Highlights • Exhaustion and tolerance represent distinct CD8 T cell differentiation states. • These distinct states are associated with unique molecular programs. • Exhaustion and tolerance are not ...fixed, but flexible and plastic cell states. • Certain characteristics are epigenetically imprinted and independent from external cues.
T cell dysfunction in solid tumors results from multiple mechanisms. Altered signaling pathways in tumor cells help produce a suppressive tumor microenvironment enriched for inhibitory cells, posing ...a major obstacle for cancer immunity. Metabolic constraints to cell function and survival shape tumor progression and immune cell function. In the face of persistent antigen, chronic T cell receptor signaling drives T lymphocytes to a functionally exhausted state. Here we discuss how the tumor and its microenvironment influences T cell trafficking and function with a focus on melanoma, and pancreatic and ovarian cancer, and discuss how scientific advances may help overcome these hurdles.
T cell dysfunction in solid tumors results from multiple mechanisms. Altered signaling pathways in tumor cells help produce a suppressive tumor microenvironment enriched for inhibitory cells, posing a major obstacle for cancer immunity. Metabolic constraints to cell function and survival shape tumor progression and immune cell function. In the face of persistent antigen, chronic T cell receptor signaling drives T lymphocytes to a functionally exhausted state. Here we discuss how the tumor and its microenvironment influences T cell trafficking and function with a focus on melanoma, pancreatic and ovarian cancer, and discuss how scientific advances may help overcome these hurdles.
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of ...humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.
Antigen-specific priming of human, naive T cells has been difficult to assess. Owing to the low initial frequency in the naive cell pool of specific T cell precursors, such an analysis has been ...obscured by the requirements for repeated stimulations and prolonged culture time. In this protocol, we describe how to evaluate antigen-specific priming of CD8(+) cells 10 d after a single specific stimulation. The assay provides reference conditions, which result in the expansion of a substantial population of antigen-specific T cells from the naive repertoire. Various conditions and modifications during the priming process (e.g., testing new cytokines, co-stimulators and so on) can now be directly compared with the reference conditions. Factors relevant to achieving effective priming include the dendritic cell preparation, the T cell preparation, the cell ratio at the time of priming, the serum source used for the experiment and the timing of addition and concentration of the cytokines used for expansion. This protocol is relevant for human immunology, vaccine biology and drug development.
The transfer of high-avidity T cell receptor (TCR) genes isolated from rare tumor-specific lymphocytes into polyclonal T cells is an attractive cancer immunotherapy strategy. However, TCR gene ...transfer results in competition for surface expression and inappropriate pairing between the exogenous and endogenous TCR chains, resulting in suboptimal activity and potentially harmful unpredicted antigen specificities of the resultant TCRs. We designed zinc-finger nucleases (ZFNs) that promoted the disruption of endogenous TCR β- and α-chain genes. Lymphocytes treated with ZFNs lacked surface expression of CD3-TCR and expanded with the addition of interleukin-7 (IL-7) and IL-15. After lentiviral transfer of a TCR specific for the Wilms tumor 1 (WT1) antigen, these TCR-edited cells expressed the new TCR at high levels, were easily expanded to near purity and were superior at specific antigen recognition compared to donor-matched, unedited TCR-transferred cells. In contrast to unedited TCR-transferred cells, the TCR-edited lymphocytes did not mediate off-target reactivity while maintaining their anti-tumor activity in vivo, thus showing that complete editing of T cell specificity generates tumor-specific lymphocytes with improved biosafety profiles.
Despite the availability of major histocompatibility complex (MHC)-binding peptide prediction algorithms, the development of T-cell vaccines against pathogen and tumor antigens remains challenged by ...inefficient identification of immunogenic epitopes. CD8⁺ T cells must distinguish immunogenic epitopes from nonimmunogenic self peptides to respond effectively against an antigen without endangering the viability of the host. Because this discrimination is fundamental to our understanding of immune recognition and critical for rational vaccine design, we interrogated the biochemical properties of 9,888 MHC class I peptides. We identified a strong bias toward hydrophobic amino acids at T-cell receptor contact residues within immunogenic epitopes of MHC allomorphs, which permitted us to develop and train a hydrophobicity-based artificial neural network (ANN-Hydro) to predict immunogenic epitopes. The immunogenicity model was validated in a blinded in vivo overlapping epitope discovery study of 364 peptides from three HIV-1 Gag protein variants. Applying the ANN-Hydro model on existing peptide-MHC algorithms consistently reduced the number of candidate peptides across multiple antigens and may provide a correlate with immunodominance. Hydrophobicity of TCR contact residues is a hallmark of immunogenic epitopes and marks a step toward eliminating the need for empirical epitope testing for vaccine development.
CD8+ T cells recognizing tumor-specific antigens are detected in cancer patients but are dysfunctional. Here we developed a tamoxifen-inducible liver cancer mouse model with a defined oncogenic ...driver antigen (SV40 large T-antigen) to follow the activation and differentiation of naive tumor-specific CD8+ T (TST) cells after tumor initiation. Early during the pre-malignant phase of tumorigenesis, TST cells became dysfunctional, exhibiting phenotypic, functional, and transcriptional features similar to dysfunctional T cells isolated from late-stage human tumors. Thus, T cell dysfunction seen in advanced human cancers may already be established early during tumorigenesis. Although the TST cell dysfunctional state was initially therapeutically reversible, it ultimately evolved into a fixed state. Persistent antigen exposure rather than factors associated with the tumor microenvironment drove dysfunction. Moreover, the TST cell differentiation and dysfunction program exhibited features distinct from T cell exhaustion in chronic infections. Strategies to overcome this antigen-driven, cell-intrinsic dysfunction may be required to improve cancer immunotherapy.
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•Tumor-specific T cells become dysfunctional at the pre- and early malignant stage•T cell dysfunction is initially reversible but later becomes irreversible•Dysfunctional T cells from pre- and early malignant lesions are similar to tumor-reactive T cells in late human tumors•Continuous antigen encounter rather than microenvironmental factors drive dysfunction
Tumor-specific CD8+ T cells found in human solid tumors are often dysfunctional, but when and how during tumorigenesis this T cell dysfunction arises was not known. Schietinger and colleagues show that CD8+ T cells become dysfunctional early during tumorigenesis at the pre-malignant stage through an antigen-driven dynamic differentiation program.
Pancreatic ductal adenocarcinomas (PDAs) erect physical barriers to chemotherapy and induce multiple mechanisms of immune suppression, creating a sanctuary for unimpeded growth. We tested the ability ...of T cells engineered to express an affinity-enhanced T cell receptor (TCR) against a native antigen to overcome these barriers in a genetically engineered model of autochthonous PDA. Engineered T cells preferentially accumulate in PDA and induce tumor cell death and stromal remodeling. However, tumor-infiltrating T cells become progressively dysfunctional, a limitation successfully overcome by serial T cell infusions that resulted in a near-doubling of survival without overt toxicities. Similarly engineered human T cells lyse PDA cells in vitro, further supporting clinical advancement of this TCR-based strategy for the treatment of PDA.
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•CD8 T cells with an enhanced affinity TCR readily infiltrate and accumulate in PDA•Mesothelin-targeted T cells induce tumor cell lysis and stromal involution•T cell therapy increases survival in KPC mice without chemotherapy or radiation•Analogously engineered T cells with mesothelin-specific TCR lyse human PDA cells
Stromnes et al. show in preclinical models that T cells engineered to express affinity-enhanced T cell receptors against mesothelin overcome physical and immunologic barriers to treat pancreatic ductal adenocarcinoma. Serial adoptive transfers of these cells are safe and significantly increase overall survival.
We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws ...collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.
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•Analysis of serial blood from 139 COVID-19 patients reveals immune coordination•A major immunological shift is seen between mild and moderate infection•Moderate and severe cases exhibit inflammation and a sharp drop in blood nutrients•Novel immune cell subsets emerge in moderate cases and increase with severity
Using serial blood draws from COVID-19 patients, Su et al. present an extensive multi-omics dataset of plasma and single PBMCs covering the first week of infection following clinical diagnosis, which includes information on plasma proteins, metabolites, and on PBMC transcriptomic and surface-protein data, immune receptor sequences, secreted proteins, and electronic health record data. Their integrated analysis identifies a major immunological shift between mild and moderate infection, which includes an increase in inflammation, drop in blood nutrients, and the emergence of novel immune cell subpopulations that intensify with disease severity.
Relapse after allogeneic hematopoietic cell transplantation (HCT) is the leading cause of death in patients with acute myeloid leukemia (AML) entering HCT with poor-risk features
. When HCT does ...produce prolonged relapse-free survival, it commonly reflects graft-versus-leukemia effects mediated by donor T cells reactive with antigens on leukemic cells
. As graft T cells have not been selected for leukemia specificity and frequently recognize proteins expressed by many normal host tissues, graft-versus-leukemia effects are often accompanied by morbidity and mortality from graft-versus-host disease
. Thus, AML relapse risk might be more effectively reduced with T cells expressing receptors (TCRs) that target selected AML antigens
. We therefore isolated a high-affinity Wilms' Tumor Antigen 1-specific TCR (TCR
) from HLA-A2
normal donor repertoires, inserted TCR
into Epstein-Bar virus-specific donor CD8
T cells (T
) to minimize graft-versus-host disease risk and enhance transferred T cell survival
, and infused these cells prophylactically post-HCT into 12 patients ( NCT01640301 ). Relapse-free survival was 100% at a median of 44 months following infusion, while a concurrent comparative group of 88 patients with similar risk AML had 54% relapse-free survival (P = 0.002). T
maintained TCR
expression, persisted long-term and were polyfunctional. This strategy appears promising for preventing AML recurrence in individuals at increased risk of post-HCT relapse.
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