Assessment of the Synaptic Interface of Primary Human T Cells from Peripheral Blood and Lymphoid Tissue

The current understanding of the dynamics and structural features of T-cell synaptic interfaces has been largely determined through the use of glass-supported planar bilayers and in vitro-derived T-cell clones or lines1,2,3,4. How these findings apply to the primary human T cells isolated from blood or lymphoid tissues is not known, partly due to significant difficulties in obtaining a sufficient number of cells for analysis5. Here we address this through the development of a technique exploiting multichannel flow slides to build planar lipid bilayers containing activating and adhesion molecules. The low height of the flow slides promotes rapid cell sedimentation in order to synchronize cell:bilayer attachment, thereby allowing researchers to study the dynamic of the synaptic interface formation and the kinetics of the granules release. We apply this approach to analyze the synaptic interface of as few as 104 to 105 primary cryopreserved T cells isolated from lymph nodes (LN) and peripheral blood (PB). The results reveal that the novel planar lipid bilayer technique enables the study of the biophysical properties of primary human T cells derived from blood and tissues in the context of health and disease.

HIV-Specific CD8+ T Cells Exhibit Reduced and Differentially Regulated Cytolytic Activity in Lymphoid Tissue

Elimination of lymphoid tissue reservoirs is a key component of HIV eradication strategies. CD8⁺ T cells play a critical role in control of HIV, but their functional attributes in lymph nodes (LNs) remain unclear. Here, we show that memory, follicular CXCR5⁺, and HIV-specific CD8⁺ T cells from LNs do not manifest the properties of cytolytic CD8⁺ T cells. While the frequency of follicular CXCR5⁺ CD8⁺ T cells was strongly inversely associated with peripheral viremia, this association was not dependent on cytolytic CXCR5⁺ CD8⁺ T cells. Moreover, the poor cytolytic activity of LN CD8⁺ T cells was linked to a compartmentalized dissociation between effector programming and the transcription factor T-bet. In line with this, activation of LN CD8⁺ T cells only partially induced the acquisition of cytolytic functions relative to peripheral blood CD8⁺ T cells. These results suggest that a state of immune privilege against CD8⁺ T cell-mediated cytolysis exists in lymphoid tissue, potentially facilitating the persistence of HIV.

Spatial distribution and function of T follicular regulatory cells in human lymph nodes

T follicular regulatory (Tfr) cells are a population of CD4⁺ T cells that express regulatory T cell markers and have been shown to suppress humoral immunity. However, the precise mechanisms and location of Tfr-mediated suppression in the lymph node (LN) microenvironment are unknown. Using highly multiplexed quantitative imaging and functional assays, we examined the spatial distribution, suppressive function, and preferred interacting partners of Tfr cells in human mesenteric LNs. We find that the majority of Tfr cells express low levels of PD-1 and reside at the border between the T cell zone and B cell follicle, with very few found in the germinal centers (GCs). Although PD-1⁺ Tfr cells expressed higher levels of CD38, CTLA-4, and GARP than PD-1^Neg Tfr cells, both potently suppressed antibody production in vitro. These findings highlight the phenotypic diversity of human Tfr cells and suggest that Tfr-mediated suppression is most efficient at the T-B border and within the follicle, not in the GC.

Novel strategies to assess the synaptic interface of primary human T cells from peripheral blood and lymphoid tissue

Our current understanding of the kinetics and structural features of T cell synaptic interfaces has largely been determined through the use of glass supported artificial bilayers and in vitro-derived T-cell clones or lines. How these findings apply to the primary human T cells isolated from blood or lymphoid tissues in unclear, given the significant difficulty in obtaining sufficient amounts of these cells for use on conventional glass-supported planar bilayers. Moreover, emerging data suggest that tissue resident T cells and T cells from lymphoid organs are significantly different in their phenotype and functional activity from those in peripheral blood, further solidifying the need to better understand the features of T cell synaptic interfaces in primary human T cells. To this end, we developed a new mini scale approach exploiting bilayers built into multichannel flow slides that allows us to perform imaging studies of T cell/bilayer interfaces with as few as 105 cells primary T cells isolated from human peripheral blood and lymphoid tissues without sacrificing the quality of the analysis. Our results indicate that while primary peripheral blood CD8+ T cells can share synaptic interface properties similar to in vitro derived T cell clones and lines, we found significant differences in the structure of the synaptic interface formed by primary lymphoid tissue compared to peripheral blood T cells, consistent with different efficiencies of these T cells.

CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells

The persistence of HIV reservoirs, including latently infected, resting CD4+ T cells, is the major obstacle to cure HIV infection. CD32a expression was recently reported to mark CD4+ T cells harboring a replication-competent HIV reservoir during antiretroviral therapy (ART) suppression. We aimed to determine whether CD32 expression marks HIV latently or transcriptionally active infected CD4+ T cells. Using peripheral blood and lymphoid tissue of ART-treated HIV+ or SIV+ subjects, we found that most of the circulating memory CD32+ CD4+ T cells expressed markers of activation, including CD69, HLA-DR, CD25, CD38, and Ki67, and bore a TH2 phenotype as defined by CXCR3, CCR4, and CCR6. CD32 expression did not selectively enrich for HIV- or SIV-infected CD4+ T cells in peripheral blood or lymphoid tissue; isolated CD32+ resting CD4+ T cells accounted for less than 3% of the total HIV DNA in CD4+ T cells. Cell-associated HIV DNA and RNA loads in CD4+ T cells positively correlated with the frequency of CD32+ CD69+ CD4+ T cells but not with CD32 expression on resting CD4+ T cells. Using RNA fluorescence in situ hybridization, CD32 coexpression with HIV RNA or p24 was detected after in vitro HIV infection (peripheral blood mononuclear cell and tissue) and in vivo within lymph node tissue from HIV-infected individuals. Together, these results indicate that CD32 is not a marker of resting CD4+ T cells or of enriched HIV DNA-positive cells after ART; rather, CD32 is predominately expressed on a subset of activated CD4+ T cells enriched for transcriptionally active HIV after long-term ART.

Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease

CD4+ T cells subsets have a wide range of important helper and regulatory functions in the immune system. Several studies have specifically suggested that circulating effector CD4+ T cells may play a direct role in control of HIV replication through cytolytic activity or autocrine β-chemokine production. However, it remains unclear whether effector CD4+ T cells expressing cytolytic molecules and β-chemokines are present within lymph nodes (LNs), a major site of HIV replication. Here, we report that expression of β-chemokines and cytolytic molecules are enriched within a CD4+ T cell population with high levels of the T-box transcription factors T-bet and eomesodermin (Eomes). This effector population is predominately found in peripheral blood and is limited in LNs regardless of HIV infection or treatment status. As a result, CD4+ T cells generally lack effector functions in LNs, including cytolytic capacity and IFNγ and β-chemokine expression, even in HIV elite controllers and during acute/early HIV infection. While we do find the presence of degranulating CD4+ T cells in LNs, these cells do not bear functional or transcriptional effector T cell properties and are inherently poor to form stable immunological synapses compared to their peripheral blood counterparts. We demonstrate that CD4+ T cell cytolytic function, phenotype, and programming in the peripheral blood is dissociated from those characteristics found in lymphoid tissues. Together, these data challenge our current models based on blood and suggest spatially and temporally dissociated mechanisms of viral control in lymphoid tissues.

CD4+ T cells have classically been divided into different subsets based on their different abilities to help and regulate specific parts of the immune system. Recent work in the HIV field has demonstrated that HIV-specific CD4+ T cells with unique effector functions, such as cytolytic activity and β-chemokine production, can play a direct role in control of HIV replication. However, HIV infection is generally considered to be a disease centered in lymphoid tissues, where unique CD4+ T helper cell subsets are present to orchestrate the maturation and priming of adaptive immunity. In this study, we identify that two specific transcription factors, T-bet and Eomes, mark cytolytic and β-chemokine producing CD4+ T cells. While this effector CD4+ T cell population is part of immunosurveillance mechanisms in blood, we find that lymph nodes largely lack this effector population–independent of HIV infection or disease progression status. These results indicate that current effector CD4+ T cell mediated correlates of HIV control are limited to blood and not representative of potential correlates of control in lymphoid tissues.

Human MAIT cells exit peripheral tissues and recirculate via lymph in steady state conditions

Mucosal-associated invariant T cells (MAIT cells) recognize bacterial metabolites as antigen and are found in blood and tissues, where they are poised to contribute to barrier immunity. Recent data demonstrate that MAIT cells located in mucosal barrier tissues are functionally distinct from their blood counterparts, but the relationship and circulation of MAIT cells between blood and different tissue compartments remains poorly understood. Previous studies raised the possibility that MAIT cells do not leave tissue and may either be retained or undergo apoptosis. To directly address if human MAIT cells exit tissues, we collected human donor-matched thoracic duct lymph and blood and analyzed MAIT cell phenotype, transcriptome, and T cell receptor (TCR) diversity by flow cytometry and RNA sequencing. We found that MAIT cells were present in the lymph, despite being largely CCR7- in the blood, thus indicating that MAIT cells in the lymph migrated from tissues and were capable of exiting tissues to recirculate. Importantly, MAIT cells in the lymph and blood had highly overlapping clonotype usage but distinct transcriptome signatures, indicative of differential activation states.

Follicular CD8 T cells accumulate in HIV infection and can kill infected cells in vitro via bispecific antibodies

Cytolytic CD8 T cells play a crucial role in the control and elimination of virus-infected cells and are a major focus of HIV cure efforts. However, it has been shown that HIV-specific CD8 T cells are infrequently found within germinal centers (GCs), a predominant site of active and latent HIV infection. We demonstrate that HIV infection induces marked changes in the phenotype, frequency, and localization of CD8 T cells within the lymph node (LN). Significantly increased frequencies of CD8 T cells in the B cell follicles and GCs were found in LNs from treated and untreated HIV-infected individuals. This profile was associated with persistent local immune activation but did not appear to be directly related to local viral replication. Follicular CD8 (fCD8) T cells, despite compromised cytokine polyfunctionality, showed good cytolytic potential characterized by high ex vivo expression of granzyme B and perforin. We used an anti-HIV/anti-CD3 bispecific antibody in a redirected killing assay and found that fCD8 T cells had better killing activity than did non-fCD8 T cells. Our results indicate that CD8 T cells with potent cytolytic activity are recruited to GCs during HIV infection and, if appropriately redirected to kill HIV-infected cells, could be an effective component of an HIV cure strategy.

Human Immunodeficiency Virus Type-1 Elite Controllers Maintain Low Co-Expression of Inhibitory Receptors on CD4+ T Cells

Human immunodeficiency virus type-1 (HIV-1) elite controllers (ELCs) represent a unique population that control viral replication in the absence of antiretroviral therapy (cART). It is well established that expression of multiple inhibitory receptors on CD8+ T cells is associated with HIV-1 disease progression. However, whether reduced co-expression of inhibitory receptors on CD4+ T cells is linked to natural viral control and slow HIV-1 disease progression remains undefined. Here, we report on the expression pattern of numerous measurable inhibitory receptors, associated with T cell exhaustion (programmed cell death-1, CTLA-4, and TIGIT), on different CD4+ T cell memory populations in ELCs and HIV-infected subjects with or without long-term cART. We found that the co-expression pattern of inhibitory receptors was significantly reduced in ELCs compared with HIV-1 cART-treated and viremic subjects, and similar to healthy controls. Markers associated with T cell exhaustion varied among different memory CD4+ T cell subsets and highest levels were found mainly on transitional memory T cells. CD4+ T cells co-expressing all inhibitory markers were positively correlated to T cell activation (CD38+ HLA-DR+) as well as the transcription factors Helios and FoxP3. Finally, clinical parameters such as CD4 count, HIV-1 viral load, and the CD4/CD8 ratio all showed significant associations with CD4+ T cell exhaustion. We demonstrate that ELCs are able to maintain lower levels of CD4+ T cell exhaustion despite years of ongoing viral replication compared with successfully cART-treated subjects. Our findings suggest that ELCs harbor a “healthy” state of inhibitory receptor expression on CD4+ T cells that might play part in maintenance of their control status.

HIV-induced modifications of TIGIT expression impair CD8 T cell polyfunctionality

HIV-specific CD8 T cells display an accumulation of inhibitory receptors that are associated with poor effector functions. Expression of the inhibitory receptor, T cell immunoglobulin and ITIM domain (TIGIT), its co-stimulatory receptor CD226 and their ligand poliovirus receptor (PVR) are altered during chronic viral infections and cancer. Here we show that the TIGIT/CD226/PVR axis is dysregulated during HIV infection and linked to poor polyfunctional activity, increased expression of inhibitory receptors and an altered effector transcriptional programming. We report that TIGIT expression is increased on CD8 T cells in untreated HIV infection. Additionally, a longitudinal increase in TIGIT expression was demonstrated despite early initiation of antiretroviral therapy during acute HIV infection. The HIV-specific TIGIT+ CD8 T cells co-expressed PD-1, CD160 and 2B4 and had an inverse expression profile of the T-box transcription factors T-bet and Eomes. The HIV-specific CD8 T cells were almost exclusively TIGIThiCD226neg/dim and the frequency of TIGIThi cells was inversely correlated with polyfunctionality. Furthermore, the TIGIT/CD226 ligand PVR was increased on CD4 T cells, especially T follicular helper (Tfh) cells in HIV-infected lymph nodes. These results demonstrate a preferential skewing of the TIGIT/CD226 axis towards the inhibitory receptor TIGIT on CD8 T cells during HIV-1 infection, which is linked to severe T cell dysfunction. The findings highlight the importance of the TIGIT/CD226/PVR axis as an immune checkpoint barrier that potentially could hinder future therapeutic “cure” strategies that require potent HIV-specific CD8 T cells and/or the clearance of HIV-1 infected Tfh cells.

Human T follicular regulatory cells (Tfr) able to inhibit antibody production are enriched at the lymph node T-B border and rare in germinal centers

T follicular helper (Tfh) cells are a subset of CD4+ T cells that are critical for the formation of germinal centers (GCs) and the development of high affinity, class-switched antibodies. Tfh cells are differentiated in a Bcl6-dependent manner and are characterized by expression of the inhibitory receptor PD-1 along with CXCR5, a chemokine receptor that directs these cells to the follicle. More recently, T follicular regulatory cells (Tfr) have been shown to express regulatory T cell (Treg) markers and suppress humoral immunity. To date, much of our understanding of the function and distribution of Tfh and Tfr cells has been obtained from animal studies. Using highly multiplexed, quantitative imaging and functional assays, we examined the spatial distribution and suppressive function of human Tfr cells obtained from mesenteric lymph nodes. Here, we report that the majority of Tfr cells reside at the border between the T cell zone and B cell follicle and are rare within the GC, being far outnumbered by Tfh cells. In contrast to Tfh cells, Tfr cells expressed low to undetectable levels of PD-1 in situ yet potently suppressed antibody production in vitro. These findings reveal that Tfh and Tfr cells are spatially segregated within human lymph nodes and caution against using PD-1 expression levels as a phenotypic marker for human Tfr cells.

This research was supported in part by NIH R01, VA, and Intramural Research Program of the NIH, NIAID.

T-bet+ B cells are induced by human viral infections and dominate the HIV gp140 response

Humoral immunity is critical for viral control, but the identity and mechanisms regulating human antiviral B cells are unclear. Here, we characterized human B cells expressing T-bet and analyzed their dynamics during viral infections. T-bet+ B cells demonstrated an activated phenotype, a distinct transcriptional profile, and were enriched for expression of the antiviral immunoglobulin isotypes IgG1 and IgG3. T-bet+ B cells expanded following yellow fever virus and vaccinia virus vaccinations and also during early acute HIV infection. Viremic HIV-infected individuals maintained a large T-bet+ B cell population during chronic infection that was associated with increased serum and cell-associated IgG1 and IgG3 expression. The HIV gp140-specific B cell response was dominated by T-bet-expressing memory B cells, and we observed a concomitant biasing of gp140-specific serum immunoglobulin to the IgG1 isotype. These findings suggest that T-bet induction promotes antiviral immunoglobulin isotype switching and development of a distinct T-bet+ B cell subset that is maintained by viremia and coordinates the HIV Env-specific humoral response.

Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals

HIV-specific CD8⁺ T cells demonstrate an exhausted phenotype associated with increased expression of inhibitory receptors, decreased functional capacity, and a skewed transcriptional profile, which are only partially restored by antiretroviral treatment (ART). Expression levels of the inhibitory receptor, T cell immunoglobulin and ITIM domain (TIGIT), the co-stimulatory receptor CD226 and their ligand PVR are altered in viral infections and cancer. However, the extent to which the TIGIT/CD226/PVR-axis is affected by HIV-infection has not been characterized. Here, we report that TIGIT expression increased over time despite early initiation of ART. HIV-specific CD8⁺ T cells were almost exclusively TIGIT⁺, had an inverse expression of the transcription factors T-bet and Eomes and co-expressed PD-1, CD160 and 2B4. HIV-specific TIGIT^hi cells were negatively correlated with polyfunctionality and displayed a diminished expression of CD226. Furthermore, expression of PVR was increased on CD4⁺ T cells, especially T follicular helper (Tfh) cells, in HIV-infected lymph nodes. These results depict a skewing of the TIGIT/CD226 axis from CD226 co-stimulation towards TIGIT-mediated inhibition of CD8⁺ T cells, despite early ART. These findings highlight the importance of the TIGIT/CD226/PVR axis as an immune checkpoint barrier that could hinder future “cure” strategies requiring potent HIV-specific CD8⁺ T cells.