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1.
Cell Rep ; 42(12): 113494, 2023 12 26.
Article in English | MEDLINE | ID: mdl-38085642

ABSTRACT

Antigen-specific T cells traffic to, are influenced by, and create unique cellular microenvironments. Here we characterize these microenvironments over time with multiplexed imaging in a melanoma model of adoptive T cell therapy and human patients with melanoma treated with checkpoint inhibitor therapy. Multicellular neighborhood analysis reveals dynamic immune cell infiltration and inflamed tumor cell neighborhoods associated with CD8+ T cells. T cell-focused analysis indicates T cells are found along a continuum of neighborhoods that reflect the progressive steps coordinating the anti-tumor immune response. More effective anti-tumor immune responses are characterized by inflamed tumor-T cell neighborhoods, flanked by dense immune infiltration neighborhoods. Conversely, ineffective T cell therapies express anti-inflammatory cytokines, resulting in regulatory neighborhoods, spatially disrupting productive T cell-immune and -tumor interactions. Our study provides in situ mechanistic insights into temporal tumor microenvironment changes, cell interactions critical for response, and spatial correlates of immunotherapy outcomes, informing cellular therapy evaluation and engineering.


Subject(s)
Melanoma , Humans , Melanoma/pathology , CD8-Positive T-Lymphocytes , Immunotherapy/methods , Cytokines , Immunity , Tumor Microenvironment
2.
Immunity ; 56(10): 2388-2407.e9, 2023 Oct 10.
Article in English | MEDLINE | ID: mdl-37776850

ABSTRACT

Chimeric antigen receptor (CAR) T cell therapy targeting CD19 has achieved tremendous success treating B cell malignancies; however, some patients fail to respond due to poor autologous T cell fitness. To improve response rates, we investigated whether disruption of the co-inhibitory receptors CTLA4 or PD-1 could restore CART function. CRISPR-Cas9-mediated deletion of CTLA4 in preclinical models of leukemia and myeloma improved CAR T cell proliferation and anti-tumor efficacy. Importantly, this effect was specific to CTLA4 and not seen upon deletion of CTLA4 and/or PDCD1 in CAR T cells. Mechanistically, CTLA4 deficiency permitted unopposed CD28 signaling and maintenance of CAR expression on the T cell surface under conditions of high antigen load. In clinical studies, deletion of CTLA4 rescued the function of T cells from patients with leukemia that previously failed CAR T cell treatment. Thus, selective deletion of CTLA4 reinvigorates dysfunctional chronic lymphocytic leukemia (CLL) patient T cells, providing a strategy for increasing patient responses to CAR T cell therapy.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Receptors, Chimeric Antigen , Humans , Receptors, Antigen, T-Cell/metabolism , CTLA-4 Antigen/genetics , CTLA-4 Antigen/metabolism , T-Lymphocytes , Immunotherapy, Adoptive , Antigens, CD19
3.
Cancer Discov ; 13(7): 1636-1655, 2023 07 07.
Article in English | MEDLINE | ID: mdl-37011008

ABSTRACT

Chimeric antigen receptor (CAR) T cell therapy has shown promise in treating hematologic cancers, but resistance is common and efficacy is limited in solid tumors. We found that CAR T cells autonomously propagate epigenetically programmed type I interferon signaling through chronic stimulation, which hampers antitumor function. EGR2 transcriptional regulator knockout not only blocks this type I interferon-mediated inhibitory program but also independently expands early memory CAR T cells with improved efficacy against liquid and solid tumors. The protective effect of EGR2 deletion in CAR T cells against chronic antigen-induced exhaustion can be overridden by interferon-ß exposure, suggesting that EGR2 ablation suppresses dysfunction by inhibiting type I interferon signaling. Finally, a refined EGR2 gene signature is a biomarker for type I interferon-associated CAR T cell failure and shorter patient survival. These findings connect prolonged CAR T cell activation with deleterious immunoinflammatory signaling and point to an EGR2-type I interferon axis as a therapeutically amenable biological system. SIGNIFICANCE: To improve CAR T cell therapy outcomes, modulating molecular determinants of CAR T cell-intrinsic resistance is crucial. Editing the gene encoding the EGR2 transcriptional regulator renders CAR T cells impervious to type I interferon pathway-induced dysfunction and improves memory differentiation, thereby addressing major barriers to progress for this emerging class of cancer immunotherapies. This article is highlighted in the In This Issue feature, p. 1501.


Subject(s)
Hematologic Neoplasms , Neoplasms , Humans , T-Lymphocytes , Neoplasms/genetics , Neoplasms/therapy , Immunotherapy, Adoptive , Signal Transduction , Hematologic Neoplasms/metabolism , Early Growth Response Protein 2/genetics , Early Growth Response Protein 2/metabolism
4.
Sci Transl Med ; 14(670): eabn7336, 2022 11 09.
Article in English | MEDLINE | ID: mdl-36350986

ABSTRACT

Chimeric antigen receptor (CAR) T cells have not induced meaningful clinical responses in solid tumors. Loss of T cell stemness, poor expansion capacity, and exhaustion during prolonged tumor antigen exposure are major causes of CAR T cell therapeutic resistance. Single-cell RNA-sequencing analysis of CAR T cells from a first-in-human trial in metastatic prostate cancer identified two independently validated cell states associated with antitumor potency or lack of efficacy. Low expression of PRDM1, encoding the BLIMP1 transcription factor, defined highly potent TCF7 [encoding T cell factor 1 (TCF1)]-expressing CD8+ CAR T cells, whereas enrichment of HAVCR2 [encoding T cell immunoglobulin and mucin-domain containing-3 (TIM-3)]-expressing CD8+ T cells with elevated PRDM1 was associated with poor outcomes. PRDM1 knockout promoted TCF7-dependent CAR T cell stemness and proliferation, resulting in marginally enhanced leukemia control in mice. However, in the setting of PRDM1 deficiency, a negative epigenetic feedback program of nuclear factor of activated T cells (NFAT)-driven T cell dysfunction was identified. This program was characterized by compensatory up-regulation of NR4A3 and other genes encoding exhaustion-related transcription factors that hampered T cell effector function in solid tumors. Dual knockout of PRDM1 and NR4A3 skewed CAR T cell phenotypes away from TIM-3+CD8+ and toward TCF1+CD8+ to counter exhaustion of tumor-infiltrating CAR T cells and improve antitumor responses, effects that were not achieved with PRDM1 and NR4A3 single knockout alone. These data underscore dual targeting of PRDM1 and NR4A3 as a promising approach to advance adoptive cell immuno-oncotherapy.


Subject(s)
Neoplasms , Receptors, Steroid , Male , Humans , Mice , Animals , Transcription Factors/genetics , Transcription Factors/metabolism , CD8-Positive T-Lymphocytes , Immunotherapy, Adoptive/methods , Hepatitis A Virus Cellular Receptor 2/genetics , Hepatitis A Virus Cellular Receptor 2/metabolism , Neoplasms/pathology , Cell Line, Tumor , DNA-Binding Proteins/metabolism , Receptors, Steroid/metabolism , Receptors, Thyroid Hormone/metabolism , Nerve Tissue Proteins/metabolism
5.
Front Immunol ; 13: 981825, 2022.
Article in English | MEDLINE | ID: mdl-36211386

ABSTRACT

Highly multiplexed, single-cell imaging has revolutionized our understanding of spatial cellular interactions associated with health and disease. With ever-increasing numbers of antigens, region sizes, and sample sizes, multiplexed fluorescence imaging experiments routinely produce terabytes of data. Fast and accurate processing of these large-scale, high-dimensional imaging data is essential to ensure reliable segmentation and identification of cell types and for characterization of cellular neighborhoods and inference of mechanistic insights. Here, we describe RAPID, a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data. RAPID deconvolves large-scale, high-dimensional fluorescence imaging data, stitches and registers images with axial and lateral drift correction, and minimizes tissue autofluorescence such as that introduced by erythrocytes. Incorporation of an open source CUDA-driven, GPU-assisted deconvolution produced results similar to fee-based commercial software. RAPID reduces data processing time and artifacts and improves image contrast and signal-to-noise compared to our previous image processing pipeline, thus providing a useful tool for accurate and robust analysis of large-scale, multiplexed, fluorescence imaging data.


Subject(s)
Image Processing, Computer-Assisted , Software , Image Processing, Computer-Assisted/methods , Microscopy, Fluorescence/methods
6.
J Hepatol ; 77(2): 397-409, 2022 08.
Article in English | MEDLINE | ID: mdl-35367533

ABSTRACT

BACKGROUND & AIMS: Despite recent translation of immunotherapies into clinical practice, the immunobiology of hepatocellular carcinoma (HCC), in particular the role and clinical relevance of exhausted and liver-resident T cells remain unclear. We therefore dissected the landscape of exhausted and resident T cell responses in the peripheral blood and tumor microenvironment of patients with HCC. METHODS: Lymphocytes were isolated from the blood, tumor and tumor-surrounding liver tissue of patients with HCC (n = 40, n = 10 treated with anti-PD-1 therapy). Phenotype, function and response to anti-PD-1 were analyzed by mass and flow cytometry ex vivo and in vitro, tissue residence was further assessed by immunohistochemistry and imaging mass cytometry. Gene signatures were analyzed in silico. RESULTS: We identified significant enrichment of heterogeneous populations of exhausted CD8+ T cells (TEX) in the tumor microenvironment. Strong enrichment of severely exhausted CD8 T cells expressing multiple immune checkpoints in addition to PD-1 was linked to poor progression-free and overall survival. In contrast, PD-1 was also expressed on a subset of more functional and metabolically active CD103+ tissue-resident memory T cells (TRM) that expressed few additional immune checkpoints and were associated with better survival. TEX enrichment was independent of BCLC stage, alpha-fetoprotein levels or age as a variable for progression-free survival in our cohort. These findings were in line with in silico gene signature analysis of HCC tumor transcriptomes from The Cancer Genome Atlas. A higher baseline TRM/TEX ratio was associated with disease control in anti-PD-1-treated patients. CONCLUSION: Our data provide information on the role of peripheral and intratumoral TEX-TRM dynamics in determining outcomes in patients with HCC. The dynamics between exhausted and liver-resident T cells have implications for immune-based diagnostics, rational patient selection and monitoring during HCC immunotherapies. LAY SUMMARY: The role of the immune response in hepatocellular carcinoma (HCC) remains unclear. T cells can mediate protection against tumor cells but are frequently dysfunctional and exhausted in cancer. We found that patients with a predominance of exhausted CD8+ T cells (TEX) had poor survival compared to patients with a predominance of tissue-resident memory T cells (TRM). This correlated with the molecular profile, metabolic and functional status of these cell populations. The enrichment of TEX was independently associated with prognosis in addition to disease stage, age and tumor markers. A high TRM proportion was also associated with better outcomes following checkpoint therapy. Thus, these T-cell populations are novel biomarkers with relevance in HCC.


Subject(s)
Carcinoma, Hepatocellular , Internship and Residency , Liver Neoplasms , CD8-Positive T-Lymphocytes , Humans , Tumor Microenvironment
7.
Nat Med ; 28(4): 724-734, 2022 04.
Article in English | MEDLINE | ID: mdl-35314843

ABSTRACT

Chimeric antigen receptor (CAR) T cells have demonstrated promising efficacy, particularly in hematologic malignancies. One challenge regarding CAR T cells in solid tumors is the immunosuppressive tumor microenvironment (TME), characterized by high levels of multiple inhibitory factors, including transforming growth factor (TGF)-ß. We report results from an in-human phase 1 trial of castration-resistant, prostate cancer-directed CAR T cells armored with a dominant-negative TGF-ß receptor (NCT03089203). Primary endpoints were safety and feasibility, while secondary objectives included assessment of CAR T cell distribution, bioactivity and disease response. All prespecified endpoints were met. Eighteen patients enrolled, and 13 subjects received therapy across four dose levels. Five of the 13 patients developed grade ≥2 cytokine release syndrome (CRS), including one patient who experienced a marked clonal CAR T cell expansion, >98% reduction in prostate-specific antigen (PSA) and death following grade 4 CRS with concurrent sepsis. Acute increases in inflammatory cytokines correlated with manageable high-grade CRS events. Three additional patients achieved a PSA reduction of ≥30%, with CAR T cell failure accompanied by upregulation of multiple TME-localized inhibitory molecules following adoptive cell transfer. CAR T cell kinetics revealed expansion in blood and tumor trafficking. Thus, clinical application of TGF-ß-resistant CAR T cells is feasible and generally safe. Future studies should use superior multipronged approaches against the TME to improve outcomes.


Subject(s)
Prostatic Neoplasms, Castration-Resistant , Receptors, Chimeric Antigen , Humans , Immunotherapy, Adoptive/adverse effects , Immunotherapy, Adoptive/methods , Male , Prostate-Specific Antigen/metabolism , Prostatic Neoplasms, Castration-Resistant/pathology , T-Lymphocytes , Transforming Growth Factor beta/metabolism , Tumor Microenvironment
8.
Cell ; 183(3): 818-834.e13, 2020 10 29.
Article in English | MEDLINE | ID: mdl-33038342

ABSTRACT

Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.


Subject(s)
Antigens, Neoplasm/immunology , Epitopes/immunology , Neoplasms/immunology , Alleles , Antigen Presentation/immunology , Cohort Studies , Humans , Peptides/immunology , Programmed Cell Death 1 Receptor , Reproducibility of Results
9.
Cell Syst ; 9(4): 375-382.e4, 2019 10 23.
Article in English | MEDLINE | ID: mdl-31606370

ABSTRACT

Despite improved methods for MHC affinity prediction, the vast majority of computationally predicted tumor neoantigens are not immunogenic experimentally, indicating that high-quality neoantigens are beyond current algorithms to discern. To enrich for neoantigens with the greatest likelihood of immunogenicity, we developed an analytic method to parse neoantigen quality through rational biological criteria across five clinical datasets for 318 cancer patients. We explored four quality metrics, including analysis of dissimilarity to the non-mutated proteome that was predictive of peptide immunogenicity. In patient tumors, neoantigens with high dissimilarity were unique, enriched for hydrophobic sequences, and correlated with survival after PD-1 checkpoint therapy in patients with non-small cell lung cancer independent of predicted MHC affinity. We incorporated our neoantigen quality analysis methodology into an open-source tool, antigen.garnish, to predict immunogenic peptides from bulk computationally predicted neoantigens for which the immunogenic "hit rate" is currently low.


Subject(s)
Antigens, Neoplasm/metabolism , Autoantigens/metabolism , Carcinoma, Non-Small-Cell Lung/diagnosis , Computational Biology/methods , Immunotherapy/methods , Lung Neoplasms/diagnosis , Software/trends , Amino Acid Sequence , Antigens, Neoplasm/chemistry , Antigens, Neoplasm/immunology , Antineoplastic Agents, Immunological/therapeutic use , Autoantigens/chemistry , Autoantigens/immunology , Biomarkers, Pharmacological , Carcinoma, Non-Small-Cell Lung/mortality , Carcinoma, Non-Small-Cell Lung/therapy , HLA Antigens/metabolism , Humans , Lung Neoplasms/mortality , Lung Neoplasms/therapy , Molecular Mimicry , Prognosis , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Proteome , Survival Analysis
10.
J Clin Invest ; 129(9): 3594-3609, 2019 06 04.
Article in English | MEDLINE | ID: mdl-31162144

ABSTRACT

Resistance to immunotherapy is one of the biggest problems of current oncotherapeutics. WhileT cell abundance is essential for tumor responsiveness to immunotherapy, factors that define the T cell inflamed tumor microenvironment are not fully understood. We conducted an unbiased approach to identify tumor-intrinsic mechanisms shaping the immune tumor microenvironment(TME), focusing on pancreatic adenocarcinoma because it is refractory to immunotherapy and excludes T cells from the TME. From human tumors, we identified EPHA2 as a candidate tumor intrinsic driver of immunosuppression. Epha2 deletion reversed T cell exclusion and sensitized tumors to immunotherapy. We found that PTGS2, the gene encoding cyclooxygenase-2, lies downstream of EPHA2 signaling through TGFß and is associated with poor patient survival. Ptgs2 deletion reversed T cell exclusion and sensitized tumors to immunotherapy; pharmacological inhibition of PTGS2 was similarly effective. Thus, EPHA2-PTGS2 signaling in tumor cells regulates tumor immune phenotypes; blockade may represent a novel therapeutic avenue for immunotherapy-refractory cancers. Our findings warrant clinical trials testing the effectiveness of therapies combining EPHA2-TGFß-PTGS2 pathway inhibitors with anti-tumor immunotherapy, and may change the treatment of notoriously therapy-resistant pancreatic adenocarcinoma.


Subject(s)
Cyclooxygenase 2/metabolism , Ephrin-A2/metabolism , Pancreatic Neoplasms/immunology , Transforming Growth Factor beta/metabolism , Adenocarcinoma/immunology , Adenocarcinoma/therapy , Animals , CD8-Positive T-Lymphocytes/immunology , Cell Line , Female , Gene Deletion , Humans , Immunosuppression Therapy , Immunotherapy , Inflammation , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Pancreatic Neoplasms/therapy , Receptor, EphA2
11.
Clin Cancer Res ; 25(14): 4363-4374, 2019 07 15.
Article in English | MEDLINE | ID: mdl-30914433

ABSTRACT

PURPOSE: Breast cancers with BRCA1/2 alterations have a relatively high mutational load, suggesting that immune checkpoint blockade may be a potential treatment option. However, the degree of immune cell infiltration varies widely, and molecular features contributing to this variability remain unknown. EXPERIMENTAL DESIGN: We hypothesized that genomic signatures might predict immunogenicity in BRCA1/2 breast cancers. Using The Cancer Genome Atlas (TCGA) genomic data, we compared breast cancers with (89) and without (770) either germline or somatic BRCA1/2 alterations. We also studied 35 breast cancers with germline BRCA1/2 mutations from Penn using WES and IHC. RESULTS: We found that homologous recombination deficiency (HRD) scores were negatively associated with expression-based immune indices [cytolytic index (P = 0.04), immune ESTIMATE (P = 0.002), type II IFN signaling (P = 0.002)] despite being associated with a higher mutational/neoantigen burden, in BRCA1/2 mutant breast cancers. Further, absence of allele-specific loss of heterozygosity (LOH negative; P = 0.01) or subclonality (P = 0.003) of germline and somatic BRCA1/2 mutations, respectively, predicted for heightened cytolytic activity. Gene set analysis found that multiple innate and adaptive immune pathways that converge on NF-κB may contribute to this heightened immunogenicity. IHC of Penn breast cancers demonstrated increased CD45+ (P = 0.039) and CD8+ infiltrates (P = 0.037) and increased PDL1 expression (P = 0.012) in HRD-low or LOH-negative cancers. Triple-negative cancers with low HRD had far greater CD8+ T cells (P = 0.0011) and Perforin 1 expression (P = 0.014) compared with hormone receptor-positive HRD-high cancers. CONCLUSIONS: HRD scores and hormone receptor subtype are predictive of immunogenicity in BRCA1/2 breast cancers and may inform the design of optimal immune therapeutic strategies.


Subject(s)
Antineoplastic Agents, Immunological/therapeutic use , BRCA1 Protein/genetics , BRCA2 Protein/genetics , Breast Neoplasms/genetics , Breast Neoplasms/immunology , CD8-Positive T-Lymphocytes/immunology , Homologous Recombination , B7-H1 Antigen/antagonists & inhibitors , B7-H1 Antigen/immunology , BRCA1 Protein/metabolism , BRCA2 Protein/metabolism , Biomarkers, Tumor/genetics , Breast Neoplasms/drug therapy , Breast Neoplasms/pathology , Female , Genomics/methods , Humans
12.
Immunity ; 49(1): 178-193.e7, 2018 07 17.
Article in English | MEDLINE | ID: mdl-29958801

ABSTRACT

The biological and functional heterogeneity between tumors-both across and within cancer types-poses a challenge for immunotherapy. To understand the factors underlying tumor immune heterogeneity and immunotherapy sensitivity, we established a library of congenic tumor cell clones from an autochthonous mouse model of pancreatic adenocarcinoma. These clones generated tumors that recapitulated T cell-inflamed and non-T-cell-inflamed tumor microenvironments upon implantation in immunocompetent mice, with distinct patterns of infiltration by immune cell subsets. Co-injecting tumor cell clones revealed the non-T-cell-inflamed phenotype is dominant and that both quantitative and qualitative features of intratumoral CD8+ T cells determine response to therapy. Transcriptomic and epigenetic analyses revealed tumor-cell-intrinsic production of the chemokine CXCL1 as a determinant of the non-T-cell-inflamed microenvironment, and ablation of CXCL1 promoted T cell infiltration and sensitivity to a combination immunotherapy regimen. Thus, tumor cell-intrinsic factors shape the tumor immune microenvironment and influence the outcome of immunotherapy.


Subject(s)
Adenocarcinoma/therapy , Immunologic Factors/immunology , Immunotherapy , Lymphocyte Subsets/immunology , Lymphocytes, Tumor-Infiltrating/immunology , Pancreatic Neoplasms/therapy , Tumor Microenvironment/immunology , Adenocarcinoma/immunology , Adenocarcinoma/pathology , Aged , Aged, 80 and over , Animals , CD8-Positive T-Lymphocytes/immunology , Epigenomics , Female , Gene Expression Profiling , Humans , Immunologic Factors/genetics , Male , Mice , Middle Aged , Pancreatic Neoplasms/immunology , Pancreatic Neoplasms/pathology , Primary Cell Culture , Pancreatic Neoplasms
13.
Cancer Res ; 78(15): 4282-4291, 2018 08 01.
Article in English | MEDLINE | ID: mdl-29844122

ABSTRACT

Immunotherapy in pancreatic ductal adenocarcinoma (PDA) remains a difficult clinical problem despite success in other disease types with immune checkpoint blockade (ICB) and chimeric antigen receptor T-cell therapy. Mechanisms driving immunosuppression and poor T-cell infiltration in PDA are incompletely understood. Here, we use genetically engineered mouse models of PDA that recapitulate hallmarks of human disease to demonstrate that CD40 pathway activation is required for clinical response to radiotherapy and ICB with αCTLA-4 and αPD-1. The combination of an agonist αCD40 antibody, radiotherapy, and dual ICB eradicated irradiated and unirradiated (i.e., abscopal) tumors, generating long-term immunity. Response required T cells and also short-lived myeloid cells and was dependent on the long noncoding RNA myeloid regulator Morrbid Using unbiased random forest machine learning, we built unique, contextual signatures for each therapeutic component, revealing that (i) radiotherapy triggers an early proinflammatory stimulus, ablating existing intratumoral T cells and upregulating MHC class I and CD86 on antigen-presenting cells, (ii) αCD40 causes a systemic and intratumoral reorganization of the myeloid compartment, and (iii) ICB increases intratumoral T-cell infiltration and improves the CD8 T-cell:regulatory T-cell ratio. Thus, αCD40 and radiotherapy nonredundantly augment antitumor immunity in PDA, which is otherwise refractory to ICB, providing a clear rationale for clinical evaluation.Significance: Radiotherapy and αCD40 disrupt key links between innate and adaptive immunity, ameliorating resistance to immune checkpoint blockade in pancreatic cancer via multiple cellular mechanisms. Cancer Res; 78(15); 4282-91. ©2018 AACR.


Subject(s)
CD40 Antigens/immunology , Carcinoma, Pancreatic Ductal/immunology , Carcinoma, Pancreatic Ductal/radiotherapy , Pancreatic Neoplasms/immunology , Pancreatic Neoplasms/radiotherapy , Adaptive Immunity/immunology , Animals , Antigen-Presenting Cells/immunology , CD8-Positive T-Lymphocytes/immunology , Carcinoma, Pancreatic Ductal/therapy , Cell Line, Tumor , Female , Immune Tolerance/immunology , Immunotherapy/methods , Immunotherapy, Adoptive/methods , Male , Mice , Mice, Inbred C57BL , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/therapy , Tumor Microenvironment/immunology , Pancreatic Neoplasms
14.
Cancer Immunol Res ; 6(3): 276-287, 2018 03.
Article in English | MEDLINE | ID: mdl-29339376

ABSTRACT

The immune system exerts antitumor activity via T cell-dependent recognition of tumor-specific antigens. Although the number of tumor neopeptides-peptides derived from somatic mutations-often correlates with immune activity and survival, most classically defined high-affinity neopeptides (CDNs) are not immunogenic, and only rare CDNs have been linked to tumor rejection. Thus, the rules of tumor antigen recognition remain incompletely understood. Here, we analyzed neopeptides, immune activity, and clinical outcome from 6,324 patients across 27 tumor types. We characterized a class of "alternatively defined neopeptides" (ADNs), which are mutant peptides predicted to bind MHC (class I or II) with improved affinity relative to their nonmutated counterpart. ADNs are abundant and molecularly distinct from CDNs. The load of ADNs correlated with intratumoral T-cell responses and immune suppression, and ADNs were also strong predictors of patient survival across tumor types. These results expand the spectrum of mutation-derived tumor antigens with potential clinical relevance. Cancer Immunol Res; 6(3); 276-87. ©2018 AACR.


Subject(s)
Antigens, Neoplasm/immunology , Histocompatibility Antigens Class II/immunology , Histocompatibility Antigens Class I/immunology , Neoplasms/immunology , Peptides/immunology , Antigens, Neoplasm/genetics , Histocompatibility Antigens Class I/genetics , Histocompatibility Antigens Class II/genetics , Humans , Mutation , Neoplasms/genetics , Peptides/genetics
16.
Proc Natl Acad Sci U S A ; 114(7): 1655-1659, 2017 02 14.
Article in English | MEDLINE | ID: mdl-28137880

ABSTRACT

Adeno-associated virus (AAV)-mediated gene therapy is currently being pursued as a treatment for the monogenic disorder α-1-antitrypsin (AAT) deficiency. Results from phase I and II studies have shown relatively stable and dose-dependent increases in transgene-derived wild-type AAT after local intramuscular vector administration. In this report we describe the appearance of transgene-specific T-cell responses in two subjects that were part of the phase II trial. The patient with the more robust T-cell response, which was associated with a reduction in transgene expression, was characterized more thoroughly in this study. We learned that the AAT-specific T cells in this patient were cytolytic in phenotype, mapped to a peptide in the endogenous mutant AAT protein that contained a common polymorphism not incorporated into the transgene, and were restricted by a rare HLA class I C alleles present only in this patient. These human studies illustrate the genetic influence of the endogenous gene and HLA haplotype on the outcome of gene therapy.


Subject(s)
Genetic Therapy/methods , Peptides/immunology , T-Lymphocytes/immunology , alpha 1-Antitrypsin Deficiency/therapy , alpha 1-Antitrypsin/immunology , Adult , Aged , Alleles , Amino Acid Sequence , Dependovirus/genetics , Female , HLA Antigens/genetics , HLA Antigens/immunology , Humans , K562 Cells , Male , Middle Aged , Peptides/genetics , Peptides/metabolism , Polymorphism, Genetic , T-Lymphocytes/metabolism , alpha 1-Antitrypsin/genetics , alpha 1-Antitrypsin/metabolism , alpha 1-Antitrypsin Deficiency/genetics , alpha 1-Antitrypsin Deficiency/immunology
17.
Clin Cancer Res ; 23(12): 3129-3138, 2017 Jun 15.
Article in English | MEDLINE | ID: mdl-28007776

ABSTRACT

Purpose: Immunotherapy has the potential to improve the dismal prognosis in pancreatic ductal adenocarcinoma (PDA), but clinical trials, including those with single-agent PD-1 or PD-L1 inhibition, have been disappointing. Our aim was to examine the immune landscape of PDA as it relates to aspects of tumor biology, including neoepitope burden.Experimental Design: We used publicly available expression data from 134 primary resection PDA samples from The Cancer Genome Atlas to stratify patients according to a cytolytic T-cell activity expression index. We correlated cytolytic immune activity with mutational, structural, and neoepitope features of the tumor.Results: Human PDA displays a range of intratumoral cytolytic T-cell activity. PDA tumors with low cytolytic activity exhibited significantly increased copy number alterations, including recurrent amplifications of MYC and NOTCH2 and recurrent deletions and mutations of CDKN2A/B In sharp contrast to other tumor types, high cytolytic activity in PDA did not correlate with increased mutational burden or neoepitope load (MHC class I and class II). Cytolytic-high tumors exhibited increased expression of multiple immune checkpoint genes compared to cytolytic-low tumors, except for PD-L1 expression, which was uniformly low.Conclusions: These data identify a subset of human PDA with high cytolytic T-cell activity. Rather than being linked to mutation burden or neoepitope load, immune activation indices in PDA were inversely linked to genomic alterations, suggesting that intrinsic oncogenic processes drive immune inactivity in human PDA. Furthermore, these data highlight the potential importance of immune checkpoints other than PD-L1/PD-1 as therapeutic targets in this lethal disease. Clin Cancer Res; 23(12); 3129-38. ©2016 AACR.


Subject(s)
Adenocarcinoma/immunology , Carcinoma, Pancreatic Ductal/immunology , Epitopes/immunology , Pancreatic Neoplasms/immunology , Adenocarcinoma/pathology , CD8-Positive T-Lymphocytes/immunology , Carcinoma, Pancreatic Ductal/pathology , Cytotoxicity, Immunologic , Gene Expression Regulation, Neoplastic/immunology , Genes, MHC Class I/immunology , Humans , Immunotherapy , Pancreatic Neoplasms/pathology , Prognosis , T-Lymphocytes, Cytotoxic/immunology , Pancreatic Neoplasms
18.
JCI Insight ; 1(14)2016 09 08.
Article in English | MEDLINE | ID: mdl-27642636

ABSTRACT

In carcinogen-driven cancers, a high mutational burden results in neoepitopes that can be recognized immunologically. Such carcinogen-induced tumors may evade this immune response through "immunoediting," whereby tumors adapt to immune pressure and escape T cell-mediated killing. Many tumors lack a high neoepitope burden, and it remains unclear whether immunoediting occurs in such cases. Here, we evaluated T cell immunity in an autochthonous mouse model of pancreatic cancer and found a low mutational burden, absence of predicted neoepitopes derived from tumor mutations, and resistance to checkpoint immunotherapy. Spontaneous tumor progression was identical in the presence or absence of T cells. Moreover, tumors arising in T cell-depleted mice grew unchecked in immune-competent hosts. However, introduction of the neoantigen ovalbumin (OVA) led to tumor rejection and T cell memory, but this did not occur in OVA immune-tolerant mice. Thus, immunoediting does not occur in this mouse model - a likely consequence, not a cause, of absent neoepitopes. Because many human tumors also have a low missense mutational load and minimal neoepitope burden, our findings have clinical implications for the design of immunotherapy for patients with such tumors.


Subject(s)
Antigens, Neoplasm/immunology , Immune Evasion , Immunotherapy , Pancreatic Neoplasms/immunology , T-Lymphocytes/immunology , Animals , Cell Line, Tumor , Epitopes/immunology , Female , Mice , Mice, Inbred C57BL
19.
Nature ; 520(7547): 373-7, 2015 Apr 16.
Article in English | MEDLINE | ID: mdl-25754329

ABSTRACT

Immune checkpoint inhibitors result in impressive clinical responses, but optimal results will require combination with each other and other therapies. This raises fundamental questions about mechanisms of non-redundancy and resistance. Here we report major tumour regressions in a subset of patients with metastatic melanoma treated with an anti-CTLA4 antibody (anti-CTLA4) and radiation, and reproduced this effect in mouse models. Although combined treatment improved responses in irradiated and unirradiated tumours, resistance was common. Unbiased analyses of mice revealed that resistance was due to upregulation of PD-L1 on melanoma cells and associated with T-cell exhaustion. Accordingly, optimal response in melanoma and other cancer types requires radiation, anti-CTLA4 and anti-PD-L1/PD-1. Anti-CTLA4 predominantly inhibits T-regulatory cells (Treg cells), thereby increasing the CD8 T-cell to Treg (CD8/Treg) ratio. Radiation enhances the diversity of the T-cell receptor (TCR) repertoire of intratumoral T cells. Together, anti-CTLA4 promotes expansion of T cells, while radiation shapes the TCR repertoire of the expanded peripheral clones. Addition of PD-L1 blockade reverses T-cell exhaustion to mitigate depression in the CD8/Treg ratio and further encourages oligoclonal T-cell expansion. Similarly to results from mice, patients on our clinical trial with melanoma showing high PD-L1 did not respond to radiation plus anti-CTLA4, demonstrated persistent T-cell exhaustion, and rapidly progressed. Thus, PD-L1 on melanoma cells allows tumours to escape anti-CTLA4-based therapy, and the combination of radiation, anti-CTLA4 and anti-PD-L1 promotes response and immunity through distinct mechanisms.


Subject(s)
B7-H1 Antigen/antagonists & inhibitors , CTLA-4 Antigen/antagonists & inhibitors , Cell Cycle Checkpoints/drug effects , Melanoma/drug therapy , Melanoma/immunology , Melanoma/radiotherapy , T-Lymphocytes/drug effects , T-Lymphocytes/radiation effects , Animals , B7-H1 Antigen/metabolism , Female , Humans , Melanoma/pathology , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Receptors, Antigen, T-Cell/drug effects , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell/metabolism , T-Lymphocytes/cytology , T-Lymphocytes/immunology , T-Lymphocytes, Regulatory/drug effects , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/radiation effects
20.
Cancer Discov ; 3(12): 1330-2, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24327693

ABSTRACT

Tumor-infiltrating T cells have recently been found to upregulate immunosuppressive pathways, such as programmed cell death protein 1 ligand 1 (PD-L1), in a paracrine fashion on tumor cells, but tumor cell-intrinsic regulation of PD-L1 is another potential mechanism. In this issue of Cancer Discovery, Akbay and colleagues show that signaling via mutant EGF receptor (EGFR) in murine lung tumor cells directly upregulates tumor PD-L1 and that therapeutic blockade of this pathway improves survival in EGFR-driven preclinical models-highlighting the dynamic interplay and therapeutic opportunities of cancer cell biology and immune biology.


Subject(s)
B7-H1 Antigen/metabolism , Carcinoma, Non-Small-Cell Lung/immunology , Cytokines/metabolism , ErbB Receptors/metabolism , Lung Neoplasms/immunology , Programmed Cell Death 1 Receptor/metabolism , T-Lymphocytes/immunology , Tumor Escape , Animals , Humans
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