Late-differentiated effector neoantigen-specific CD8+ T cells are enriched in peripheral blood of non-small cell lung carcinoma patients responding to atezolizumab treatment

Abstract

BackgroundThere is strong evidence that immunotherapy-mediated tumor rejection can be driven by tumor-specific CD8+ T cells reinvigorated to recognize neoantigens derived from tumor somatic mutations. Thus, the frequencies or characteristics of tumor-reactive, mutation-specific CD8+ T cells could be used as biomarkers of an anti-tumor response. However, such neoantigen-specific T cells are difficult to reliably identify due to their low frequency in peripheral blood and wide range of potential epitope specificities.MethodsPeripheral blood mononuclear cells (PBMC) from 14 non-small cell lung cancer (NSCLC) patients were collected pre- and post-treatment with the anti-PD-L1 antibody atezolizumab. Using whole exome sequencing and RNA sequencing we identified tumor neoantigens that are predicted to bind to major histocompatibility complex class I (MHC-I) and utilized mass cytometry, together with cellular ‘barcoding’, to profile immune cells from patients with objective response to therapy (n = 8) and those with progressive disease (n = 6). In parallel, a highly-multiplexed combinatorial tetramer staining was used to screen antigen-specific CD8+ T cells in peripheral blood for 782 candidate tumor neoantigens and 71 known viral-derived control peptide epitopes across all patient samples.ResultsNo significant treatment- or response associated phenotypic difference were measured in bulk CD8+ T cells. Multiplexed peptide-MHC multimer staining detected 20 different neoantigen-specific T cell populations, as well as T cells specific for viral control antigens. Not only were neoantigen-specific T cells more frequently detected in responding patients, their phenotypes were also almost entirely distinct. Neoantigen-specific T cells from responder patients typically showed a differentiated effector phenotype, most like Cytomegalovirus (CMV) and some types of Epstein-Barr virus (EBV)-specific CD8+ T cells. In contrast, more memory-like phenotypic profiles were observed for neoantigen-specific CD8+ T cells from patients with progressive disease.ConclusionThis study demonstrates that neoantigen-specific T cells can be detected in peripheral blood in non-small cell lung cancer (NSCLC) patients during anti-PD-L1 therapy. Patients with an objective response had an enrichment of neoantigen-reactive T cells and these cells showed a phenotype that differed from patients without a response. These findings suggest the ex vivo identification, characterization, and longitudinal follow-up of rare tumor-specific differentiated effector neoantigen-specific T cells may be useful in predicting response to checkpoint blockade.Trial registrationPOPLAR trial NCT01903993.Electronic supplementary materialThe online version of this article (10.1186/s40425-019-0695-9) contains supplementary material, which is available to authorized users.

CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entire SARS-CoV-2 proteome and show kinetics of early differentiation

“…Hundreds of candidate epitopes spanning the complete SARS-CoV-2 genome were recently identified as potential targets for a CD8+ T cell response to SARS-CoV-2 14 , 15 . A triple-coded multiplexed peptide-MHC tetramer staining approach was used to screen 408 potential epitopes for recognition by T cell responses across 6 different HLA alleles: HLA-A*01:01, HLA-A*02:01, HLA-A03:01, HLA-A*11:01, HLA-A*24:02 and HLA-B*07:02 16 , 17 . In addition, CD8+ T cells were probed for reactivity against up to 20 different SARS-CoV-2-unrelated control peptides per HLA for each sample (CMV-, EBV-, Influenza-, Adenovirus-, and MART-1-derived epitopes; Table S3 ).…”

“…Antigen-specific triple tetramer positive cells (hits) were identified by an automated peptide-MHC gating method 17 and each hit was confirmed and refined using manual gating. The designation of bona fide antigen-specific T cells was further dependent on (i) the detection cut-off threshold (≥2 events to be detected in each staining configuration), (ii) the frequency correspondence between the two tetramer staining configurations ( ratio between the frequencies of a hit in either staining configuration to be ≤2) and (iii) the background noise (frequencies of specific CD8 T+ cell events must be greater than events from the corresponding CD4 T cell population), as unbiased objective criteria for antigen-specificity assessment 16 . Bulk T cells and true hits from both staining configurations were combined for assessing frequencies, phenotypic and statistical analysis.…”

Identification of Clonal Neoantigens Derived From Driver Mutations in an EGFR-Mutated Lung Cancer Patient Benefitting From Anti-PD-1

“…Previous studies had shown that memory T cells from peripheral blood could respond to neoantigens in tumor tissue (38), and CD8 + PD-1 +/high T-cell subsets were preferentially enriched upon neoantigen stimulation (39,40). Analyzing features of CD8 + T cells seemed to be an alternative choice for monitoring immune response.…”

Adoptive Cell Therapy—Harnessing Antigen-Specific T Cells to Target Solid Tumours

“…Neoantigen-specific T cells can be identified in patients not only with melanoma, but also with epithelial cancers, such as lung cancer [119,120], gastrointestinal cancer [121][122][123], ovarian cancer [124][125][126], breast cancer [127] and pancreatic cancer [128]. Case reports have demonstrated that treatment of the gastrointestinal and breast cancer patients with a T cell population highly enriched in neoepitope-specific T cells caused tumour regression [121,123,127].…”