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Generating responses to tumor antigens poses a challenge for immunotherapy. This phase II trial (NCT02129075) tested fms-like tyrosine kinase 3 (Flt3) ligand pre-treatment enhancement of responses to dendritic cell (DC)-targeting vaccines. We evaluated a regimen of Flt3L (CDX-301) to increase DCs and other antigen-presenting cells, poly-ICLC (TLR3 agonist that activates DCs) and a vaccine comprising anti-DEC-205-NY-ESO-1, a fusion antibody targeting CD205, linked to NY-ESO-1. High-risk melanoma patients were randomized to vaccine, with and without CDX-301. The end point was immune response to NY-ESO-1. Flt3L increased peripheral monocytes and conventional DCs (cDCs), including cross-presenting cDC1 and cDC2 and plasmacytoid DCs. Significant increases in humoral and T-cell responses and activation of DCs, natural killer cells and T cells were elicited. Transcriptional analyses revealed gene signatures associated with CDX-301 induction of an early, durable immune response. This study reveals in vivo effects of Flt3L on innate immune cells in the setting of vaccination, leading to an immunogenic vaccine regimen. Bhardwaj et al. report that adding Flt3 ligand to the treatment strategy effectively increased DC populations and increased T-cell responses in a randomized phase II trial of a DC-targeted vaccine for the melanoma antigen NY-ESO-1.

To uncover underlying mechanisms associated with failure of indoleamine 2,3-dioxygenase 1 (IDO1) blockade in clinical trials, we conducted a pilot, window-of-opportunity clinical study in 17 patients with newly diagnosed advanced high-grade serous ovarian cancer before their standard tumor debulking surgery. Patients were treated with the IDO1 inhibitor epacadostat, and immunologic, transcriptomic, and metabolomic characterization of the tumor microenvironment was undertaken in baseline and posttreatment tumor biopsies. IDO1 inhibition resulted in efficient blockade of the kynurenine pathway of tryptophan degradation and was accompanied by a metabolic adaptation that shunted tryptophan catabolism toward the serotonin pathway. This resulted in elevated nicotinamide adenine dinucleotide (NAD + ), which reduced T cell proliferation and function. Because NAD + metabolites could be ligands for purinergic receptors, we investigated the impact of blocking purinergic receptors in the presence or absence of NAD + on T cell proliferation and function in our mouse model. We demonstrated that A2a and A2b purinergic receptor antagonists, SCH58261 or PSB1115, respectively, rescued NAD + -mediated suppression of T cell proliferation and function. Combining IDO1 inhibition and A2a/A2b receptor blockade improved survival and boosted the antitumor immune signature in mice with IDO1 overexpressing ovarian cancer. These findings elucidate the downstream adaptive metabolic consequences of IDO1 blockade in ovarian cancers that may undermine antitumor T cell responses in the tumor microenvironment.

Summary We introduce a new method for single-cell cytometry studies, FAUST, which performs unbiased cell population discovery and annotation. FAUST processes experimental data on a per-sample basis and returns biologically interpretable cell phenotypes, making it well suited for the analysis of complex datasets. We provide simulation studies that compare FAUST with existing methodology, exemplifying its strength. We apply FAUST to data from a Merkel cell carcinoma anti-PD-1 trial and discover pre-treatment effector memory T cell correlates of outcome co-expressing PD-1, HLA-DR, and CD28. Using FAUST, we then validate these correlates in cryopreserved peripheral blood mononuclear cell samples from the same study, as well as an independent CyTOF dataset from a published metastatic melanoma trial. Finally, we show how FAUST's phenotypes can be used to perform cross-study data integration in the presence of diverse staining panels. Together, these results establish FAUST as a powerful new approach for unbiased discovery in single-cell cytometry., Highlights • An interpretable machine-learning method for cytometry data analysis is developed • Using this, candidate biomarkers of response to therapy are identified and visualized • The method is used to validate our findings on two additional cytometry datasets • It is shown how to integrate findings across datasets with heterogeneous marker panels, The bigger picture Our article introduces a new method, FAUST, which combines novel algorithms for clustering, cluster matching, variable selection, and feature selection. While these algorithms were developed for application to high-dimensional single-cell data—and our article validates this application area with multiple case studies—they are general purpose and can be applied to any collection of related real-valued matrices one wishes to partition. Some useful features of these algorithms to the broader data science community include the following: they estimate the number of clusters across a dataset, they can be applied independently to each matrix in the set of matrices one wishes to cluster, they match clusters across matrices on the basis of data-driven annotations, and the annotations are interpretable in relation to the initial measurement variables. We provide an open-source implementation of our method, https://github.com/RGLab/FAUST, targeting data structures optimized for use in cytometry data analysis., A novel interpretable machine-learning method is developed and applied to discover and visualize candidate biomarkers of response to immunotherapy in single-cell data from a Merkel cell carcinoma clinical trial. We provide demonstrations of how to validate findings on independent cytometry datasets, simulation and benchmark studies comparing our method with existing approaches, and illustrations of how to integrate findings across datasets with diverse staining panels.

Cutaneous T cell lymphomas (CTCL) are rare but aggressive cancers without effective treatments. While a subset of patients derive benefit from PD-1 blockade, there is a critically unmet need for predictive biomarkers of response. Herein, we perform CODEX multiplexed tissue imaging and RNA sequencing on 70 tumor regions from 14 advanced CTCL patients enrolled in a pembrolizumab clinical trial (NCT02243579). We find no differences in the frequencies of immune or tumor cells between responders and non-responders. Instead, we identify topographical differences between effector PD-1+ CD4+ T cells, tumor cells, and immunosuppressive Tregs, from which we derive a spatial biomarker, termed the SpatialScore, that correlates strongly with pembrolizumab response in CTCL. The SpatialScore coincides with differences in the functional immune state of the tumor microenvironment, T cell function, and tumor cell-specific chemokine recruitment and is validated using a simplified, clinically accessible tissue imaging platform. Collectively, these results provide a paradigm for investigating the spatial balance of effector and suppressive T cell activity and broadly leveraging this biomarker approach to inform the clinical use of immunotherapies., PD-1 blockade is effective for only a subset of patients with cutaneous T cell lymphomas. Here, the authors report a spatial biomarker that uses immune and cancer cell topography to predict response to PD-1 blockade in this disease.

BackgroundSipuleucel-T (sip-T) is a Food and Drug Administration (FDA)-approved autologous cellular immunotherapy for metastatic castration-resistant prostate cancer (mCRPC). We hypothesized that combining sip-T with interleukin (IL)-7, a homeostatic cytokine that enhances both B and T cell development and proliferation, would augment and prolong antigen-specific immune responses against both PA2024 (the immunogen for sip-T) and prostatic acid phosphatase (PAP).MethodsFifty-four patients with mCRPC treated with sip-T were subsequently enrolled and randomized 1:1 into observation (n=26) or IL-7 (n=28) arms of a phase II clinical trial (NCT01881867). Recombinant human (rh) IL-7 (CYT107) was given weekly×4. Immune responses were evaluated using flow cytometry, mass cytometry (CyTOF), interferon (IFN)-γ ELISpot, 3H-thymidine incorporation, and ELISA.ResultsTreatment with rhIL-7 was well tolerated. For the rhIL-7-treated, but not observation group, statistically significant lymphocyte subset expansion was found, with 2.3–2.6-fold increases in CD4+T, CD8+T, and CD56bright NK cells at week 6 compared with baseline. No significant differences in PA2024 or PAP-specific T cell responses measured by IFN-γ ELISpot assay were found between rhIL-7 and observation groups. However, antigen-specific T cell proliferative responses and humoral IgG and IgG/IgM responses significantly increased over time in the rhIL-7-treated group only. CyTOF analyses revealed pleiotropic effects of rhIL-7 on lymphocyte subsets, including increases in CD137 and intracellular IL-2 and IFN-γ expression. While not powered to detect clinical outcomes, we found that 31% of patients in the rhIL-7 group had prostate specific antigen (PSA) doubling times of >6 months, compared with 14% in the observation group.ConclusionsTreatment with rhIL-7 led to a significant expansion of CD4+ and CD8+ T cells, and CD56bright natural killer (NK) cells compared with observation after treatment with sip-T. The rhIL-7 treatment also led to improved antigen-specific humoral and T cell proliferative responses over time as well as to increased expression of activation markers and beneficial cytokines. This is the first study to evaluate the use of rhIL-7 after sip-T in patients with mCRPC and demonstrates encouraging results for combination approaches to augment beneficial immune responses.

PURPOSE To assess the efficacy of pembrolizumab in patients with advanced relapsed or refractory mycosis fungoides (MF) or Sézary syndrome (SS). PATIENTS AND METHODS CITN-10 is a single-arm, multicenter phase II trial of 24 patients with advanced MF or SS. Patients were treated with pembrolizumab 2 mg/kg every 3 weeks for up to 24 months. The primary end point was overall response rate by consensus global response criteria. RESULTS Patients had advanced-stage disease (23 of 24 with stage IIB to IV MF/SS) and were heavily pretreated with a median of four prior systemic therapies. The overall response rate was 38% with two complete responses and seven partial responses. Of the nine responding patients, six had 90% or more improvement in skin disease by modified Severity Weighted Assessment Tool, and eight had ongoing responses at last follow-up. The median duration of response was not reached, with a median response follow-up time of 58 weeks. Immune-related adverse events led to treatment discontinuation in four patients. A transient worsening of erythroderma and pruritus occurred in 53% of patients with SS. This cutaneous flare reaction did not result in treatment discontinuation for any patient. The flare reaction correlated with high PD-1 expression on Sézary cells but did not associate with subsequent clinical responses or lack of response. Treatment responses did not correlate with expression of PD-L1, total mutation burden, or an interferon-γ gene expression signature. CONCLUSION Pembrolizumab demonstrated significant antitumor activity with durable responses and a favorable safety profile in patients with advanced MF/SS.

Anti-PD-1 immunotherapies have transformed cancer treatment, yet the determinants of clinical response are largely unknown. We performed CODEX multiplexed tissue imaging and RNA sequencing on 70 tumor regions from 14 advanced cutaneous T cell lymphoma (CTCL) patients enrolled in a clinical trial of pembrolizumab therapy. Clinical response was not associated with the frequency of tumor-infiltrating T cell subsets, but rather with striking differences in the spatial organization and functional immune state of the tumor microenvironment (TME). After treatment, pembrolizumab responders had a localized enrichment of tumor and CD4+ T cells, which coincided with immune activation and cytotoxic PD-1+ CD4+ T cells. In contrast, non-responders had a localized enrichment of Tregs pre- and post-treatment, consistent with a persistently immunosuppressed TME and exhausted PD-1+ CD4+ T cells. Integrating these findings by computing the physical distances between PD-1+ CD4+ T cells, tumor cells, and Tregs revealed a spatial biomarker predictive of pembrolizumab response. Finally, the chemokine CXCL13 was upregulated in tumor cells in responders post-treatment, suggesting that chemoattraction of PD-1+ CD4+ T cells towards tumor cells facilitates a positive outcome. Together, these data show that T cell topography reflects the balance of effector and suppressive activity within the TME and predicts clinical response to PD-1 blockade in CTCL.

BackgroundClinical benefit from programmed cell death 1 receptor (PD-1) inhibitors relies on reinvigoration of endogenous antitumor immunity. Nonetheless, robust immunological markers, based on circulating immune cell subsets associated with therapeutic efficacy are yet to be validated.MethodsWe isolated peripheral blood mononuclear cell from three independent cohorts of melanoma and Merkel cell carcinoma patients treated with PD-1 inhibitor, at baseline and longitudinally after therapy. Using multiparameter flow cytometry and cell sorting, we isolated four subsets of CD8+ T cells, based on PD-1 and TIGIT expression profiles. We performed phenotypic characterization, T cell receptor sequencing, targeted transcriptomic analysis and antitumor reactivity assays to thoroughly characterize each of these subsets.ResultsWe documented that the frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T-cells after 1 month of anti-PD-1 therapy was associated with clinical response and overall survival. This DPOS T-cell population was enriched in highly activated T-cells, tumor-specific and emerging T-cell clonotypes and T lymphocytes overexpressing CXCR5, a key marker of the CD8 cytotoxic follicular T cell population. Additionally, transcriptomic profiling defined a specific gene signature for this population as well as the overexpression of specific pathways associated with the therapeutic response.ConclusionsOur results provide a convincing rationale for monitoring this PD-1+TIGIT+ circulating population as an early cellular-based marker of therapeutic response to anti-PD-1 therapy.

Background Sipuleucel-T (Provenge) is the first therapeutic vaccination approved by the FDA so far, indicated for advanced metastatic prostate cancer patients. Despite an improvement of the overall survival, the benefits of the therapy are still short-term so increasing the duration of the efficacy is necessary. Specifically, T-cell anergy is one of the challenges that we need to overcome to improve the overall efficacy. IL-7 is known to promote the naive T cell activation and to increase the proliferation and activation of the T cell memory subsets. Therefore, in this phase II clinical trial, we tested the therapeutic potential of a human recombinant glycosylated IL-7 after completion of the Provenge therapy on asymptomatic advanced prostate cancer patients. Methods To get a comprehensive analysis of the immune landscape in these patients, we performed CyTOF analysis on PBMC samples obtained at week 1 (baseline) and week 6 after the beginning of the IL-7 therapy. After stimulation with PMA/Ionomycin, we proceeded to surface and intracellular cytokine staining before acquisition on the CyTOF. The data were then analyzed by expert gating on Cytobank. Results At 6 weeks post therapy, our data showed an increase in the number of circulating T lymphocytes in the IL-7 cohort, especially CD8 T cells, in accordance with previous literature. Even though of the frequency of CD4 T cells did not increase, the cells showed greater functionalities, with increased expression of IL-2, TNFα and IL-6 upon stimulation by PMA-Ionomycine. Cytotoxic subsets were also positively affected, with increased expression of IFNγ in CD8 T cells, TNFα in NK cells and IL-2 in γδ T cells. Moreover, PD-1 expression was decreased on CD4, CD8 and γδ T cells while CD137 increased on CD4, CD8 and NK cells. In addition, despite a reduction in the pool of circulating monocytes, we observed higher TNFα expression in these cells. Conclusions Altogether, our data revealed multiple effects of IL-7 in these patients, highlighting a complex set of in vivo mechanisms. In the future, knowledge of these effects may help in choosing the best agents to use in combination with IL-7 and/or the best patients to benefit from IL-7 as part of their therapeutic approach. Trial Registration NCT01881867 Ethics Approval The study was last approved by Fred Hutchinson Cancer Research Center Institutional Review Board, IR file 8037, on January 23, 2020

Key Points PD-L1 structural variants are recurrent in mycosis fungoides with large cell transformation. PD-L1 structural variants in relapsed/refractory mycosis fungoides should prompt consideration of treatment with PD-1 inhibitors.

Background We recently reported a 56% objective response rate in patients with advanced Merkel cell carcinoma (MCC) receiving pembrolizumab. However, a biomarker predicting clinical response was not identified. Methods Pretreatment FFPE tumor specimens (n = 26) were stained for CD8, PD-L1, and PD-1 by immunohistochemistry/immunofluorescence (IHC/IF), and the density and distribution of positive cells was quantified to determine the associations with anti-PD-1 response. Multiplex IF was used to test a separate cohort of MCC archival specimens (n = 16), to identify cell types expressing PD-1. Results Tumors from patients who responded to anti-PD-1 showed higher densities of PD-1+ and PD-L1+ cells when compared to non-responders (median cells/mm2, 70.7 vs. 6.7, p = 0.03; and 855.4 vs. 245.0, p = 0.02, respectively). There was no significant association of CD8+ cell density with clinical response. Quantification of PD-1+ cells located within 20 μm of a PD-L1+ cell showed that PD-1/PD-L1 proximity was associated with clinical response (p = 0.03), but CD8/PD-L1 proximity was not. CD4+ and CD8+ cells in the TME expressed similar amounts of PD-1. Conclusions While the binomial presence or absence of PD-L1 expression in the TME was not sufficient to predict response to anti-PD-1 in patients with MCC, we show that quantitative assessments of PD-1+ and PD-L1+ cell densities as well as the geographic interactions between these two cell populations correlate with clinical response. Cell types expressing PD-1 in the TME include CD8+ T-cells, CD4+ T-cells, Tregs, and CD20+ B-cells, supporting the notion that multiple cell types may potentiate tumor regression following PD-1 blockade. Electronic supplementary material The online version of this article (10.1186/s40425-018-0404-0) contains supplementary material, which is available to authorized users.

BackgroundMerkel cell carcinoma (MCC) is an aggressive human skin cancer primarily induced by Merkel Cell Polyomavirus (MCPyV) driven by expression of the oncogenic T antigens (T-Ags): Large T and Small T antigen. Checkpoint inhibition therapy blocking the programmed cell death protein-1 (PD-1) pathway has proven effective with a clinical response rate up to 58%,1 highlighting the critical role of immune surveillance for tumor control. Yet, evidence for the impact of T-Ag-specific T cells following immunotherapy is still limited.MethodsPotential CD8+ T cell epitopes derived from the T-Ags and the Viral capsid protein 1 (VP1) were predicted with netMHCpan 4.0 as 9- and 10-mer peptides with a rank score ResultsAcross all patients, 40 T-Ag-specific CD8+ T-cell populations were detected recognizing 31 epitopes restriction to 14 different HLA class I types. T-Ag-specific CD8+ T cells were detected in responders (complete and partial response, n=17) during therapy with a trend of increased number of responses observed after therapy initiation. Whereas only a single T-Ag-specific population was detectable in non-responders (stable and progressive disease, n=7). Moreover, the T cell repertoire after therapy initiation was significantly increased in the responder group compared to non-responder with the T-Ag-specific T cells showing an activated effector memory phenotype.ConclusionsThe current study indicates that the T-Ag-specific T cells are associated with clinical benefit to checkpoint inhibitor therapy. Furthermore, the broad identification of novel T-Ag-derived T cell epitopes could potentially facilitate the use of targeted T cell therapy to enhance T cell recognition and clearance of MCC in combination with checkpoint inhibition.AcknowledgementsSupported by the Cancer Immunotherapy Trials Network (CITN)ReferenceNghiem P, Bhatia S, Lipson E. Three-year survival, correlates and salvage therapies in patients receiving first-line pembrolizumab for advanced Merkel cell carcinoma. J Immunother cancer 2021;9:e002478.

High-dimensional single-cell cytometry is routinely used to characterize patient responses to cancer immunotherapy and other treatments. This has produced a wealth of datasets ripe for exploration but whose biological and technical heterogeneity make them difficult to analyze with current tools. We introduce a new interpretable machine learning method for single-cell mass and flow cytometry studies, FAUST, that robustly performs unbiased cell population discovery and annotation. FAUST processes data on a per-sample basis and returns biologically interpretable cell phenotypes that can be compared across studies, making it well-suited for the analysis and integration of complex datasets. We demonstrate how FAUST can be used for candidate biomarker discovery and validation by applying it to a flow cytometry dataset from a Merkel cell carcinoma anti-PD-1 trial and discover new CD4+ and CD8+ effector-memory T cell correlates of outcome co-expressing PD-1, HLA-DR, and CD28. We then use FAUST to validate these correlates in an independent CyTOF dataset from a published metastatic melanoma trial. Importantly, existing state-of-the-art computational discovery approaches as well as prior manual analysis did not detect these or any other statistically significant T cell sub-populations associated with anti-PD-1 treatment in either data set. We further validate our methodology by using FAUST to replicate the discovery of a previously reported myeloid correlate in a different published melanoma trial, and validate the correlate by identifying itde novoin two additional independent trials. FAUST’s phenotypic annotations can be used to perform cross-study data integration in the presence of heterogeneous data and diverse immunophenotyping staining panels, enabling hypothesis-driven inference about cell sub-population abundance through a multivariate modeling framework we callPhenotypic andFunctionalDifferentialAbundance (PFDA). We demonstrate this approach on data from myeloid and T cell panels across multiple trials. Together, these results establish FAUST as a powerful and versatile new approach for unbiased discovery in single-cell cytometry.

PURPOSE Merkel cell carcinoma (MCC) is an aggressive skin cancer often caused by the Merkel cell polyomavirus. Clinical trials of programmed cell death-1 pathway inhibitors for advanced MCC (aMCC) demonstrate increased progression-free survival (PFS) compared with historical chemotherapy data. However, response durability and overall survival (OS) data are limited. PATIENTS AND METHODS In this multicenter phase II trial (Cancer Immunotherapy Trials Network-09/Keynote-017), 50 adults naïve to systemic therapy for aMCC received pembrolizumab (2 mg/kg every 3 weeks) for up to 2 years. Radiographic responses were assessed centrally per Response Evaluation Criteria in Solid Tumors (RECIST) v1.1. RESULTS Among 50 patients, the median age was 70.5 years, and 64% had Merkel cell polyomavirus–positive tumors. The objective response rate (ORR) to pembrolizumab was 56% (complete response [24%] plus partial response [32%]; 95% CI, 41.3% to 70.0%), with ORRs of 59% in virus-positive and 53% in virus-negative tumors. Median follow-up time was 14.9 months (range, 0.4 to 36.4+ months). Among 28 responders, median response duration was not reached (range, 5.9 to 34.5+ months). The 24-month PFS rate was 48.3%, and median PFS time was 16.8 months (95% CI, 4.6 months to not estimable). The 24-month OS rate was 68.7%, and median OS time was not reached. Although tumor viral status did not correlate with ORR, PFS, or OS, there was a trend toward improved PFS and OS in patients with programmed death ligand-1–positive tumors. Grade 3 or greater treatment-related adverse events occurred in 14 (28%) of 50 patients and led to treatment discontinuation in seven (14%) of 50 patients, including one treatment-related death. CONCLUSION Here, we present the longest observation to date of patients with aMCC receiving first-line anti–programmed cell death-1 therapy. Pembrolizumab demonstrated durable tumor control, a generally manageable safety profile, and favorable OS compared with historical data from patients treated with first-line chemotherapy.

BackgroundMerkel cell carcinoma (MCC) is an aggressive skin cancer associated with poor survival. Programmed cell death-1 (PD-1) pathway inhibitors have shown high rates of durable tumor regression compared with chemotherapy for MCC. The current study was undertaken to assess baseline and on-treatment factors associated with MCC regression and 3-year survival, and to explore the effects of salvage therapies in patients experiencing initial non-response or tumor progression after response or stable disease following first-line pembrolizumab therapy on Cancer Immunotherapy Trials Network-09/KEYNOTE-017.MethodsIn this multicenter phase II trial, 50 patients with advanced unresectable MCC received pembrolizumab 2 mg/kg every 3 weeks for ≤2 years. Patients were followed for a median of 31.8 months.ResultsOverall response rate to pembrolizumab was 58% (complete response 30%+partial response 28%; 95% CI 43.2 to 71.8). Among 29 responders, the median response duration was not reached (NR) at 3 years (range 1.0+ to 51.8+ months). Median progression-free survival (PFS) was 16.8 months (95% CI 4.6 to 43.4) and the 3-year PFS was 39.1%. Median OS was NR; the 3-year OS was 59.4% for all patients and 89.5% for responders. Baseline Eastern Cooperative Oncology Group performance status of 0, greater per cent tumor reduction, completion of 2 years of treatment and low neutrophil-to-lymphocyte ratio were associated with response and longer survival. Among patients with initial disease progression or those who developed progression after response or stable disease, some had extended survival with subsequent treatments including chemotherapies and immunotherapies.ConclusionsThis study represents the longest available follow-up from any first-line anti-programmed death-(ligand) 1 (anti-PD-(L)1) therapy in MCC, confirming durable PFS and OS in a proportion of patients. After initial tumor progression or relapse following response, some patients receiving salvage therapies survived. Improving the management of anti-PD-(L)1-refractory MCC remains a challenge and a high priority.Trial registration numberNCT02267603.

Cutaneous T-cell lymphoma (CTCL) is a rare, incurable CD4+ T cell malignancy of the skin with a 5-year survival rate of less than 30% in advanced stages. Immune checkpoint inhibitors, such as anti-PD-1 antibodies, have shown dramatic clinical efficacy in multiple advanced cancers, but the majority of cancer patients do not respond to these treatments. The clinical use of immunotherapies will increase considerably in the near future; therefore, predictive biomarkers of response to stratify patients for treatment are needed to limit potentially devastating adverse effects and reduce costs for healthcare systems. A clinical trial of the anti-PD-1 antibody pembrolizumab in CTCL showed that 38% of patients have a durable clinical response. However, standard tests, including comprehensive immunohistochemistry and single-cell quantification of PD-1 expression, have so far failed to identify a predictive biomarker for pembrolizumab response in this cohort. We reasoned that deep profiling of the CTCL tumor microenvironment (TME) using CODEX–a novel technology that allows for highly multiplexed tissue microscopy with >50 simultaneous parameters–could provide insight into the mechanisms of pembrolizumab response and enable prediction. We analyzed the CTCL TME using a tissue microarray of matched biopsies taken before and after pembrolizumab therapy in 7 responders and 7 non-responders. Imaging of 55 markers allowed discriminating malignant CD4+ tumor cells from reactive CD4+ T cells based on nuclear size and differential expression of CD7, CD25 and Ki-67. Unsupervised machine learning followed by supervised curation identified 21 different cell type clusters with spatial information. Integrating these data using advanced computational analysis revealed 10 distinct, conserved cellular neighborhoods (CNs) in the CTCL TME that changed in frequency and distribution during pembrolizumab therapy. In responders, effector-type CNs, including a tumor/dendritic cell CN and a tumor/CD4+ T cell CN, were significantly increased after treatment. In contrast, in non-responders, an immunosuppressive-type CN enriched in regulatory T cells was significantly increased before and after therapy. Importantly, the global frequencies in the tissues of the cell types defining these CNs were not different between patient groups. In addition, RNA sequencing of matched tissue sections revealed higher expression of effector-type cytokines and chemokines in responders. In sum, highly multiplexed analysis of the CTCL TME architecture in combination with RNA sequencing allows discovering novel, predictive spatial biomarkers of immunotherapy response and will pave the way for future studies that functionally address the identified cell types and cellular interactions. Citation Format: Christian M. Schürch, Darci J. Phillips, Belén Rivero Gutierrez, Magdalena Matusiak, Salil S. Bhate, Graham L. Barlow, Steven P. Fling, Nirasha Ramchurren, Robert H. Pierce, Martin A. Cheever, Michael S. Khodadoust, Robert West, Youn H. Kim, Garry P. Nolan. Cellular neighborhoods predict pembrolizumab response in cutaneous T cell lymphoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6669.

Immunotherapies targeting the PD-1 pathway have profoundly transformed the clinical care of cancer patients for a growing variety of cancer types. However, most patients do not experience durable clinical benefit. The definition of robust and convenient biomarkers of PD-1 therapy efficacy to stratify patients beforehand or early after initiation of the therapy that could guide therapeutic management is still lacking while being a very active research field. Biomarkers described to date include tumor burden, neoantigen load, presence and number of PD-1+ CD8+ at the tumor margin, T-cell inflamed tumor microenvironment and PD-L1 expression by the tumor cells or other immune cells and composition of the gut microbiota. Most of these parameters are closely related/influenced by the presence, activation status and functional capacities of CD8+ T cells infiltrating the tumor site demonstrating their pivotal role for anti-PD-1 mediated anti-tumor efficacy. A population of PD-1high CD8 TILs was consequently described as predictive of PD-1 blockade in NSCLC. The exact contribution for clinical efficacy of TILs versus distinct CD8+ T cells from peripheral origins recirculating to the tumor site remains to be elucidated. Notably, immunological responses to PD-1 blockade at the periphery were described within the very first days following the first therapy dose. Therefore, describing circulating cellular population predictive of PD-1 inhibitor efficacy could represent a convenient, non-invasive and rapid method to assess anti-tumor benefits. Original findings reported in this study identified a circulating CD8 T cell population delineated by the co-expression of TIGIT and PD-1 inhibitory receptors as an early immune marker of anti-PD-1 efficacy in three independent cohorts of cancer patients (two melanoma patient's cohorts and one Merkel-cell carcinoma patient's cohort). The frequency of this double positive (DPOS) population even appeared predictive of PD-1 inhibitor therapy efficacy at baseline in the MCC cohort. Furthermore, to understand the mechanistical relevance of this subset for PD-1 blockade efficacy, we thoroughly described this DPOS T cell subset by flow cytometry, gene expression analysis, anti-tumor reactivity assay and TCR repertoire analysis, and compared it to its double negative (DNEG), PD-1 and TIGIT single positive counterparts. This DPOS subset was enriched in activated and proliferative T cells, retained expression of co-stimulatory molecules and was enriched for common features with Tfc. Moreover, this subpopulation exhibited a specific gene signature, strongly predictive of long-term survival in melanoma patients (TCGA analyses). We demonstrated that this subpopulation was enriched in tumor-specific T-cells (ELISPOT analysis against 11 antigen-derived peptides). Finally, clustering of TCR clonotypes revealed that the DPOS T cell population was significantly enriched in emerging clonotypes in responding patients, after 1 month of anti-PD-1 therapy echoing recent work from others. Our findings provide a compelling rationale to measure PD-1+TIGIT+ CD8 T-cell subset in the blood of cancer patients to monitor early anti-PD1 mediated clinical efficacy, and to use DPOS T cells as a window to study the dynamic changes that underly successful antitumor immunity. Citation Format: Sylvain Simon, Valentin Voillet, Virginie Vignard, Zhong Wu, Camille Dabrowski, Nicolas Jouand, Tiffany Beauvais, Amir Khammari, Cecile Braudeau, Regis Josien, Olivier Adotevi, Caroline Laheurte, Francçois Aubin, Charles Nardin, Samuel Rulli, Raphaël Gottardo, Nirasha Ramchurren, Cheever Martin, Steven P. Fling, Candice D. Church, Paul Nghiem, Brigitte Dreno, Stanley R. Riddell, Nathalie Labarriere. PD-1 and TIGIT co-expression identifies a circulating CD8 T cell population predictive of response to anti-PD-1 therapy in melanoma and Merkel-cell carcinoma patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4476.

Background Merkel cell carcinoma (MCC) is an aggressive skin cancer that frequently responds to anti-PD-1 therapy. MCC is associated with sun exposure and, in 80% of cases, Merkel cell polyomavirus (MCPyV). MCPyV-specific T and B cell responses provide a unique opportunity to study cancer-specific immunity throughout PD-1 blockade therapy. Methods Immune responses were assessed in patients (n = 26) with advanced MCC receiving pembrolizumab. Peripheral blood mononuclear cells (PBMC) were collected at baseline and throughout treatment. MCPyV-oncoprotein antibodies were quantified and T cells were assessed for MCPyV-specificity via tetramer staining and/or cytokine secretion. Pre-treatment tumor biopsies were analyzed for T cell receptor clonality. Results MCPyV oncoprotein antibodies were detectable in 15 of 17 (88%) of virus-positive MCC (VP-MCC) patients. Antibodies decreased in 10 of 11 (91%) patients with responding tumors. Virus-specific T cells decreased over time in patients who had a complete response, and increased in patients who had persistent disease. Tumors that were MCPyV(+) had a strikingly more clonal (less diverse) intratumoral TCR repertoire than virus-negative tumors (p = 0.0001). Conclusions Cancer-specific T and B cell responses generally track with disease burden during PD-1 blockade, in proportion to presence of antigen. Intratumoral TCR clonality was significantly greater in VP-MCC than VN-MCC tumors, suggesting expansion of a limited number of dominant clones in response to fewer immunogenic MCPyV antigens. In contrast, VN-MCC tumors had lower clonality, suggesting a diverse T cell response to numerous neoantigens. These findings reveal differences in tumor-specific immunity for VP-MCC and VN-MCC, both of which often respond to anti-PD-1 therapy. Electronic supplementary material The online version of this article (10.1186/s40425-018-0450-7) contains supplementary material, which is available to authorized users.

Figure S1. CD8+ cell densities correlate with the presence of McPyV, but PD-1 densities do not correlate with viral status. Figure S2. PD-1+ cell densities in both the peritumoral and intratumoral regions correlate with anti-PD-1 response, but CD8+ cell densities in these regions do not. Figure S3. Pathologist scores for PD-L1 expression levels did not associate with response to anti-PD-1 in patients with MCC. Figure S4. Computer-assisted quantitation of PD-L1 in the PT and IT regions of tumor can help distinguish anti-PD-1 responders (R) from non-responders (NR). Figure S5. CD8+, PD-1+, and PD-L1+ TME cell densities by quartile from MCC patients receiving anti-PD1. Figure S6. The density of PD-L1+ cells adjacent to a PD-1+ cell correlates with clinical response to anti-PD-1. (PDF 611Â kb)

Cutaneous T cell lymphoma (CTCL) is a CD4+ T cell malignancy of the skin with heterogeneous outcomes and limited treatment options. Monoclonal antibodies directed against PD-1, such as pembrolizumab, have shown impressive efficacy in multiple advanced malignancies, and are currently tested in clinical trials in patients with CTCL. Initial data indicate that about half of the patients experience treatment response, whereas the other half are non-responders. Non-responders can be further divided into patients with stable disease versus rapid progressors. It is currently unknown why some CTCL patients respond to pembrolizumab while others rapidly progress, and no predictive biomarkers are available. Single-cell analysis approaches to identify biomarkers of response, for example quantifying the expression of PD-1 on tumor cells vs. reactive immune cells, have not enabled stratification of patients. We therefore hypothesized that more complex spatial cellular interactions within the immune tumor microenvironment (iTME) of CTCL could provide insight into the mechanisms of pembrolizumab response and enable prediction. We applied CODEX (CO-Detection by indEXing) highly multiplexed tissue imaging to study the CTCL iTME in matched biopsies before and after pembrolizumab therapy in 7 responders and 7 non-responders (see the Figure). Using 54 markers simultaneously allowed discriminating malignant CD4+ tumor cells from reactive CD4+ T cells and identified 30 different cell clusters with spatial information, including an M2 macrophage cluster that was enriched in non-responders before therapy. Unexpectedly, in pembrolizumab responders compared to non-responders, PD-1 expression levels were higher in multiple clusters of tumor cells and reactive T cells. Computational spatial analysis revealed ten distinct, conserved cellular neighborhoods in the CTCL iTME that changed in composition and frequency during therapy. Interestingly, one cellular neighborhood to be presented dramatically increased after therapy only in responders. Therefore, highly multiplexed spatial analysis of the CTCL iTME allows discovering novel, predictive biomarkers of immunotherapy response and will pave the way for future studies that functionally address the identified cell types and cellular interactions. Disclosures Khodadoust: Corvus Pharmaceuticals: Research Funding. Kim:miRagen: Research Funding; Merck: Research Funding; Medivir: Honoraria, Membership on an entity's Board of Directors or advisory committees; Innate Pharma: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Soligenix: Research Funding; Forty Seven Inc: Research Funding; Neumedicine: Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Trillium: Research Funding; Elorac: Research Funding; Galderma: Research Funding; Corvus: Honoraria, Membership on an entity's Board of Directors or advisory committees; Portola Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Seattle Genetics: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Kyowa Hakko Kirin: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Eisai: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Horizon: Research Funding. Nolan:Akoya Biosciences Inc.: Consultancy, Equity Ownership, Patents & Royalties.

Twenty-one invasive squamous-cell carcinomas (SCC) of the bladder from Schistosoma-hematobium-infected patients were examined immunohistochemically for the expression of p53, Rb, EGFR and c-erbB-2 proteins; and screened by single-strand conformation polymorphism and sequencing for mutations in the ras (H, N, K) codon hotspots (12, 13, 61) and p53 (exons 4-9) genes. Positive staining for p53, EGFR and c-erbB-2 was reported in 38, 67 and 28% of tumors respectively. Only one of the tumors, the only one that was poorly differentiated, displayed an absence of nuclear Rb staining. Ras alterations were detected in the H-ras gene in 3 tumors, 2 of which harbored a codon-13 (Gly-->Arg) and one a codon-12 (Gly-->Ser) point mutation. p53 mutations were recorded in 12 tumors (57%), 6 of which stained positively for p53. Four tumors had exon-7 mutations (codons 235, 241 and 249; one tumor had 2 exon-7 mutations). Eight tumors were mutated in exon 8 (codons 264, 271, 273, 285, 286, 288 and 294), 5 of which harbored multiple mutations. One tumor had an insertion/deletion event in exon 9. The frequency of detection of over-expression of EGFR and c-erbB-2 in bilharzial-bladder lesions is comparable to that reported in TCC, contrasting with the infrequent loss of Rb expression found in invasive lesions associated with schistosomiasis infection. However, the detection of multiple p53 mutations in these lesions is suggestive of the involvement of a carcinogenic agent with maintenance of preferential activation of the H-ras gene.

The identification of novel T cell antigens is central to basic and translational research in autoimmunity, tumor immunology, transplant immunology, and vaccine design for infectious disease. However, current methods for T cell antigen discovery are low throughput, and fail to explore a wide range of potential antigen-receptor interactions. To overcome these limitations, we developed a method in which programmable microarrays are used to cost-effectively synthesize complex libraries of thousands of minigenes that collectively encode the content of hundreds of candidate protein targets. Minigene-derived mRNA are transfected into autologous antigen presenting cells and used to challenge complex populations of purified peripheral blood CD8+ T cells in multiplex, parallel ELISPOT assays. In this proof-of-concept study, we apply synthetic minigene screening to identify two novel pancreatic islet autoantigens targeted in a patient with Type I Diabetes. To our knowledge, this is the first successful screen of a highly complex, synthetic minigene library for identification of a T cell antigen. In principle, responses against the full protein complement of any tissue or pathogen can be assayed by this approach, suggesting that further optimization of synthetic libraries holds promise for high throughput antigen discovery.

Background: Urinary cytology has long been used as a noninvasive screen for the detection of urinary tract cancer but is limited by the generation of false positive and false negative results. More recently, molecular changes associated with urothelial neoplastic progression have been identified in DNA from urine sediments, demonstrating an alternative approach for identifying neoplastic change in the bladder. Purpose: The purpose of this prospective study was to determine the value of detection of H-ras (also known as HRAS) mutations in urine sediment DNA as a clinical indicator of tumor presence, recurrence, and/or progression. Methods: Urine sediments were collected from 100 patients presenting with bladder tumors, with follow-up samples collected from 19 patients. DNA extracted from urine sediments was analyzed for changes in exon 1 of the H-ras gene, using single-strand conformation polymorphism (SSCP) analysis. A representative number of aberrant H-ras/SSCP migrating bands were excised and sequenced to confirm the presence of a mutation. Human bladder specimens were obtained from patients (93 of the 100 patients initially and 18 of the 19 patients studied by follow-up) and histologically evaluated for tumor content and grade. Results: Mutations in exon 1 of the H-ras gene were detected in urine sediments from 44% (44 of 100) of the patients; concordant results were obtained by cytologic analysis, where 33% (31 of 93) of the patients displayed positive cytology. Analysis of the distribution of abnormalities with tumor grade revealed greater detection of low-grade (1-2) lesions using ras analysis (47%) compared with cytology (16%). In contrast, cytology was more effective in identifying the presence of carcinoma in situ. Combined results from these two approaches substantially increased the sensitivity of tumor detection, resulting in the identification of tumors in 60% of patients. Conclusions: Identification of H-ras mutations in DNA from urine sediments facilitates the detection of low-grade bladder tumors and, in combination with cytology, increases the overall tumor detection from 33% to 60%. Preliminary results in patient follow-up suggest that detection of H-ras mutations may have some clinical utility in detecting the presence of abnormal cells in the absence of an overt lesion following cytoscopy or positive cytology

Objective: To establish whether specific K- ras alterations are predictive of less aggressive tumor behavior and subsequently those patients who are most likely to benefit from resection of hepatic metastases from colorectal carcinoma. Design: Evaluation of long-term survivors of hepatic resection for metastases of colorectal carcinoma (median survival, 85 months). Results: DNA, extracted from 26 paraffin-embedded hepatic metastases from 19 patients, was analyzed using single-strand conformation polymorphism and direct sequence analysis of codons 12 and 13 of the K- ras gene. Seven of 19 patients were found to harbor K- ras mutations. A similar frequency and spectrum of K- ras mutational events was detected in 14 patients with short-term survival following pathologic diagnosis of hepatic metastasis. Conclusions: Neither the presence of a K- ras mutational event nor the precise nucleotide change are predictive of less aggressive tumor behavior, and genetic alterations at this locus alone cannot be used to select patients undergoing resection of hepatic metastases from colorectal carcinoma. (Arch Surg. 1995;130:9-14)

Recent identification of genetic alterations in colon polyps and tumors has allowed construction of a hypothesis for the molecular basis of colon carcinogenesis. The consistency of observed genetic changes has inspired enthusiastic anticipation of new diagnostic tools and interventions for colon cancer. Appropriate animal models are crucial to the testing of molecular postulates as well as the development of markers and therapies for colon carcinogenesis. We discuss herein the various animal models that are currently used for the study of colon cancer as well as those that hold promise for the future. The contributions, drawbacks, and potential uses for the chemical carcinogen model, the multiple intestinal neoplasia model, transgenic animals, and the reconstruction model in the study of colon carcinoma are presented. (Arch Surg. 1993;128:647-653)

The growth of the cultured human breast carcinoma cell line NUB 1 as well as that of other cultured malignant cells has been shown to be inhibited by addition of gamma-linolenic acid (GLA) to the culture medium. It has previously been suggested that these findings may be attributed to correction of a GLA deficiency in malignant cells, with supplementation of this fatty acid leading to increased prostaglandin (PG) production and consequent growth inhibition. To test this hypothesis the effect of 50 ug/ml concentrations of GLA and its sequential metabolite dihomo-gamma-linolenic acid (DGLA) and cell growth, morphology and prostaglandin (PGE and PGF) production by NUB 1 cells was investigated. GLA increased PGE and PGF production, inhibited cell growth and caused accumulation of lipid containing cytoplasmic granules. While treatment with DGLA increased PG production to a significantly greater extent than GLA administration it had no apparent effect on cell growth of morphology and did not inhibit cell growth. These findings suggest that some action other than the ability to increase PG production may be responsible for the inhibitory effects produced by GLA in malignant cells.

Prostaglandin production by two continuous human esophageal carcinoma cell lines HCU 18 and HCU 39 derived from poorly and moderately differentiated source tumors, respectively, was investigated. Behavior of both lines in vitro and upon sc inoculation into athymic randombred BALB/c nude mice was also assessed. Approximately half the xenografts induced by HCU 18 cells were invasive, whereas those initiated by HCU 39 cells were all well encapsulated. Although metastases were not detected in mice given injections of HCU 39 cells, metastatic tumors developed in 2 mice inoculated with HCU 18 cells. In addition, HCU 18 cells produced significantly more prostaglandin E (PGE) and prostaglandin F (PGF) than HCU 39 cells. These findings suggest a relationship between PGE and PGF production by human esophageal carcinoma cells and their invasive and metastatic potential in athymic mice.

Frequency of tetramer+ CD8 T cells. Frequency of MCPyV tetramer positive CD8 T cells are reported in percent of all CD8s with background subtracted. Abbreviations for RECIST 1.1 response criteria are as follows: CR = complete response; PR = partial response; PD = progressive disease. (DOCX 69 kb)

Class I HLA Tetramers and MCPyV peptide pools. Description of data: A) Summary of HLA and peptide combinations used for CD8 class I tetramers including which position of the MCPyV oncoprotein (small, common, or large T antigen) the peptide corresponds to. B) Schematic of MCPyV peptide pools and locations of tetramer epitopes. Details of peptide pools are available in Iyer et al., 2011. (DOCX 364â kb)

Frequency of IFN-γ and/or IL-2 secreting CD8 T cells in response to Merkel polyomavirus peptide pools. IFN-γ and/or IL-2 in A) 2 of 13 VP-MCC responders and B) 1 of 4 VP-MCC non-responders was detectible via flow cytometry after a 16 h stimulation with MCPyV peptide pools. Dotted line represents background signal cutoff. *Post = first blood draw after initiation of treatment. (DOCX 425 kb)

Frequency of tetramer+ CD8 T cells. Frequency of MCPyV tetramer positive CD8 T cells are reported in percent of all CD8s with background subtracted. Abbreviations for RECIST 1.1 response criteria are as follows: CR = complete response; PR = partial response; PD = progressive disease. (DOCX 69 kb)

Class I HLA Tetramers and MCPyV peptide pools. Description of data: A) Summary of HLA and peptide combinations used for CD8 class I tetramers including which position of the MCPyV oncoprotein (small, common, or large T antigen) the peptide corresponds to. B) Schematic of MCPyV peptide pools and locations of tetramer epitopes. Details of peptide pools are available in Iyer et al., 2011. (DOCX 364â kb)

Serology results. Raw results for MCPyV-specific oncoprotein antibodies were reported as Standard Titer Units (STUs). Patient with a value of 75 or greater were considered oncoprotein antibody producers and values below 74 were considered negative. Abbreviations for RECIST 1.1 response criteria are as follows: CR = complete response; PR = partial response; PD = progressive disease. (DOCX 114 kb)

Serology results. Raw results for MCPyV-specific oncoprotein antibodies were reported as Standard Titer Units (STUs). Patient with a value of 75 or greater were considered oncoprotein antibody producers and values below 74 were considered negative. Abbreviations for RECIST 1.1 response criteria are as follows: CR = complete response; PR = partial response; PD = progressive disease. (DOCX 114 kb)

Frequency of IFN-γ and/or IL-2 secreting CD8 T cells in response to Merkel polyomavirus peptide pools. IFN-γ and/or IL-2 in A) 2 of 13 VP-MCC responders and B) 1 of 4 VP-MCC non-responders was detectible via flow cytometry after a 16 h stimulation with MCPyV peptide pools. Dotted line represents background signal cutoff. *Post = first blood draw after initiation of treatment. (DOCX 425 kb)