CD4+ T cell help is required for the formation of a cytolytic CD8+ T cell subset that protects against chronic viral infection and cancer

CD8 T cells responding to chronic viral infection can be classified into two major subsets, with a TCF-1+ subset serving as a self-renewing progenitor population that can give rise to a more terminally exhausted PD-1hi subset. However, whether additional heterogeneity exists amongst virus-specific CD8 T cells remains unclear. Here, using single cell RNA-sequencing and flow cytometric approaches, we demonstrate that in addition to the progenitor and exhausted subsets, CD8 T cells responding to persistent LCMV infection also encompass a previously unrecognized T cell subset that exhibits potent cytolytic activity in vitro, and is required for viral control in vivo. This cytotoxic subset is characterized by high expression of killer cell lectin-like receptors, the chemokine receptor CX3CR1, and the transcription factors T-bet and Zeb2. Notably, we further demonstrate a critical role for CD4 help via IL-21 production in facilitating the differentiation of this cytotoxic subset, as depletion of CD4 T cells or deletion of IL-21R signaling in P14 cells (which express a transgenic TCR specific for GP33–41) wholly abrogated the development of CX3CR1+CD8 T cells. Moreover, PD-L1 blockade, an immunotherapy known to partially reverse T cell exhaustion, failed to rescue this differentiation defect of “un-helped” CD8 T cells. Lastly, using a B16 melanoma model, we found that provision of IL-21+CD4 T cells was sufficient to induce over a 2-fold increase in the development of CX3CR1+CD8 TILs, which was associated with enhanced control over tumor growth. Collectively, our findings demonstrate a critical role for CD4 help in the generation of protective CX3CR1+CD8 T cells, and that this differentiation checkpoint may be exploited for immunotherapy.

Abstract B64: CD4 help is required for the generation of a transcriptionally distinct cytolytic CD8 T-cell subset to control chronic infection and tumor

“CD4 help” is crucial to sustain the function of exhausted CD8 T cells, yet the detailed mechanisms by which CD4 help regulates CD8 T-cell differentiation and function during chronic viral infection remains elusive. Here, using single-cell RNA-sequencing (scRNA-seq) we show that CD8 T cells responding to chronic viral infection are more heterogeneous than previously appreciated, with three transcriptionally distinct subsets dominating the late phase of the antiviral response. Importantly, our findings uncover the formation of a previously unrecognized CD8 T-cell subset that exhibits potent cytolytic function. This subset is characterized by high expression of killer cell lectin-like receptors Klre1 and Klra9, the chemokine receptor CX3CR1, and the transcription factors T-bet and Zeb2. Notably, our data further demonstrate that the formation of this cytotoxic subset is critically dependent on CD4 help and that exploitation of this developmental pathway may be used therapeutically to enhance cytotoxic CD8 T-cell infiltration into the tumor. These findings uncover novel cellular and molecular mechanisms of how “CD4 help” regulates CD8 T-cell differentiation during persistent infection and have implications towards optimizing the generation of protective CD8 T cells in immunotherapy.

Citation Format: Ryan Zander, David Schauder, Weiguo Cui. CD4 help is required for the generation of a transcriptionally distinct cytolytic CD8 T-cell subset to control chronic infection and tumor [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B64.

CD4+ T Cell Help Is Required for the Formation of a Cytolytic CD8+ T Cell Subset that Protects against Chronic Infection and Cancer

Although CD4⁺ T cell "help" is crucial to sustain antiviral immunity, the mechanisms by which CD4⁺ T cells regulate CD8⁺ T cell differentiation during chronic infection remain elusive. Here, using single-cell RNA sequencing, we show that CD8⁺ T cells responding to chronic infection were more heterogeneous than previously appreciated. Importantly, our findings uncovered the formation of a CX₃CR1-expressing CD8⁺ T cell subset that exhibited potent cytolytic function and was required for viral control. Notably, our data further demonstrate that formation of this cytotoxic subset was critically dependent on CD4⁺ T cell help via interleukin-21 (IL-21) and that exploitation of this developmental pathway could be used therapeutically to enhance the killer function of CD8⁺ T cells infiltrated into the tumor. These findings uncover additional molecular mechanisms of how "CD4⁺ T cell help" regulates CD8⁺ T cell differentiation during persistent infection and have implications toward optimizing the generation of protective CD8⁺ T cells in immunotherapy.

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain

Neuronal cell types are the nodes of neural circuits that determine the flow of information within the brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of cell type and reveals how individual neurons route their output across the brain. Despite the importance of morphology, few projection neurons in the mouse brain have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the brain. We used this platform to reconstruct more than 1,000 projection neurons in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed neurons constitute more than 85 meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of projection neurons and suggest organizational principles of long-range connectivity.

Abstract B200: Single-cell RNA-sequencing (ScRNA-seq) reveals broad heterogeneity among CD8 T-cells during chronic viral infection and identifies a critical role for CD4 help in promoting the differentiation of a potent cytotoxic CD8 T-cell subset

During chronic viral infection and cancer, CD8 T-cells undergo a differentiation process commonly referred to as T-cell exhaustion. This process is traditionally defined by a stepwise loss of effector functions, eventually leading to cell death. Despite their inability to completely clear the infection, exhausted T-cells are still necessary for limiting viral replication during infection. Thus, it has been proposed that functional adaptation is a more appropriate term for T-cell exhaustion, as CD8 T-cells may be undergoing a multifaceted process of differentiation to better meet the needs of a chronic infection. In line with this hypothesis, it has recently been demonstrated that CD8 T-cells responding to chronic infection are non-homogenous and can be compartmentalized into at least two major subsets, with a TCF-1+ subset serving as a progenitor population that can give rise to a more terminally exhausted TCF-1- subset. However, whether additional heterogeneity exists among CD8 T-cells responding to persistent infection remains unclear. Here, we used ScRNA-seq to fully characterize the heterogeneity of CD8 T-cells during chronic LCMV Cl13 infection. We identified that several transcriptionally distinct subsets of CD8 T-cells develop during chronic LCMV infection, with 3 particular clusters, Slamf6, Pdcd1, and Cx3cr1 cell subsets dominating the antiviral CD8 T-cell response. Importantly both ScRNA-seq and flow cytometric analyses demonstrated that differential expression of cell surface receptors CX3CR1 and Ly108 (encoded by Slamf6) can distinguish these 3 major T-cell subsets. Notably, Ly108 cells shared similar characteristics to the previously described progenitor population and displayed elevated expression of TCF-1. Conversely, CX3CR1 CD8 T-cells displayed increased expression of killer cell lectin-like receptors Klre1 and Klra9, and the TFs T-bet and Zeb2, whereas CX3CR1-Ly108- (DN) cells exhibited elevated expression of multiple co-inhibitory receptors and the TFs Eomes and Nr4a2. Ex vivo functional analyses further indicated that Ly108 CD8 T-cells exhibit an enhanced capacity to co-produce IFN-γ and TNF-α upon GP33 peptide stimulation, whereas CX3CR1 CD8 T-cells display augmented cytotoxicity against peptide-pulsed targeT-cells. Sc trajectory modeling using Monocle analyses predicted that Ly108 CD8 T-cells give rise to both CX3CR1 and DN subsets, with the DN subset branch appearing closer in pseudotime to the Ly108 progenitor subset. To determine the in vivo differentiation trajectory, proliferative potential, and phenotypic stability of these 3 subsets, we performed adoptive transfer experiments using congenically marked CD8 T-cells. Importantly, and consistent with our Monocle predictions, our results demonstrate that Ly108 CD8 T-cells display robust secondary proliferation and give rise to both CX3CR1 and DN subsets. By contrast, CX3CR1 cells retained high CX3CR1 and T-bet expression and did not differentiate into Ly108 or DN CD8 T-cells. Intriguingly, although the DN subset appeared to be the most phenotypically and functionally exhausted subset, more than half of their progeny acquired high CX3CR1 and T-bet expression, indicating that this subset may not be as terminally differentiated as its CX3CR1 counterpart. Notably, our ScRNA-seq analyses also identified that DN cells displayed the highest levels of IL-21R expression, suggesting a potential role for CD4 help in regulating the differentiation of this subset. Strikingly, depletion of CD4 T-cells or deletion of IL-21R signaling in P14 transgenic CD8 T-cells abrogated the development of the CX3CR1 CD8 subset, indicating a critical role for CD4 help in facilitating the differentiation of exhausted CD8 T-cells into a potent cytotoxic CD8 subset. Collectively, our work supports a new model of CD8 T-cell differentiation during chronic viral infection and has important implications for T-cell-based immunotherapies aimed at treating persistent infections and/or cancer.

Citation Format: Ryan Zander, David Schauder, Gang Xin, Christine Nguyen, Xiaopeng Wu, Weiguo Cui. Single-cell RNA-sequencing (ScRNA-seq) reveals broad heterogeneity among CD8 T-cells during chronic viral infection and identifies a critical role for CD4 help in promoting the differentiation of a potent cytotoxic CD8 T-cell subset [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B200.

Abstract B201: Exploration and exploitation of macrophage death pathways: Infection by Mycobacterium tuberculosis as a model

Macrophages can impact the development of tumors and their responses to therapy. However, we lack a full understanding of how macrophage activation and survival are regulated and might be therapeutically modulated. To address these questions, we turned to a host-pathogen interaction that is likely to have impacted the evolution of these processes: infection by Mycobacterium tuberculosis (Mtb), the leading cause of death from infection. Once internalized by macrophages, Mtb resists killing by macrophages and replicates within them. Ultimately, Mtb infection results in death of macrophages, allowing dissemination of the pathogen to other cells. To explore how Mtb induces macrophage cell death and how macrophage cell death might impact host defense against Mtb, we performed a genome-wide CRISPR-Cas9 recessive genetic screen in RAW264.7 macrophages. We discovered that the absence of components of the type I interferon signaling pathway, including the IFN-α/β receptor (IFNAR), delays Mtb-induced cell death. It is known that Mtb infection induces macrophages to produce type I interferon. Our finding directly links type I interferon signaling pathway and Mtb-induced macrophage death. We are currently working on the mechanism of the type I IFN-induced death of bacterially-stimulated macrophages. Meanwhile, we are testing blockers of this pathway as host-directed therapy against TB and have seen striking protective effects of anti-IFNAR1 mAb in Mtb-infected mice, whether the mAb is administered before or after infection. Further exploration of the protective effect of anti-IFNAR mAb could point to an antibody-based, host-directed therapy. Acknowledgment: We thank Prof. R. Schreiber, Washington University, for facilitating access to anti-IFNAR mAb.

Citation Format: Ryan Zander, David Schauder, Gang Xin, Christine Nguyen, Xiaopeng Wu, Weiguo Cui. Exploration and exploitation of macrophage death pathways: Infection by Mycobacterium tuberculosis as a model [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B201.

Frontline Science: PECAM-1 (CD31) expression in naïve and memory, but not acutely activated, CD8+ T cells

Inhibitory cell surface proteins on T cells are often dynamically regulated, which contributes to their physiologic function. PECAM-1 (CD31) is an inhibitory receptor that facilitates TGF-β-mediated suppression of T cell activity. It is well established in CD4+ T cells that PECAM-1 is expressed in naïve recent thymic emigrants, but is down-regulated after acute T cell activation and absent from memory cells. The extent to which PECAM-1 expression is similarly regulated in CD8+ T cells is much less well characterized. We evaluated T cells recovered from mice after infection with a model intracellular pathogen and determined that, in CD8+ T cells, PECAM-1 expression was strongly down-regulated during acute infection but re-expressed to intermediate levels in memory cells. Down-regulation of PECAM-1 expression in CD8+ T cells was transcriptionally regulated and affected by the strength and nature of TCR signaling. PECAM-1 was also detected on the surface of human activated/memory CD8+ , but not CD4+ T cells. These data demonstrate that PECAM-1 expression is dynamically regulated, albeit differently, in both CD4+ and CD8+ T cells. Furthermore, unlike memory CD4+ T cells, memory CD8+ T cells retain PECAM-1 expression and have the potential to be modulated by this inhibitory receptor.

T follicular helper cell-derived IL-10 sustains humoral immunity during chronic viral infection

Although it is well-appreciated that Tfh cells play a critical role in regulating antiviral humoral immunity, the detailed cellular and molecular pathways that govern their differentiation and function during chronic viral infection remains incompletely understood. In this study, we generated IL-10 and IL-21 double-reporter mice to study the dynamic expression of the immunoregulatory cytokines IL-10 and IL-21, which are known to differentially regulate T cell-mediated control over viral replication. Infection of these double-reporter mice with either an acute or chronic strain of LCMV, revealed a unique subset of IL-10+IL-21+co-producing Tfh cells that arise only during chronic viral infection. Notably, compared to IL-21-single producing Tfh cells, IL-10+IL-21+co-producing Tfh cells exhibited an enhanced germinal center (GC) Tfh-like profile, as exemplified by their increased per cell expression of PD-1, CXCR5, and Bcl-6. Additional analyses identified that IL-10-producing Tfh cells have an increased capacity to form stable Tfh-B cell conjugates compared to their IL-10− Tfh counterparts, suggesting that IL-10+ Tfh cells may specialize in providing help signals to B cells during chronic infection. Importantly, depletion of IL-10+IL-21+ co-producing CD4 T cells or deletion of Il10 specifically from Tfh cells resulted in impaired GC B cell responses, LCMV-specific antibody production and viral control. Mechanistically, we show that B cell intrinsic IL-10 signaling is indispensable for GC B cell differentiation and function. Collectively, our findings delineate a heterogeneous population of Tfh cells and elucidate a critical role for Tfh-derived IL-10 in promoting humoral immunity during persistent viral infection.

Abstract A02: A pathogen boosted adoptive cell transfer immunotherapy to treat solid tumors

Despite the remarkable success in treating hematological malignancies, adoptive cell transfer (ACT) still faces several challenges in treating solid tumor. The main stumbling blocks include insufficient quantity of tumor-specific T cells for transfer, impaired migration of transferred T cells into the tumor and the immunosuppressive microenvironment within the tumor. To overcome these problems, we designed an innovative approach that not only overcomes immunosuppression, but also induces robust anti-tumor T cell responses in the tumor. We first genetically engineered dual-specific CD8 T cells that can recognize both a tumor associated antigen and a bacterial antigen in vitro. Then, we treated tumor-bearing mice with ACT using a small number of the dual-specific CD8 T cells. This was accompanied by intratumoral injection of a low dose of the bacteria, which was sufficient to break local immunosuppression. The dual-specific CD8 T cells expanded robustly and migrated to the tumor bed in response to the infection. At the same time, the second TCR of these effector CD8 T cells recognized tumor antigen and executed effector function, causing tumor regression. As a result of this enhanced anti-tumor effects, 60% of the treated mice successfully eradicated their solid tumor at the primary site. Our approach not only overcomes immunosuppression, but also recruits robust anti-tumor T cell responses to the tumor. Overall, our study harnesses the power of multiple arms of the immune system with promising translational value, which can be used to target many types of solid tumors.

Citation Format: Gang Xin, David Schauder, Aimin Jiang, Nikhil Joshi, Weiguo Cui. A pathogen boosted adoptive cell transfer immunotherapy to treat solid tumors. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A02.

Redirected Adoptive Cell Transfer (ReACT)- A Multi-pronged Strategy to Treat Solid Tumors

Adoptive cell transfer (ACT) of genetically engineered T cells provides unprecedented opportunities to treat hematological malignancies. However, due to insufficient migration and anti-tumor function of transferred T cells, especially inside the immunosuppressive tumor microenvironment (TME), the efficacy of ACT is much curtailed in treating solid tumors. Pathogen-based cancer vaccines can break immunosuppression in TME, but often fail to mobilize tumor-specific T cell response with ample magnitude to eradicate established tumors. To overcome these challenges, we genetically engineered tumor-specific CD8 T cells in vitro with a second T cell receptor (TCR) that recognizes a bacterial antigen. We then transfer these dual-specific T cells in combination with intratumoral bacteria injection in an approach called redirected-ACT (ReACT) to treat melanoma in mice. The dual-specific CD8 T cells expand robustly in response to bacteria, migrate to the very site of infection/tumor, and confer tumor eradication in the majority of tumor-bearing mice. The mice cured from ReACT also develop immunological memory against subsequent tumor rechallenge. Additionally, we found that this combined approach reverts the immunosuppressive TME and recruits redirected CD8 T cells with enhanced killing ability to the very site of tumor. Overall, we provide the proof-of-principle of a promising strategy to treat various malignancies.

Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging

Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired immunodeficiency syndrome (AIDS) ². Infection begins when the HIV Envelope glycoprotein "spike" makes contact with the CD4 receptor on the surface of the CD4+ T-cell. This interaction induces a conformational change in the spike, which promotes interaction with a second cell surface co-receptor ^5,9. The significance of these protein interactions in the HIV infection pathway makes them of profound importance in fundamental HIV research, and in the pursuit of an HIV vaccine.

The need to better understand the molecular-scale interactions of HIV cell contact and neutralization motivated the development of a technique to determine the structures of the HIV spike interacting with cell surface receptor proteins and molecules that block infection. Using cryo-electron tomography and 3D image processing, we recently demonstrated the ability to determine such structures on the surface of native virus, at ˜20 Å resolution ^9,14. This approach is not limited to resolving HIV Envelope structures, and can be extended to other viral membrane proteins and proteins reconstituted on a liposome. In this protocol, we describe how to obtain structures of HIV envelope glycoproteins starting from purified HIV virions and proceeding stepwise through preparing vitrified samples, collecting, cryo-electron microscopy data, reconstituting and processing 3D data volumes, averaging and classifying 3D protein subvolumes, and interpreting results to produce a protein model. The computational aspects of our approach were adapted into modules that can be accessed and executed remotely using the Biowulf GNU/Linux parallel processing cluster at the NIH (http://biowulf.nih.gov). This remote access, combined with low-cost computer hardware and high-speed network access, has made possible the involvement of researchers and students working from school or home.