Expression and clinical significance of PD-L1, B7-H3, B7-H4 and TILs in human small cell lung Cancer (SCLC)

Background

Small cell lung cancer (SCLC) accounts for 10–15% of all lung malignancies and its prognosis is dismal. Although early studies have shown promising clinical activity of immune checkpoint blockers, the immune composition and expression of potentially actionable immunostimulatory targets in this malignancy are poorly understood.

Methods

Using multiplexed quantitative immunofluorescence (QIF), we measured the levels of 3 different B7 family ligands PD-L1, B7-H3, B7-H4 and major tumor infiltrating lymphocyte (TIL) subsets in 90 SCLC samples represented in tissue microarray format. Associations between the marker levels, clinicopathological variables and survival were studied.

Results

PD-L1 protein was detected in 7.3%, B7-H3 in 64.9% and B7-H4 in 2.6% of SCLC cases. The markers showed limited co-expression and were not associated with the level of TILs, age, gender and stage. Elevated B7-H4 was associated with shorter 5-year overall survival. The levels of CD3+, CD8+ and CD20+ TILs and the ratio of total/effector T-cells were significantly lower in SCLC than in non-small cell lung cancer. High levels of CD3+, but not CD8+ or CD20+ TILs were significantly associated with longer survival.

Conclusions

Taken together, our study indicate variable expression and clinical role of B7-family ligands in SCLC with predominant expression of the candidate target B7-H3 and the presence of a limited cytotoxic anti-tumor immune response. These results support the evaluation of B7-H3 blockers and/or pro-inflammatory therapies in SCLC.

Immune Checkpoint Inhibitor-Associated Pericarditis

Side effects of immune checkpoint inhibitors, termed immune-related adverse events, are relatively common, but immune checkpoint inhibitor-mediated cardiotoxicities are rare; however, they can be serious and potentially fatal. Pericarditis is an infrequent cardiac toxicity of immunotherapy and predisposing factors remain unknown. Here we report three patients with NSCLC who developed pericarditis during therapy with programmed death 1/programmed death ligand 1+/- CTLA-4 inhibitors. We review the clinical presentation of these three cases and histopathologic findings from autopsies from the first two patients and a pericardial sampling that has been obtained from a pericardial window procedure in the third patient who recovered from the pericarditis episode. We also discuss the potential mechanisms, as well as what is known about pericarditis secondary to immune-related adverse events.

Siglec-15 as an immune suppressor and potential target for normalization cancer immunotherapy

Overexpression of the B7-H1 (PD-L1) molecule in the tumor microenvironment (TME) is a major immune evasion mechanism in some patients with cancer, and antibody blockade of the B7-H1/PD-1 interaction can normalize compromised immunity without excessive side-effects. Using a genome-scale T cell activity array, we identified Siglec-15 as a critical immune suppressor. While only expressed on some myeloid cells normally, Siglec-15 is broadly upregulated on human cancer cells and tumor-infiltrating myeloid cells, and its expression is mutually exclusive to B7-H1, partially due to its induction by macrophage colony-stimulating factor and downregulation by IFN-γ. We demonstrate that Siglec-15 suppresses antigen-specific T cell responses in vitro and in vivo. Genetic ablation or antibody blockade of Siglec-15 amplifies anti-tumor immunity in the TME and inhibits tumor growth in some mouse models. Taken together, our results support Siglec-15 as a potential target for normalization cancer immunotherapy.

Spatial Architecture and Arrangement of Tumor-Infiltrating Lymphocytes for Predicting Likelihood of Recurrence in Early-Stage Non-Small Cell Lung Cancer

PURPOSE

The presence of a high degree of tumor-infiltrating lymphocytes (TIL) has been proven to be associated with outcome in patients with non-small cell lung cancer (NSCLC). However, recent evidence indicates that tissue architecture is also prognostic of disease-specific survival and recurrence. We show a set of descriptors (spatial TIL, SpaTIL) that capture density, and spatial colocalization of TILs and tumor cells across digital images that can predict likelihood of recurrence in early-stage NSCLC.

EXPERIMENTAL DESIGN

The association between recurrence in early-stage NSCLC and SpaTIL features was explored on 301 patients across four different cohorts. Cohort D1 (n = 70) was used to identify the most prognostic SpaTIL features and to train a classifier to predict the likelihood of recurrence. The classifier performance was evaluated in cohorts D2 (n = 119), D3 (n = 112), and D4 (n = 112). Two pathologists graded each sample of D1 and D2; intraobserver agreement and association between manual grading and likelihood of recurrence were analyzed.

RESULTS

SpaTIL was associated with likelihood of recurrence in all test sets (log-rank P < 0.02). A multivariate Cox proportional hazards analysis revealed an HR of 3.08 (95% confidence interval, 2.1-4.5, P = 7.3 × 10-5). In contrast, agreement among expert pathologists using tumor grade was moderate (Kappa = 0.5), and the manual TIL grading was only prognostic for one reader in D2 (P = 8.0 × 10-3).

CONCLUSIONS

A set of features related to density and spatial architecture of TILs was found to be associated with a likelihood of recurrence of early-stage NSCLC. This information could potentially be used for helping in treatment planning and management of early-stage NSCLC.See related commentary by Peled et al., p. 1449.

Multiplexed (18-Plex) Measurement of Signaling Targets and Cytotoxic T Cells in Trastuzumab-Treated Patients using Imaging Mass Cytometry

PURPOSE

Imaging mass cytometry (IMC) uses metal-conjugated antibodies to provide multidimensional, objective measurement of protein targets. We used this high-throughput platform to perform an 18-plex assessment of HER2 ICD/ECD, cytotoxic T-cell infiltration and other structural and signaling proteins in a cohort of patients treated with trastuzumab to discover associations with trastuzumab benefit.

EXPERIMENTAL DESIGN

An antibody panel for detection of 18 targets (pan-cytokeratin, HER2 ICD, HER2 ECD, CD8, vimentin, cytokeratin 7, β-catenin, HER3, MET, EGFR, ERK 1-2, MEK 1-2, PTEN, PI3K p110 α, Akt, mTOR, Ki67, and Histone H3) was used with a selection of trastuzumab-treated patients from the Hellenic Cooperative Oncology Group 10/05 trial (n = 180), and identified a case-control series.

RESULTS

Patients that recurred after adjuvant treatment with trastuzumab trended toward a decreased fraction of HER2 ECD pixels over threshold compared with cases without recurrence (P = 0.057). After exclusion of the lowest HER2 expressers, 5-year recurrence events were associated with reduced total extracellular domain (ECD)/intracellular domain (ICD) ratio intensity in tumor (P = 0.044). These observations are consistent with our previous work using quantitative immunofluorescence, but represent the proof on identical cell content. We also describe the association of the ECD of HER2 with CD8 T-cell infiltration on the same slide.

CONCLUSIONS

The proximity of CD8 cells as a function of the expression of the ECD of HER2 provides further evidence for the role of the immune system in the mechanism of action of trastuzumab.

Abstract P4-02-01: Analytical validation of an automated digital scoring protocol for Ki67: International multicenter collaboration study

Background/Goal: Ki67 expression has been a valuable prognostic marker in breast cancer, but has not seen broad adoption due to lack of standardization between institutions. Automation could represent a solution. Here we tested 3 automated digital image analysis (DIA) platforms including an open source platform to: (i) Investigate the reproducibility of Ki67 measurement across platforms with supervised classifiers performed by the same operator and by multiple operators. (ii) Compare accuracy of the 3 DIA platforms against outcome (prognostic potential). (iii) Assess inter-laboratory reproducibility of a calibrated DIA tool to evaluate Ki67 in breast cancer among 10 participating labs of the International Ki67 in Breast Cancer Working Group (IKWG).

Methods: The Mib-1 antibody (Dako) was used to detect Ki67 (dilution 1:100). HALO (H) (IndicaLabs), QuantCenter (QC) (3DHistech), QuPath (QP) (open-source software) digital image analysis (DIA) platforms were used to evaluate Ki67 expression. As a ground truth, we evaluated Ki67 LI with meticulous manual tissue segmentation using the Spectrum Webscope (SW) (Aperio). Calibration was performed using 30 ER+ breast cancer cases from phase 3 of the IKWG initiative where blocks were centrally cut and stained for Ki67. The inter-laboratory analysis was done with 10 participating laboratories divided into 2 groups where members within the same group were given the same set of images. The outcome cohort consisted of 149 breast cancer cases from the Yale Pathology archives in tissue microarray format. Intra-class correlation coefficient (ICC) was used to measure reproducibility with the pre-specified criterion for success being to exceed 0.80. Kaplan-Meier analysis supported with log-rank test was performed to assess prognostic potential.

Results: All 3 DIA platforms showed excellent inter-platform reproducibility (ICC: 0.933, CI: 0.879-0.966). Also, excellent reproducibility was found between all DIA platforms and the reference standard Ki67 values of SW (QP ICC: 0.970, CI: 0.936-0.986; H ICC: 0.968, CI: 0.933-0.985; QC ICC: 0.964, CI: 0.919-0.983). The intra-DIA reproducibility was also excellent for all platforms (QP ICC: 0.992, CI: 0.986-0.996; H ICC: 0.972, CI: 0.924-0.988; QC ICC: 0.978, CI: 0.932-0.991). Comparing each DIA against outcome, the hazard ratios were similar (QP=3.309, H=3.077, QC=3.731). The inter-operator reproducibility was particularly high (ICC: 0.962-0.995). As QP is open source software and also showed the lowest intra-DIA platform variability, we selected the QP platform to investigate inter-laboratory reproducibility among 10 IKWG labs. The different-section ICC across the 10 labs was 0.974 (CI: 0.954 - 0.986). The same-section ICC estimate was 0.984 (CI: 0.971-0.992) for group 1 and 0.978 (CI: 0.956-0.989) for group 2.

Conclusions: Our results showed outstanding reproducibility both within and between DIA platforms. We also found the platforms essentially indistinguishable with respect to prediction of breast cancer patient outcome. Automated Ki67 evaluation using a calibrated, open-source DIA platform (QuPath) met the pre-specified criterion of success in the multi-institutional setting. Assessment of clinical utility is planned.

Citation Format: Acs B, Leung SC, Pelekanou V, Bai Y, Martinez-Morilla S, Toki M, Chang MC, Gholap A, Jadhav A, Hugh JC, Bigras G, Laurinavicius A, Augulis R, Levenson R, Todd A, Piper T, Virk S, van der Vegt B, Hayes DF, Dowsett M, Nielsen TO, Rimm DL. Analytical validation of an automated digital scoring protocol for Ki67: International multicenter collaboration study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-02-01.

An international multicenter study to evaluate reproducibility of automated scoring for assessment of Ki67 in breast cancer

The nuclear proliferation biomarker Ki67 has potential prognostic, predictive, and monitoring roles in breast cancer. Unacceptable between-laboratory variability has limited its clinical value. The International Ki67 in Breast Cancer Working Group investigated whether Ki67 immunohistochemistry can be analytically validated and standardized across laboratories using automated machine-based scoring. Sets of pre-stained core-cut biopsy sections of 30 breast tumors were circulated to 14 laboratories for scanning and automated assessment of the average and maximum percentage of tumor cells positive for Ki67. Seven unique scanners and 10 software platforms were involved in this study. Pre-specified analyses included evaluation of reproducibility between all laboratories (primary) as well as among those using scanners from a single vendor (secondary). The primary reproducibility metric was intraclass correlation coefficient between laboratories, with success considered to be intraclass correlation coefficient >0.80. Intraclass correlation coefficient for automated average scores across 16 operators was 0.83 (95% credible interval: 0.73-0.91) and intraclass correlation coefficient for maximum scores across 10 operators was 0.63 (95% credible interval: 0.44-0.80). For the laboratories using scanners from a single vendor (8 score sets), intraclass correlation coefficient for average automated scores was 0.89 (95% credible interval: 0.81-0.96), which was similar to the intraclass correlation coefficient of 0.87 (95% credible interval: 0.81-0.93) achieved using these same slides in a prior visual-reading reproducibility study. Automated machine assessment of average Ki67 has the potential to achieve between-laboratory reproducibility similar to that for a rigorously standardized pathologist-based visual assessment of Ki67. The observed intraclass correlation coefficient was worse for maximum compared to average scoring methods, suggesting that maximum score methods may be suboptimal for consistent measurement of proliferation. Automated average scoring methods show promise for assessment of Ki67 scoring, but requires further standardization and subsequent clinical validation.

Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement

Immunotherapies targeting the PD-1 pathway produce durable responses in many cancers, but the tumor-intrinsic factors governing response and resistance are largely unknown. MHC-II expression on tumor cells can predict response to anti-PD-1 therapy. We therefore sought to determine how MHC-II expression by tumor cells promotes PD-1 dependency. Using transcriptional profiling of anti-PD-1-treated patients, we identified unique patterns of immune activation in MHC-II+ tumors. In patients and preclinical models, MHC-II+ tumors recruited CD4+ T cells and developed dependency on PD-1 as well as Lag-3 (an MHC-II inhibitory receptor), which was upregulated in MHC-II+ tumors at acquired resistance to anti-PD-1. Finally, we identify enhanced expression of FCRL6, another MHC-II receptor expressed on NK and T cells, in the microenvironment of MHC-II+ tumors. We ascribe this to what we believe to be a novel inhibitory function of FCRL6 engagement, identifying it as an immunotherapy target. These data suggest a MHC-II-mediated context-dependent mechanism of adaptive resistance to PD-1-targeting immunotherapy.

Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement

Immunotherapies targeting the PD-1 pathway produce durable responses in many cancers, but the tumor-intrinsic factors governing response and resistance are largely unknown. MHC-II expression on tumor cells can predict response to anti-PD-1 therapy. We therefore sought to determine how MHC-II expression by tumor cells promotes PD-1 dependency. Using transcriptional profiling of anti-PD-1-treated patients, we identified unique patterns of immune activation in MHC-II+ tumors. In patients and preclinical models, MHC-II+ tumors recruited CD4+ T cells and developed dependency on PD-1 as well as Lag-3 (an MHC-II inhibitory receptor), which was upregulated in MHC-II+ tumors at acquired resistance to anti-PD-1. Finally, we identify enhanced expression of FCRL6, another MHC-II receptor expressed on NK and T cells, in the microenvironment of MHC-II+ tumors. We ascribe this to what we believe to be a novel inhibitory function of FCRL6 engagement, identifying it as an immunotherapy target. These data suggest a MHC-II-mediated context-dependent mechanism of adaptive resistance to PD-1-targeting immunotherapy.

CD68, CD163, and matrix metalloproteinase 9 (MMP-9) co-localization in breast tumor microenvironment predicts survival differently in ER-positive and -negative cancers

Background

The role of tumor-associated macrophages (TAMs) in the cancer immune landscape and their potential as treatment targets or modulators of response to treatment are gaining increasing interest. TAMs display high molecular and functional complexity. Therefore their objective assessment as breast cancer biomarkers is critical. The aims of this study were to objectively determine the in situ expression and significance of TAM biomarkers (CD68, CD163, and MMP-9) in breast cancer and to identify subclasses of patients who could benefit from TAM-targeting therapies.

Methods

We measured CD68, CD163, and MMP-9 protein expression in formalin-fixed paraffin-embedded tissues of breast carcinomas represented in tissue microarray format using multiplexed quantitative immunofluorescence (QIF) in two independent Yale cohorts: cohort A—n = 398, estrogen receptor–positive (ER⁺) and ER⁻ cases—and the triple-negative breast cancer (TNBC)-only cohort B (n = 160). Associations between macrophage markers, ER status, and survival were assessed. Protein expression measured by QIF was compared with mRNA expression data from the METABRIC study.

Results

All three macrophage markers were co-expressed, displaying higher expression in ER⁻ cancers. High pan-macrophage marker CD68 correlated with poorer overall survival (OS) only in ER⁻ cases of cohort A (P = 0.02). High expression of CD163 protein in TAMs was associated with improved OS in ER⁻ cases (cohort A, P = 0.03 and TNBC cohort B, P = 0.04, respectively) but not in ER⁺ cancers. MMP-9 protein was not individually associated with OS. High expression of MMP-9 in the CD68⁺/CD163⁺ TAMs was associated with worse OS in ER⁺ tumors (P <0.001) but not in ER⁻ cancers. In the METABRIC dataset, mRNA levels followed the co-expression pattern observed in QIF but did not always show the same trend regarding OS.

Conclusions

Macrophage activity markers correlate with survival differently in ER⁺ and ER⁻ cancers. The association between high co-expression and co-localization of MMP-9/CD163/CD68 and poor survival in ER⁺ cancers suggests that these cancers may be candidates for macrophage-targeted therapies.

Electronic supplementary material

The online version of this article (10.1186/s13058-018-1076-x) contains supplementary material, which is available to authorized users.

Association of B7-H4, PD-L1, and tumor infiltrating lymphocytes with outcomes in breast cancer

B7-H4 (VTCN1) is a member of the CD28/B7 family of immune co-inhibitory molecules. The relationship of tumor and stromal B7-H4 protein expression with PD-L1, tumor infiltrating lymphocytes (TILs) and its association with clinico-pathological variables are not well defined. Herein, we explore the expression level of B7-H4 protein in breast cancer and evaluate its association with TILs, levels of PD-L1 expression, and clinico-pathological characteristics in two independent populations. In this study, we used multiplexed automated quantitative immunofluorescence (QIF) to measure the levels of B7-H4 and PD-L1 protein and determined TILs through pathologist assessment of H&E-stained preparations in over a thousand breast cancer cases from two institutions represented in tissue microarray format. Associations between the marker levels, major clinico-pathological variables, and survival were analyzed. We detected B7-H4 protein was highly expressed in both breast cancer and stromal cells. Its expression was independent of breast cancer intrinsic subtypes. PD-L1 expression was higher in triple negative breast cancers. Neither B7-H4 nor PD-L1 were associated with survival in breast cancer. Our study shows there is a mutually exclusive pattern of B7-H4 with both tumor PD-L1 expression and TILs in all breast cancers, independent of breast cancer intrinsic subtype. This exclusive pattern suggests that some breast tumors may preferentially use one B7-related immune evasion mechanism/pathway. This could explain the clinical benefit that is seen only in a fraction of patients with immune checkpoint inhibitors directed exclusively towards PD-L1 in breast cancer.

Quantitative Spatial Profiling of PD-1/PD-L1 Interaction and HLA-DR/IDO-1 Predicts Improved Outcomes of Anti-PD-1 Therapies in Metastatic Melanoma

Purpose: PD-1/L1 axis-directed therapies produce clinical responses in a subset of patients; therefore, biomarkers of response are needed. We hypothesized that quantifying key immunosuppression mechanisms within the tumor microenvironment by multiparameter algorithms would identify strong predictors of anti-PD-1 response.Experimental Design: Pretreatment tumor biopsies from 166 patients treated with anti-PD-1 across 10 academic cancer centers were fluorescently stained with multiple markers in discovery (n = 24) and validation (n = 142) cohorts. Biomarker-positive cells and their colocalization were spatially profiled in pathologist-selected tumor regions using novel Automated Quantitative Analysis algorithms. Selected biomarker signatures, PD-1/PD-L1 interaction score, and IDO-1/HLA-DR coexpression were evaluated for anti-PD-1 treatment outcomes.Results: In the discovery cohort, PD-1/PD-L1 interaction score and/or IDO-1/HLA-DR coexpression was strongly associated with anti-PD-1 response (P = 0.0005). In contrast, individual biomarkers (PD-1, PD-L1, IDO-1, HLA-DR) were not associated with response or survival. This finding was replicated in an independent validation cohort: patients with high PD-1/PD-L1 and/or IDO-1/HLA-DR were more likely to respond (P = 0.0096). These patients also experienced significantly improved progression-free survival (HR = 0.36; P = 0.0004) and overall survival (HR = 0.39; P = 0.0011). In the combined cohort, 80% of patients exhibiting higher levels of PD-1/PD-L1 interaction scores and IDO-1/HLA-DR responded to PD-1 blockers (P = 0.000004). In contrast, PD-L1 expression was not predictive of survival.Conclusions: Quantitative spatial profiling of key tumor-immune suppression pathways by novel digital pathology algorithms could help more reliably select melanoma patients for PD-1 monotherapy. Clin Cancer Res; 24(21); 5250-60. ©2018 AACR.

Immune Marker Profiling and Programmed Death Ligand 1 Expression Across NSCLC Mutations

INTRODUCTION

Programmed death 1/programmed death ligand 1 (PD-L1) axis inhibitors have been proven effective, especially in patients with tumors expressing PD-L1. Their clinical efficacy in patients with EGFR-activating mutations is still unclear, whereas KRAS mutations seem to be associated with good response.

METHODS

We used multiplexed quantitative immunofluorescence to investigate PD-L1 expression and to characterize tumor infiltrating lymphocyte (TIL) populations and their activation status in more than 150 NSCLC patients with known mutation status.

RESULTS

PD-L1 expression was significantly lower in EGFR-mutant compared to KRAS-mutant, and EGFR/KRAS wild-type (WT) tumors. KRAS mutant tumors were more inflamed with higher CD4+, CD8+ and CD20+ TILs. Subgroup analysis by TIL activation status revealed that EGFR mutants had a high frequency of inactive TILs even though lymphocytes were present in the tumor microenvironment. In contrast, in KRAS mutants, when TILs were present they were almost always active. Additionally, we found differences between EGFR mutation sites in CD8+ expression and the TIL activation profile. Finally, activated EGFR correlated with increased PD-L1 expression in EGFR mutants but not in EGFR WT, whereas TIL activation was associated with higher PD-L1 only in EGFR/KRAS WT.

CONCLUSIONS

Our findings show the unique immune profile of EGFR-mutant tumors. The high frequency of inactive TILs could explain the low immunotherapy response rates in these patients, whereas PD-L1 as a predictive biomarker may reflect the constitutive oncogenic signaling rather than immune signaling, which would be associated with high PD-L1 levels and TILs activation.

Correlating nuclear morphometric patterns with estrogen receptor status in breast cancer pathologic specimens

In this pilot study, we introduce a machine learning framework to identify relationships between cancer tissue morphology and hormone receptor pathway activation in breast cancer pathology hematoxylin and eosin (H&E)-stained samples. As a proof-of-concept, we focus on predicting clinical estrogen receptor (ER) status-defined as greater than one percent of cells positive for estrogen receptor by immunohistochemistry staining-from spatial arrangement of nuclear features. Our learning pipeline segments nuclei from H&E images, extracts their position, shape and orientation descriptors, and then passes them to a deep neural network to predict ER status. After training on 57 tissue cores of invasive ductal carcinoma (IDC), our pipeline predicted ER status in an independent test set of patient samples (AUC ROC = 0.72, 95%CI = 0.55-0.89, n = 56). This proof of concept shows that machine-derived descriptors of morphologic histology patterns can be correlated to signaling pathway status. Unlike other deep learning approaches to pathology, our system uses deep neural networks to learn spatial relationships between pre-defined biological features, which improves the interpretability of the system and sheds light on the features the neural network uses to predict ER status. Future studies will correlate morphometry to quantitative measures of estrogen receptor status and, ultimately response to hormonal therapy.

A dormant TIL phenotype defines non-small cell lung carcinomas sensitive to immune checkpoint blockers

The biological determinants of sensitivity and resistance to immune checkpoint blockers are not completely understood. To elucidate the role of intratumoral T-cells and their association with the tumor genomic landscape, we perform paired whole exome DNA sequencing and multiplexed quantitative immunofluorescence (QIF) in pre-treatment samples from non-small cell lung carcinoma (NSCLC) patients treated with PD-1 axis blockers. QIF is used to simultaneously measure the level of CD3+ tumor infiltrating lymphocytes (TILs), in situ T-cell proliferation (Ki-67 in CD3) and effector capacity (Granzyme-B in CD3). Elevated mutational load, candidate class-I neoantigens or intratumoral CD3 signal are significantly associated with favorable response to therapy. Additionally, a "dormant" TIL signature is associated with survival benefit in patients treated with immune checkpoint blockers characterized by elevated TILs with low activation and proliferation. We further demonstrate that dormant TILs can be reinvigorated upon PD-1 blockade in a patient-derived xenograft model.

The Society for Immunotherapy of Cancer consensus statement on immunotherapy for the treatment of non-small cell lung cancer (NSCLC)

Lung cancer is the leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for over 85% of all cases. Until recently, chemotherapy – characterized by some benefit but only rare durable responses – was the only treatment option for patients with NSCLC whose tumors lacked targetable mutations. By contrast, immune checkpoint inhibitors have demonstrated distinctly durable responses and represent the advent of a new treatment approach for patients with NSCLC. Three immune checkpoint inhibitors, pembrolizumab, nivolumab and atezolizumab, are now approved for use in first- and/or second-line settings for selected patients with advanced NSCLC, with promising benefit also seen in patients with stage III NSCLC. Additionally, durvalumab following chemoradiation has been approved for use in patients with locally advanced disease. Due to the distinct features of cancer immunotherapy, and rapid progress in the field, clinical guidance is needed on the use of these agents, including appropriate patient selection, sequencing of therapies, response monitoring, adverse event management, and biomarker testing. The Society for Immunotherapy of Cancer (SITC) convened an expert Task Force charged with developing consensus recommendations on these key issues. Following a systematic process as outlined by the National Academy of Medicine, a literature search and panel voting were used to rate the strength of evidence for each recommendation. This consensus statement provides evidence-based recommendations to help clinicians integrate immune checkpoint inhibitors into the treatment plan for patients with NSCLC. This guidance will be updated following relevant advances in the field.

Abstract 3638: Quantitative assessment of tumor-infiltrating lymphocytes and immunotherapy outcome in metastatic melanoma

Background: Durable responses to immune checkpoint blockade against programmed cell death 1 (PD-1) are limited to a subset of metastatic melanoma patients, so there is a need for predictive biomarkers. Tumor-infiltrating lymphocytes (TILs) are the major cellular target of anti-PD-1 therapy, so we hypothesized that pretreatment TIL profiles would be associated with response.

Methods: Pretreatment whole-tissue sections from 94 melanoma patients treated with anti-PD-1 therapy (pembrolizumab, nivolumab, or ipilimumab plus nivolumab) from 2011-17 were collected from Yale Pathology archives, and stained to visualize nuclei (DAPI) and melanoma cells (S100 & HMB45) in combination with two multiplex immunofluorescence panels to: (1) perform TIL quantitation of helper T cells by CD4 (SP35, Spring), cytotoxic T cells by CD8 (C8/144B, Dako), and B cells by CD20 (L26, Dako); and (2) assess TIL activation by identifying T cells by CD3 (SP7, Novus), cytolytic activity by GZMB (4E6, Abcam), and proliferation by Ki67 (MIB-1, Dako). Cell phenotyping and counting were performed using inForm software (PerkinElmer) and protein expression was measured by the AQUA method of quantitative immunofluorescence (QIF). Response Evaluation Criteria In Solid Tumors (RECIST) 1.1 were used to classify best overall response as complete response (CR), partial response (PR), stable disease (SD), or progressive disease (PD). Objective response rate (ORR; CR/PR), disease control rate (DCR; CR/PR/SD), and progression-free survival (PFS) were correlated with TIL parameters measured by both methodologies.

Results: Pretreatment lymphocytic infiltration, by cell counts or QIF, was significantly higher in CR/PR than in SD/PD, particularly for CD3 and CD8 (P &lt; 0.0001). Neither TIL activation (CD3 high, Ki67 and/or GZMB high) nor TIL dormancy (CD3 high, Ki67 and GZMB low) was significantly associated with outcome. Multivariable analyses revealed significant CD8 associations (HR &gt; 3) with PFS independent of age, sex, mutation, stage, treatment, and prior immune checkpoint blockade, which accounted for similar CD3 PFS associations as expected. The favorable predictive performance of CD8 cell count (and QIF) had an area under the receiver operating characteristic (ROC) curve of 0.75 for ORR and 0.78 for DCR, which reached 0.83 (ORR or DCR) for dual therapy (ipilimumab plus nivolumab). Interestingly, in contrast to previous hypothetical classifications, there were a number of responders (CR/PR) in the CD3 or CD8 low (immune desert) category.

Conclusions: Pretreatment lymphocytic infiltration, by cell counts or QIF, is associated with anti-PD-1 response in metastatic melanoma. Multiplex analysis of the tumor microenvironment has the potential to be used as a companion diagnostic test for precision immunotherapy.

Citation Format: Pok Fai Wong, James W. Smithy, Kim R. Blenman, Harriet M. Kluger, David L. Rimm. Quantitative assessment of tumor-infiltrating lymphocytes and immunotherapy outcome in metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3638.

Abstract 3621: High-plex immune marker spatial profiling quantitation by NanoString Digital Spatial Profiling technology and quantitative immunofluorescence

Background: Quantitative immunofluorescence (QIF) offers the advantage of multiple target measurement on a single slide, but is limited by the number of fluorescence channels. NanoString's Digital Spatial Profiling (DSP)* can detect and quantify immune markers at higher multiplex with spatial resolution within specific regions of interest on FFPE tissue. Here, we compare NanoString DSP to automated QIF (AQUA), for immune marker compartment specific measurement. Additionally, we assess their agreement on the prognostic value of commonly used biomarkers in Non-Small Cell Lung Cancer (NSCLC). Finally, we explore the predictive value of a 30-plex panel of immune markers on two cohorts of treated patients.

Methods: NanoString DSP technology uses a cocktail of primary antibodies conjugated to indexing DNA oligos. Regions of interest (ROI) on the tissue are selected with fluorescently labeled antibodies, and oligos from that region are UV cleaved and quantified on the nCounter platform. The comparator for this technology was the AQUA method of QIF. We retrospectively examined a NSCLC cohort of over 100 patients for prognostic markers and two treated patient cohorts for associations between immune markers expression and response to treatment, all in tissue microarray format. The treated cohorts included an Epidermal Growth Factor Receptor Tyrosine kinase inhibitor (EGFR TKI) treated NSCLC cohort and a melanoma immunotherapy (ITx) treated cohort.

Results: Multiple immune markers (CD3, CD4, CD8, CD20, PD-L1) were assessed and a high correlation was found between NanoString DSP counts and QIF scores, when the measurements were performed in the same ROIs (tumor or stroma). The prognostic value of the immune markers tested was concordant between the two assays with high expression of CD3 assessed by either assay showing a statistically significantly better overall survival (OS). For the EGFR TKI treated NSCLC cohort none of the immune markers was correlated with response to treatment or favorable outcome. However, in the ITx treated melanoma patients, PD-L1, PD-1, CD68, CD3, CD8A and b2-microglobulin tumor expression predicted response to treatment. Each marker also predicted better outcome, but only CD8A was an independent predictive marker of prolonged survival.

Conclusion: NanoString DSP offers the capacity of highly multiplexed immune marker measurements on selected compartments. It shows high concordance with AQUA, which was further validated by comparing prognostic significance. The pilot study of the Melanoma ITx cohort also illustrates the potential to simultaneously evaluate a range of markers and possibly construct new predictive signatures based on a cohort represented by very small tissue samples. *FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

Citation Format: Maria I. Toki, Pok Fai Wong, Harriet Kluger, Yuting Liu, Chris Merritt, Giang Ong, Sarah Warren, Joseph M. Beechem, David L. Rimm. High-plex immune marker spatial profiling quantitation by NanoString Digital Spatial Profiling technology and quantitative immunofluorescence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3621.

Pathway level alterations rather than mutations in single genes predict response to HER2-targeted therapies in the neo-ALTTO trial

Background

We performed whole-exome sequencing of pretreatment biopsies and examined whether genome-wide metrics of overall mutational load, clonal heterogeneity or alterations at variant, gene, and pathway levels are associated with treatment response and survival.

Patients and Methods

Two hundred and three biopsies from the NeoALTTO trial were analyzed. Mutations were called with MuTect, and Strelka, using pooled normal DNA. Associations between DNA alterations and outcome were evaluated by logistic and Cox-proportional hazards regression.

Results

There were no recurrent single gene mutations significantly associated with pathologic complete response (pCR), except PIK3CA [odds ratio (OR) = 0.42, P = 0.0185]. Mutations in 33 of 714 pathways were significantly associated with response, but different genes were affected in different individuals. PIK3CA was present in 23 of these pathways defining a ‘trastuzumab resistance-network’ of 459 genes. Cases with mutations in this network had low pCR rates to trastuzumab (2/50, 4%) compared with cases with no mutations (9/16, 56%), OR = 0.035; P < 0.001. Mutations in the ‘Regulation of RhoA activity’ pathway were associated with higher pCR rate to lapatinib (OR = 14.8, adjusted P = 0.001), lapatinib + trastuzumab (OR = 3.0, adjusted P = 0.09), and all arms combined (OR = 3.77, adjusted P = 0.02). Patients (n = 124) with mutations in the trastuzumab resistance network but intact RhoA pathway had 2% (1/41) pCR rate with trastuzumab alone (OR = 0.026, P = 0.001) but adding lapatinib increased pCR rate to 45% (17/38, OR = 1.68, P = 0.3). Patients (n = 46) who had no mutations in either gene set had 6% pCR rate (1/15) with lapatinib, but had the highest pCR rate, 52% (8/15) with trastuzumab alone.

Conclusions

Mutations in the RhoA pathway are associated with pCR to lapatinib and mutations in a PIK3CA-related network are associated with resistance to trastuzumab. The combined mutation status of these two pathways could define patients with very low response rate to trastuzumab alone that can be augmented by adding lapatinib or substituting trastuzumab with lapatinib.

Tumor-Infiltrating Lymphocytes and PD-L1 Expression in Pre- and Posttreatment Breast Cancers in the SWOG S0800 Phase II Neoadjuvant Chemotherapy Trial

Our aim was to examine the association of pretreatment tumor-infiltrating lymphocyte (TIL) count and PD-L1 levels with pathologic complete response (pCR) and assess immune marker changes following treatment in tumor specimens from the S0800 clinical trial, which randomized patients to bevacizumab + nab-paclitaxel, followed by doxorubicin/cyclophosphamide (AC) versus two control arms without bevacizumab (varying sequence of AC and nab-paclitaxel). TILs were assessed in 124 pre- and 62 posttreatment tissues (including 59 pairs). PD-L1 was assessed in 120 pre- and 43 posttreatment tissues (including 39 pairs) using the 22C3 antibody. Baseline and treatment-induced immune changes were correlated with pCR and survival using estrogen receptor (ER) and treatment-adjusted logistic and Cox regressions, respectively. At baseline, the mean TIL count was 17.4% (17% had zero TILs, 9% had ≥50% TILs). Posttreatment, mean TIL count decreased to 11% (5% had no TILs, 2% had >50% TILs). In paired samples, the mean TIL change was 15% decrease. Baseline PD-L1 was detected in 43% of cases (n = 5 in tumor cells, n = 29 stroma, n = 18 tumor + stroma). Posttreatment, PD-L1 expression was not significantly lower (33%). Higher baseline TIL count and PD-L1 positivity rate were associated with higher pCR rate even after adjustment for treatment and ER status (P = 0.018). There was no association between TIL counts, PD-L1 expression, and survival due to few events. In conclusion, TIL counts, but not PD-L1 expression, decreased significantly after treatment. Continued PD-L1 expression in some residual cancers raises the possibility that adjuvant immune checkpoint inhibitor therapy could improve survival in this patient population. Mol Cancer Ther; 17(6); 1324-31. ©2018 AACR.

An assessment of neuronal calcium sensor-1 and response to neoadjuvant chemotherapy in breast cancer patients

Neuronal calcium sensor-1 (NCS-1) has been identified as a binding partner of the taxane, paclitaxel. Our previous study showed that overexpression of NCS-1 increased the efficacy of paclitaxel in vitro, but was associated with poor clinical outcome. Here, we determine if NCS-1 expression is associated with pathological complete response (pCR) to taxane-based neoadjuvant chemotherapy in 105 pre-treatment breast cancer biopsies. Elevated expression of NCS-1 was found to be positively associated with pCR. These results suggest that NCS-1 may be a predictive biomarker for response to taxane-based neoadjuvant chemotherapy in breast cancer.

Abstract P2-09-18: Multiplexed (18-Plex) measurement of protein targets in trastuzumab-treated patients using imaging mass cytometry

Introduction: Recent studies have shown that the molecular heterogeneity of HER2 intracellular (ICD) and extracellular (ECD) domains, as well as overall immune infiltration, are associated with response to adjuvant trastuzumab. Traditional strategies for in situ measurement in the tumor microenvironment allow the combination of up to 6 targets, limiting our capability for in-depth interrogation of tissues. Imaging Mass Cytometry (IMC) uses metal-conjugated antibodies to provide multidimensional, objective measurement of protein targets. We used this high-throughput multiplexing platform to perform an 18-plex assessment of HER2 ICD/ECD, cytotoxic T cell infiltration and other structural and signaling proteins in a cohort of patients treated with trastuzumab.

Methods: An antibody panel for detection of 18 targets (Pancytokeratin, HER2 ICD, HER2 ECD, CD8, vimentin, cytokeratin 7, beta-catenin, HER3, MET, EGFR, ERK 1-2, MEK 1-2, PTEN, PI3K p110 alpha, Akt, mTOR, Ki67 and Histone H3) was conjugated to unique metals for detection in an IMC instrument (Fluidigm). All assays were objectively standardized and validated using quantitative immunofluoresce (QIF). Finally, the IMC technique was validated against HER2 single marker assays by QIF. We used a collection of trastuzumab-treated patients from the HeCOG 10/05 trial (n=180), and identified a case:control series using 5-year recurrence events (n=19), which were matched to controls (n=41) by age and TNM stage. Formalin-fixed, paraffin embedded tissues in tissue microarray format were ablated in the IMC attachment to the CyTOF flow cytometer for simultaneous detection of markers. Image visualization was conducted using MCD Viewer (Fluidigm). Statistical analyses were performed using a range of platforms.

Results: Patients that recurred after adjuvant treatment with trastuzumab showed a decreased fraction of HER2 ECD pixels over threshold in a compartment determined by CK and HER2 ICD compared to cases without recurrence (p=0.057). After exclusion of the lowest HER2 expressers (that would have fallen below the threshold for positive by current HER2 assays), 5-year recurrence events where associated with reduced total ECD/ ICD ratio intensity in tumor (p=0.044). Patients below the median for total ECD/ICD ratio showed a trend for decreased benefit from trastuzumab (p=0.066). Levels of cytotoxic T cell infiltration, depicted by total CD8 intensity, were lower in patients with recurrences (p=0.05).

Conclusion: Objective measurement of highly multiplexed protein targets in routine, fixed breast cancer tissues shows that a decreased ratio of HER2 ECD/ ICD is associated with 5-year recurrence after trastuzumab treatment. This observation is consistent with our previous work using QIF but represents the first time this has been done on identical cell content (on a single tissue section). Additionally, on the same section we found that lower levels of overall cytotoxic T cell infiltration were associated with worse outcome. Further analysis of the multiplexed data, including both correlative and distance-based analyses are underway.

Citation Format: Carvajal-Hausdorf DE, Stanton KP, Patsenker J, Villarroel-Espindola F, Esch A, Montgomery RR, Psyrri A, Kalogeras KT, Kotoula V, Fountzilas G, Schalper KA, Kluger Y, Rimm DL. Multiplexed (18-Plex) measurement of protein targets in trastuzumab-treated patients using imaging mass cytometry [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-18.

Abstract P1-08-02: Breast tumor-specific MHC-II expression drives a unique pattern of adaptive resistance to antitumor immunity through MHC-II receptor checkpoint engagement

Background: We have previously shown that some breast cancers express major histocompatibility complex II (MHC-II), correlating with enhanced immune infiltration. In other tumor types, we have shown that MHC-II expression on tumor cells predicts clinical response to checkpoint inhibition. We sought to determine the direct effects of MHC-II on anti-tumor immunity and characterize mechanisms of immune escape in this breast cancer subset.

Methods: To determine the functional effects of MHC-II on tumor cells, we generated isogenic mouse breast tumor cells with enforced MHC-II expression and determined their ability to generate tumors in syngeneic mice, the impact on immunity, and their response to checkpoint inhibition. In a series of molecularly-characterized HER2+ (n=8) and triple-negative breast cancers (TNBC; n=103), we performed immunohistochemistry (IHC) and quantitative immunofluorescence (QIF) for Lag-3, PD-L1, CD4, CD8, FCRL6, and granzyme B.

Results: Following injection in syngeneic immunocompetent mice, MHC-II+ mouse breast tumors were more frequently rejected (p=0.04) and recruited greater numbers of CD4+ TILs. When MHC-II+ tumors escaped rejection, they expressed higher degrees of PD-1 and Lag-3 in the tumor and in the draining lymph node. Since Lag-3 is a checkpoint that specifically targets MHC-II, we hypothesized that MHC-II+ breast cancers escape anti-tumor immunity through suppressing MHC-II-mediated antigen presentation. Combinations of anti-Lag-3 and anti-Pd-1 antibodies inhibited growth of MHC-II+ tumors. These findings led us to also explore Fc receptor-like 6 (FCRL6), a previously reported MHC-II receptor expressed on NK and cytotoxic T cells. Residual MHC-II+ TNBC post-neoadjuvant chemotherapy (NAC) recruited greater numbers of CD4+ and CD8+ TILs (p=0.0001 and p=0.0002), suggesting enhanced immune recognition. However, MHC-II+ TNBCs also demonstrated a greater frequency of Lag-3+ and FCRL6+ TILs (p&lt;0.001 and p=0.01, respectively) which frequently co-occurred (p=0.003). Thus, our data suggest that MHC-II expression in breast tumors supports recruitment of MHC-II-specific checkpoint-positive TILs. In line with this concept, QIF analysis demonstrated that the presence of Lag3+ and/or FCRL6+ TILs was strongly associated with suppression of T cell cytotoxicity as assessed by granzyme-B+ CD8+ T cells (p=0.0001 and p=0.002, respectively). Functional analyses of FCRL6 on human NK cell lines and peripheral blood mononuclear cells (PBMCs) demonstrated that like Lag3, FCRL6 is a checkpoint which engages MHC-II and suppresses cytotoxic NK and T cell activity.

Conclusions: These data suggest that MHC-II+ breast tumors are immunologically active and circumvent anti-tumor immunity by targeting MHC-II antigen presentation through recruitment of Lag-3+ and FCRL6+ TILs. We describe herein FCRL6 as a novel bona fide immune checkpoint which targets MHC-II, which may impact a variety of cancers. MHC-II expression status may be a useful biomarker for patient stratification on anti-PD-1/anti-Lag-3 combination, and eventually, anti-PD-1/anti-FCRL6 combinations in patients with breast cancer.

Citation Format: Balko JM, Johnson DB, Ericsson-Gonzalez P, Nixon MJ, Salgado R, Sanchez V, Shreeder DM, Rimm DL, Loi S, Kim JY, Bordeaux J, Sanders ME, Davis RS. Breast tumor-specific MHC-II expression drives a unique pattern of adaptive resistance to antitumor immunity through MHC-II receptor checkpoint engagement [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-08-02.

Abstract P2-09-06: Quantitative spatial profiling of tumor associated macrophages and the PD-1/PD-L1 interaction in breast cancer

Background: Although immunotherapy approaches are being successfully administered in some breast cancer (BC) patients (pts), biomarkers of response remain elusive. Tumor associated macrophages (TAMs) are the most prominent immune cells in breast tumors, mediating the cross-talk between tumor cells and tumor infiltrating lymphocytes (TILs). Specific biomarkers of breast TAMs' functional status remain to be defined. CSF-1R, is a TAMs regulator and key target across cancers clinically tested, alone or combined with anti-PD-1 checkpoint inhibitors.

The goals of the study were: 1) to objectively measure CSF-1R expression within all CD68+ and M2-like CD163+TAMs, as well as PD-L1/PD-1 spatial interaction and 2) to determine whether objectively quantifying these key immune mechanisms related to TAMs immunomodulation within the tumor microenvironment can predict outcome and potentially response to immunotherapy.

Methods: Tissue Microarrays (TMAs) from two Yale BC cohorts (Cohort A, all breast cases, n=320) (Cohort B, TNBC, n=132) were assessed by quantitative immunofluorescence (QIF) for CSF-1R/CD163/CD68; PD-1/PD-L1 interaction score (proportion of PD-1+ cells co-localized with PD-L1) and co-expression of the multiplexed biomarker panels. Biomarker positive cells and their co-localization were objectively measured using the AQUA method of QIF. QIF scores were compared by linear regression coefficients (R2). Overall and recurrence-free survival (OS and RFS) were assessed. Our protein data were compared with transcriptome data from the METABRIC study obtained from www.cbioportal.org.

Results: CSF-1R expression was associated with expression of both CD68 and CD163 in both cohorts (A: R2=0.64, B: R2=0.49). CSF-1R in CD163/CD68 was higher in TNBC Cohort B (p&lt;0.01) and in ER- cases of Cohort A (p=0.004). In Cohort A high CSF-1R expression (top 10%) in CD163+/CD68+ cells was associated with worse OS and RFS (All cases, p=0.015 and p=0.0005, respectively). After ER-status adjustment, high CSF-1R (in CD68 and CD163) was associated with worse OS and RFS only in ER- cases. High CSF-1R/CD68 (top 10%) was associated with ER- (p=0.0078), PR- (p=0.004) and increased recurrence rate (p=0.009). High CSF-1R/CD163 (top 10%) was also associated with increased recurrence rate (p=0.004). In TNBC, high CSF-1R correlated with worse OS (p=0.01) only in CD163+ TAMs. High CSF-1R scored as a continuous variable was related with worse RFS in both CD68+ (p=0.0026, RR 1.00/2.86) and CD163+ TAMs (p=0.006, RR 1.00/2.76). However, in multivariate analysis CSF-1R was not an independent prognostic factor for OS or RFS.

PD-L1 mostly co-localized with CD68 TAMs (R2=0.7). Tumor PD-L1 tended to be mutually exclusive of CSF-1R. PD-L1/PD-1 colocalization was higher in TNBC (p&lt;0.01) and associated with better OS (p=0.01). CSF-1R in TAMs tended to be higher when PD-1/PD-L1 colocalization was low.

The trend of mutual exclusivity between CSF-1R in TAMs and PD-1/PD-L1 was confirmed by expression (mRNA) data from METABRIC study.

Discussion: This novel multiplexed method profiling key tumor-immune suppression pathways could identify BC pts likely to respond to anti-PD-1/anti-CSF-1R therapy. This method could help stratify pts for mono- or combined therapy in future clinical trials.

Citation Format: Pelekanou V, Neumeister V, Pusztai L, Rimm DL. Quantitative spatial profiling of tumor associated macrophages and the PD-1/PD-L1 interaction in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-06.

Abstract P2-03-02: Macrodissection prior to closed system RT-qPCR is not necessary for estrogen receptor and HER2 concordance with IHC/FISH in breast cancer

Background: An on-demand, closed system RT-qPCR (the GeneXpert system, Cepheid, Sunnyvale, CA) has the potential to provide biomarker information in low resourced settings. The system consists of an inexpensive, single-use, disposable, macrofluidic cartridge and an instrument that automates RT-qPCR. Here we use it with a research use only cartridge (STRAT4) that measures the mRNA expression levels of ESR1, PGR, ERBB2, and MKi67 using a single 5uM thick FFPE tissue section from an excisional or core biopsy specimen containing invasive carcinoma of the breast. The assay, results are expressed as a delta cycle threshold (dCt) value, defined as the Ct of a control gene (CYFIP1) minus the Ct of the target gene (ESR1, PGR, ERBB2, or MKi67). We determine whether the dCt result for each marker is equivalent using the entire non-macrodissected section (non m-d) to the dCt results obtained following tumor macro-dissection (m-d) to eliminate non-tumor elements from the assay.

Methods: We evaluated the impact of m-d versus non m-d using STRAT4 on a cohort of 62 formalin-fixed paraffin-embedded (FFPE) tumor core needle biopsy specimens with a range of HER2 expression determined by clinical immunohistochemistry and fluorescence in situ hybridization (IHC/FISH). Concordance (sensitivity and specificity) of the STRAT4 ESR1 and HER2 mRNA versus ER and HER2 IHC/FISH measurements were also assessed.

Results: We observed excellent agreement of the resulting dCt between the paired samples, m-d versus non m-d, for ESR1 (R2=0.92), PGR (R2=0.90), ERBB2 (R2=0.94) and MKi67 (R2=0.90). No significant difference (P value &gt; 0.99) was observed when we compared the dCt between the paired samples m-d versus non m-d. In addition, using the predefined STRAT4 dCt cutoff for ESR and ERBB2 positivity, we found a significant concordance between RT-qPCR and IHC/FISH for ESR-positivity for the paired samples, m-d (P value &lt; 0.001; sensitivity = 0.98; specificity = 1; PPV = 1; NPV = 0.95) versus non m-d (P value &lt; 0.001; sensitivity = 0.98; specificity = 1; PPV = 1; NPV = 0.95) and HER2-positivity for the paired samples, m-d (P value &lt; 0.001; sensitivity = 0.85; specificity = 0.98; PPV = 0.92; NPV = 0.96) versus non m-d (P value &lt; 0.001; sensitivity = 0.71; specificity = 0.98; PPV = 0.90; NPV = 0.92), respectively.

Conclusion: These data suggest that mRNA for ESR and ERBB2 is sufficiently low in surrounding tissues that m-d of whole sections is not required for accurate assessment of key breast cancer mRNA markers in a closed system RT-qPCR assay. The simplicity of the assay workflow may be particularly valuable in low resourced settings where routine access to pathology expertise and to high quality IHC/FISH is challenging.

Citation Format: Gupta S, Carvajal-Hausdorf DE, Wasserman BE, Ho K, Weidler J, Wong W, Rhees B, Bates M, Rimm DL. Macrodissection prior to closed system RT-qPCR is not necessary for estrogen receptor and HER2 concordance with IHC/FISH in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-02.

Implications of the tumor immune microenvironment for staging and therapeutics

Characterizing the tumor immune microenvironment enables the identification of new prognostic and predictive biomarkers, the development of novel therapeutic targets and strategies, and the possibility to guide first-line treatment algorithms. Although the driving elements within the tumor microenvironment of individual primary organ sites differ, many of the salient features remain the same. The presence of a robust antitumor milieu characterized by an abundance of CD8+ cytotoxic T-cells, Th1 helper cells, and associated cytokines often indicates a degree of tumor containment by the immune system and can even lead to tumor elimination. Some of these features have been combined into an 'Immunoscore', which has been shown to complement the prognostic ability of the current TNM staging for early stage colorectal carcinomas. Features of the immune microenvironment are also potential therapeutic targets, and immune checkpoint inhibitors targeting the PD-1/PD-L1 axis are especially promising. FDA-approved indications for anti-PD-1/PD-L1 are rapidly expanding across numerous tumor types and, in certain cases, are accompanied by companion or complimentary PD-L1 immunohistochemical diagnostics. Pathologists have direct visual access to tumor tissue and in-depth knowledge of the histological variations between and within tumor types and thus are poised to drive forward our understanding of the tumor microenvironment. This review summarizes the key components of the tumor microenvironment, presents an overview of and the challenges with PD-L1 antibodies and assays, and addresses newer candidate biomarkers, such as CD8+ cell density and mutational load. Characteristics of the local immune contexture and current pathology-related practices for specific tumor types are also addressed. In the future, characterization of the host antitumor immune response using multiplexed and multimodality biomarkers may help predict which patients will respond to immune-based therapies.

Exceptional Response to Pembrolizumab in a Metastatic, Chemotherapy/Radiation-Resistant Ovarian Cancer Patient Harboring a PD-L1-Genetic Rearrangement

Purpose: Ovarian carcinoma no longer responsive to surgery and chemotherapy remains an incurable disease. Alternative therapeutic options remain desperately needed.Patients and Methods: We describe a heavily pretreated patient with ovarian cancer with recurrent disease experiencing a remarkable clinical response to treatment with the anti-PD1 immune checkpoint inhibitor pembrolizumab. The clinical, pathological, and genomic characteristics of this exceptional ovarian cancer responder were carefully investigated using immunohistochemistry (IHC), quantitative multiplex fluorescence methods (i.e., automated quantitative analysis, AQUA) and whole-exome sequencing (WES) techniques.Results: The patient harbored a recurrent/metastatic radiation and chemotherapy-resistant high-grade ovarian carcinoma with clear cell features. While progressing on any standard treatment modality, she demonstrated a remarkable complete response to the anti-PD1 immune checkpoint inhibitor pembrolizumab. WES results were notable for the presence a relative low number of mutations (tumor mutation load/Mb = 4.31, total mutations = 164) and a peculiar structural variant disrupting the 3' region of the PD-L1 gene causing aberrant PD-L1 surface expression as confirmed by IHC and AQUA technology. Heavy infiltration of the PD-L1-mutated and PD-L1-overexpressing tumor with T-cell lymphocytes (i.e., CD4⁺/CD8⁺ TIL), CD68⁺ macrophages, and CD20⁺ B cells was detected in the surgical specimen strongly suggesting immune evasion as a key mechanism of tumor growth and survival. Patient's complete clinical responses remain unchanged at the time of the writing of this report with no significant side effects reported to date.Conclusions: Anti-PD1 inhibitors may represent a novel treatment option for recurrent/metastatic human tumors refractory to salvage treatment harboring PD-L1 gene structural variations causing aberrant PD-L1 expression. Clin Cancer Res; 24(14); 3282-91. ©2018 AACRSee related commentary by Lheureux, p. 3233.

Worldwide Frequency of Commonly Detected EGFR Mutations

CONTEXT

- Recurrent epidermal growth factor receptor ( EGFR) mutations are seen in a subset of pulmonary adenocarcinomas. These mutations are targeted by EGFR inhibitors and are a biomarker for response to EGFR inhibitor therapies. Initial data have indicated an increased frequency of activating EGFR mutations in nonsmoking Asian females. However, there are very few studies of global scope that address the question of mutation distribution across the population of lung cancer.

OBJECTIVE

- To determine the frequency of EGFR mutations in exons 18 through 21 detected in clinical laboratories participating in the College of American Pathologists proficiency testing program for EGFR in calendar year 2013.

DESIGN

- We reviewed the surveys from 170 clinical laboratories from 20 countries that participated in the College of American Pathologists EGFR proficiency testing program. The proficiency testing includes questions regarding the total numbers of tests performed at each common mutation site, including both activating and resistance mutations, and their frequency. Countries were grouped into regional groups in order to assess frequency of mutation by type, and to indirectly assess ethnic differences in mutation frequencies.

RESULTS

- Among the treatment-sensitive activating mutations, the most common are exon 19 mutations (n = 10 802 of 136 533 cases; 7.9% of total cases tested) and the exon 21 L858R mutation (n = 10 351 of 136 533 cases; 7.6% of total cases tested) and the least common are exon 20 mutations (n = 466 of 136 533 cases; 0.3% of total cases tested). The T790M mutation in exon 20 is the more common resistance mutation (n = 1010 of 136 533 cases; 0.7% of all cases tested). The highest activating mutation frequency is seen in southern Asia (n = 4260 of 9337 cases; 46%) and the lowest activating mutation frequencies are in South and North America (n = 113 of 1439 cases and 7926 of 86 654 cases; 8% and 9%, respectively).

CONCLUSIONS

- Our data confirm that activating EGFR mutations are more common in southern Asia and that the distribution of activating EGFR mutations varies significantly across the regions. Similarly, the frequency and distribution of resistance mutations also show significant variation when comparing southern Asia with other regions.

Objective measurement and clinical significance of IDO1 protein in hormone receptor-positive breast cancer

Background

Immunostimulatory therapies targeting immune-suppressive pathways produce durable responses in advanced solid tumors. Indoleamine 2,3-dioxygenase (IDO) is the rate-limiting oxidoreductase that catalyzes the degradation of tryptophan to kynurenine. IDO induces immune tolerance by downregulating CD8+ and effector CD4+ T cell responses. IDO1, the most active isoform, is expressed in diverse tumor types and can be targeted using small molecule inhibitors. We used an objective, in situ assay to measure IDO1 in a collection of hormone receptor-positive breast cancers (HR+ BC).

Methods

IDO1 protein was measured using quantitative immunofluorescence in 362 stage I-III HR+ BC represented in tissue microarrays. IDO1 levels were determined in the tumor and stroma, and stratified using median cut-point. Associations between IDO1, clinico-pathological features and CD3+, CD8+, CD20+ and FOXP3 tumor-infiltrating lymphocytes were examined using χ² and Mann-Whitney tests. Survival was studied using Kaplan-Meier estimator and a proportional hazards model. All tests were two-sided.

Results

IDO1 protein was observed in 76.2% of HR+ BC. There was no association between IDO1 and major clinico-pathological characteristics. Increased IDO1 correlated with decreased CD20+ infiltration (P = 0.0004) but not with CD3+, CD8+ or FOXP3 levels. Elevated IDO1 expression was associated with worse 20-year overall survival (log-rank P = 0.02, HR = 1.39, 95% C.I.: 1.05-1.82). IDO1 scores were independently associated with outcome in multivariable analysis.

Conclusions

IDO1 protein is expressed in the majority of HR+ BC and is an independent negative prognostic marker. Additionally, IDO1 expression is negatively associated with tumor B-cell infiltration. Measurement of IDO1 has the potential to identify a population that might derive benefit from IDO1 blockade.

Electronic supplementary material

The online version of this article (10.1186/s40425-017-0285-7) contains supplementary material, which is available to authorized users.

Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer

Mechanisms of acquired resistance to immune checkpoint inhibitors (ICI) are poorly understood. We leveraged a collection of 14 ICI-resistant lung cancer samples to investigate whether alterations in genes encoding HLA Class I antigen processing and presentation machinery (APM) components or interferon signaling play a role in acquired resistance to PD-1 or PD-L1 antagonistic antibodies. Recurrent mutations or copy-number changes were not detected in our cohort. In one case, we found acquired homozygous loss of B2M that caused lack of cell-surface HLA Class I expression in the tumor and a matched patient-derived xenograft (PDX). Downregulation of B2M was also found in two additional PDXs established from ICI-resistant tumors. CRISPR-mediated knockout of B2m in an immunocompetent lung cancer mouse model conferred resistance to PD-1 blockade in vivo, proving its role in resistance to ICIs. These results indicate that HLA Class I APM disruption can mediate escape from ICIs in lung cancer.Significance: As programmed death 1 axis inhibitors are becoming more established in standard treatment algorithms for diverse malignancies, acquired resistance to these therapies is increasingly being encountered. Here, we found that defective antigen processing and presentation can serve as a mechanism of such resistance in lung cancer. Cancer Discov; 7(12); 1420-35. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1355.

A Prospective, Multi-institutional, Pathologist-Based Assessment of 4 Immunohistochemistry Assays for PD-L1 Expression in Non-Small Cell Lung Cancer

Importance

Four assays registered with the US Food and Drug Administration (FDA) detect programmed cell death ligand 1 (PD-L1) to enrich for patient response to anti-programmed cell death 1 and anti-PD-L1 therapies. The tests use 4 separate PD-L1 antibodies on 2 separate staining platforms and have their own scoring systems, which raises questions about their similarity and the potential interchangeability of the tests.

Objective

To compare the performance of 4 PD-L1 platforms, including 2 FDA-cleared assays, 1 test for investigational use only, and 1 laboratory-developed test.

Design, Setting, and Participants

Four serial histologic sections from 90 archival non-small cell lung cancers from January 1, 2008, to December 31, 2010, were distributed to 3 sites that performed the following immunohistochemical assays: 28-8 antibody on the Dako Link 48 platform, 22c3 antibody on the Dako Link 48 platform, SP142 antibody on the Ventana Benchmark platform, and E1L3N antibody on the Leica Bond platform. The slides were scanned and scored by 13 pathologists who estimated the percentage of malignant and immune cells expressing PD-L1. Statistical analyses were performed from December 1, 2015, to August 30, 2016, to compare antibodies and pathologists' scoring of tumor and immune cells.

Main Outcomes and Measures

Percentages of malignant and immune cells expressing PD-L1.

Results

Among the 90 samples, the SP142 assay was an outlier, with a significantly lower mean score of PD-L1 expression in both tumor and immune cells (tumor cells: 22c3, 2.96; 28-8, 3.26; SP142, 1.99; E1L3N, 3.20; overall mean, 2.85; and immune cells: 22c3, 2.15; 28-8, 2.28; SP142, 1.62; E1L3N, 2.28; overall mean, 2.08). Pairwise comparisons showed that the scores from the 28-8 and E1L3N tests were not significantly different but that the 22c3 test showed a slight (mean difference, 0.24-0.30) but statistically significant reduction in labeling of PD-L1 expression in tumor cells. Evaluation of intraclass correlation coefficients (ICCs) between antibodies to quantify interassay variability for PD-L1 expression in tumor cells showed high concordance between antibodies for tumor cell scoring (0.813; 95% CI, 0.815-0.839) and lower levels of concordance for immune cell scoring (0.277; 95% CI, 0.222-0.334). When examining variability between pathologists for any single assay, the concordance between pathologists' scoring for PD-L1 expression in tumor cells ranged from ICCs of 0.832 (95% CI, 0.820-0.844) to 0.882 (95% CI, 0.873-0.891) for each assay, while the ICCs from immune cells for each assay ranged from 0.172 (95% CI, 0.156-0.189) to 0.229 (95% CI, 0.211-0.248).

Conclusions and Relevance

The assay using the SP142 antibody is an outlier that detected significantly less PD-L1 expression in tumor cells and immune cells. The assay for antibody 22c3 showed slight yet statistically significantly lower staining than either 28-8 or E1L3N, but this significance was detected only when using the mean of 13 pathologists' scores. The pathologists showed excellent concordance when scoring tumor cells stained with any antibody but poor concordance for scoring immune cells stained with any antibody. Thus, for tumor cell assessment of PD-L1, 3 of the 4 tests are concordant and reproducible as read by pathologists.

ErbB activation signatures as potential biomarkers for anti-ErbB3 treatment in HNSCC

Head and neck squamous cell carcinoma (HNSCC) accounts for 3–5% of all tumor types and remains an unmet medical need with only two targeted therapies approved to date. ErbB3 (HER3), the kinase-impaired member of the EGFR/ErbB family, has been implicated as a disease driver in a number of solid tumors, including a subset of HNSCC. Here we show that the molecular components required for ErbB3 activation, including its ligand neuregulin-1 (NRG1), are highly prevalent in HNSCC and that HER2, but not EGFR, is the major activating ErbB3 kinase partner. We demonstrate that cetuximab treatment primarily inhibits the ERK signaling pathway and KTN3379, an anti-ErbB3 monoclonal antibody, inhibits the AKT signaling pathway, and that dual ErbB receptor inhibition results in enhanced anti-tumor activity in HNSCC models. Surprisingly, we found that while NRG1 is required for ErbB3 activation, it was not sufficient to fully predict for KTN3379 activity. An evaluation of HNSCC patient samples demonstrated that NRG1 expression was significantly associated with expression of the EGFR ligands amphiregulin (AREG) and transforming growth factor α (TGFα). Furthermore, NRG1-positive HNSCC cell lines that secreted high levels of AREG and TGFα or contained high levels of EGFR homodimers (H11D) demonstrated a better response to KTN3379. Although ErbB3 and EGFR activation are uncoupled at the receptor level, their respective signaling pathways are linked through co-expression of their respective ligands. We propose that NRG1 expression and EGFR activation signatures may enrich for improved efficacy of anti-ErbB3 therapeutic mAb approaches when combined with EGFR-targeting therapies in HNSCC.

Abstract 5657: Objective measurement and significance of VISTA (PD-1H) expression in non-small cell lung cancer (NSCLC)

Introduction: VISTA (PD-1H) is a member of the B7 family of immune co-regulatory molecules and has been proposed as a novel anti-cancer immunotherapy target. The intra- and extracellular domains of VISTA show homology to PD-1 and PD-L1, respectively, suggesting a role in anti-tumor immune evasion. The expression of VISTA, its association with PD-1 axis components and biological role in human NSCLC are unknown.

Methods: Using multiplex quantitative immunofluorescence (QIF), we simultaneously measured the levels of VISTA (clone D1L2G, CST), PD-L1 (clone 405.9A11, CST) and PD-1 (clone EH33, CST) protein in 732 stage I-IV NSCLCs from 3 retrospective collections represented in tissue microarray format (cohort #1 [n=297, Yale], cohort #2 [n=329, Greece]; and cohort #3 [n=106, Yale]). To evaluate the tumor tissue distribution, VISTA was also selectively measured in cytokeratin+ tumor cells, CD3+ T-cells, CD4+ T-helper cells, CD8+ cytotoxic T-cells and CD20+ B-lymphocytes. Associations between the marker levels, clinico-pathological-molecular variables and survival were studied.

Results: VISTA protein was detected in all NSCLCs, showed a membranous staining pattern and was localized predominantly in the tumor cells in 27.4% of cases; and in the stromal compartment in 98.5%. Although VISTA was detected in all major tumor infiltrating lymphocyte (TIL) subsets, the signal was higher in CD20+ B-cells than in CD3+ T-lymphocytes (P&lt;0.05); and in CD4+ helper than in CD8+ cytotoxic T-cells (P&lt;0.001). Using the median score as cut point, elevated VISTA in tumor and/or stromal cells was significantly associated with high PD-L1, PD-1 protein expression and increased CD8+TILs in the cohorts (P&lt;0.001 - P&lt;0.05). No consistent association between VISTA levels and age, gender, smoking status, specific NSCLC histology, stage, EGFR/KRAS mutations and overall survival was found.

Conclusion: VISTA is expressed in the majority of NSCLCs and shows differential distribution in tumor/stromal cells and TIL subsets, suggesting a complex function as a ligand and receptor. Elevated expression of VISTA in NSCLC is associated with increased PD-1 axis targets and cytotoxic T-cell density, indicating its possible modulation by pro-inflammatory signals. Our results support VISTA as a candidate target for anti-cancer immunotherapy in NSCLC alone or in combination with PD-1 axis blockers.

Citation Format: Franz Villarroel-Espindola, Ila J. Datar, Vamsidhar Velcheti, David L. Rimm, Roy S. Herbst, Kurt A. Schalper. Objective measurement and significance of VISTA (PD-1H) expression in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5657. doi:10.1158/1538-7445.AM2017-5657

Abstract 5600: Simultaneous measurement and clinical significance of PD-1, LAG-3 and TIM-3 in non-small cell lung cancer (NSCLC)

Introduction: The ineffective anti-tumor immune response is characterized by increased immune suppressive signals in the tumor microenvironment. In particular, T-cells recognizing tumor antigens can express diverse immune inhibitory receptors mediating lymphocyte inactivation and limiting tumor rejection. Blockade of these receptors such as PD-1 induces prominent clinical benefit in patients with NSCLC. However, the expression and significance of additional potentially actionable immune inhibitory receptors in lung cancer is poorly understood.

Methods: After careful validation of assays and using multiplexed quantitative immunofluorescence (QIF) we measured the levels of CD3 (rabbit polyclonal, Dako), PD-1 (clone EH33, CST), LAG-3 (Clone 17B4, Abcam) and TIM-3 (clone D5D5R, CST) in 698 stages I-IV formalin-fixed paraffin embedded (FFPE) lung carcinomas represented in three tissue microarrays (cohort #1 [Yale n=186], cohort #2 [Yale n=192, and cohort #3 [Greece n=320]). We also included a collection of lung adenocarcinomas with molecular annotation (cohort #4 [Yale n=106]). The targets were measured in all cells of the preparation using fluorescence co-localization with DAPI and specifically in CD3-positive T-lymphocytes. Associations between the markers and with major clinico-pathological variables, driver mutations and survival were studied.

Results: All the targets were detected predominantly in CD3+ T-cells with membranous staining. Expression of PD-1, LAG-3 and TIM-3 in T-cells across all NSCLC cohorts was 68.7%, 39.7% and 55.8%, respectively. Elevated levels of PD-1, LAG-3 or TIM-3 were significantly associated with increased tumor infiltrating lymphocytes and with the co-expression of one or more of the other inhibitory receptors (P&lt;0.001). Simultaneous co-expression of all 3 markers was identified in 32.6% of cases. No consistent association was seen between the targets and patient age, gender, smoking status, clinical stage, tumor histology and overall survival. PD-1, TIM-3 and CD3 expression was significantly lower in EGFR and KRAS mutant lung adenocarcinomas than in tumors lacking mutations in these oncogenic drivers (P&lt;0.05).

Conclusion: PD-1, LAG-3 and TIM-3 are differentially expressed in NSCLC, show frequent co-expression and association with elevated CD3+ T-cells. Our results support the biological role of PD-1, LAG-3 and TIM-3 in NSCLC and suggest co-activation of these immune inhibitory pathways in a proportion of cases. Modulation of these receptors could enhance the anti-tumor immune response in lung cancer.

Citation Format: Ila J. Datar, Jun Wang, Nikita Mani, Franz Villarroel-Espindola, Patrick Ryan, Miguel F. Sanmamed, Kristen McEachern, David Jenkins, David L. Rimm, Leiping Chen, Roy Herbst, Kurt Schalper. Simultaneous measurement and clinical significance of PD-1, LAG-3 and TIM-3 in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5600. doi:10.1158/1538-7445.AM2017-5600

B7-H3 Expression in NSCLC and Its Association with B7-H4, PD-L1 and Tumor-Infiltrating Lymphocytes

Purpose: The immune checkpoint PD-1 and its receptor B7-H1 (PD-L1) are successful therapeutic targets in cancer but less is known about other B7 family members. Here, we determined the expression level of B7-H3 protein in non-small cell lung cancer (NSCLC) and evaluated its association with tumor-infiltrating lymphocytes (TIL), PD-L1, B7-H4, and major clinicopathologic characteristics is in 3 NSCLC cohorts.Experimental design: We used multiplexed automated quantitative immunofluorescence (QIF) to assess the levels of B7-H3, PD-L1, B7-H4, and TILs in 634 NSCLC cases with validated antibodies. Associations between the marker levels, major clinicopathologic variables and survival were analyzed.Results: Expression of B7-H3 protein was found in 80.4% (510/634) of the cases. High B7-H3 protein level (top 10 percentile) was associated with poor overall survival (P < 0.05). Elevated B7-H3 was consistently associated with smoking history across the 3 cohorts, but not with sex, age, clinical stage, and histology. Coexpression of B7-H3 and PD-L1 was found in 17.6% of the cases (112/634) and with B7-H4 in 10% (63/634). B7-H4 and PD-L1 were simultaneously detected only in 1.8% of NSCLCs (12/634). The expression of B7-H3 was not associated with the levels of CD3-, CD8-, and CD20-positive TILs.Conclusions: B7-H3 protein is expressed in the majority of NSCLCs and is associated with smoking history. High levels of B7-H3 protein have a negative prognostic impact in lung carcinomas. Coexpression of B7-H3 with PD-L1 and B7-H4 is relatively low, suggesting a nonredundant biological role of these targets. Clin Cancer Res; 23(17); 5202-9. ©2017 AACR.

Quantitative spatial profiling of PD-1/PD-L1 interaction and HLA-DR/IDO1 to predict outcomes to anti-PD-1 in metastatic melanoma (MM)

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Background: Although PD-1/L1 axis directed therapies induce durable responses in some mm patients (pts), biomarkers of response remain elusive. We hypothesized that quantifying key immune suppression mechanisms within the tumor microenvironment would provide superior predictors of response to anti-PD-1 compared with single marker assessment. Methods: Pre-treatment tumor biopsies from 124 mm pts treated with anti-PD-1 at 7 academic centers were fluorescently stained with multiple immune markers in discovery (n = 24) and validation (n = 100) cohorts. Selected biomarker signatures, PD-1/PD-L1 interaction score (proportion of PD-1+ cells co-localized with PD-L1) and IDO1/HLA-DR co-expression were evaluated for anti-PD-1 treatment response and survival. Slides were imaged using Vectra; biomarker positive cells and their co-localization were objectively quantified in pathologist-selected regions using novel Automated Quantitative Analysis (AQUA) algorithms. Results: In the discovery cohort, high levels of PD-1/PD-L1 interaction score and/or IDO1/HLA-DR coexpression was strongly positively associated with response to anti-PD-1 (p = 0.0005). In contrast, other individual biomarkers (PD-1, PD-L1, CD8) were not associated with response or survival (p > 0.10). This finding was replicated in the validation cohort: pts with high PD-1/PD-L1 and/or IDO1/HLA-DR were more likely to respond to treatment (p = 0.009). These pts also experienced a three-fold increase in progression free survival (hazards ratio (HR) = 0.33; p = 0.003) and overall survival (HR = 0.34; p = 0.004). Multivariate analyses revealed that these findings were independent of BRAF mutation, stage, LDH and prior therapy. In the combined cohort (n = 124), 80% of responding pts had higher levels of PD-1/PD-L1 interaction scores and/or IDO1/HLA-DR. In contrast, PD-L1 expression alone (≥1% or ≥50%) was not predictive of PFS or OS (p > 0.1). Conclusions: This novel multiplexed method profiling key tumor-immune suppression pathways identified mm pts likely to respond to anti-PD-1 therapy. This method could help stratify patients for PD-1 monotherapy and be useful in guiding future clinical trials.

Measurement of PD-1, TIM-3 and LAG-3 protein in non-small cell lung carcinomas (NSCLCs) with acquired resistance to PD-1 axis blockers

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Background: PD-1 axis blockade induces lasting clinical responses in ~20% of patients with advanced NSCLC. However, most patients eventually develop resistance. Acquired resistance is poorly understood, but may be mediated by alternative immune suppressive pathways. Methods: Using multiplex immunofluorescence we simultaneously measured levels of DAPI, CD3 (D7AE6), PD-1 (EH33), TIM-3 (D5D5R) and LAG-3 (17B4) in 11 whole tissue sections obtained from patients with NSCLC before PD-1 axis blockade and after acquired resistance (8 cases with progression on-treatment and 3 with progression off-therapy). Markers were measured in the whole tumor area or in CD3+ T-cells using fluorescence co-localization. The association between markers and changes upon acquired resistance were studied. Results: Expression of PD-1, TIM-3 and LAG-3 was seen in all cases with membranous staining pattern and signal predominantly located in CD3+ T-cells. Levels of TIM-3 and LAG-3 in T-cells were significantly correlated (Spearman’s R = 0.65, P = 0.001), but were not associated with PD-1 (R = -0.03, P = 0.86 for TIM-3 and PD-1; and R = 0.24, P = 0.28 for LAG-3 and PD-1). Compared to pre-treatment samples, 6 cases (55%) showed significantly higher levels of PD-1 or LAG-3 on acquired resistance and 5 cases (45%) had higher TIM-3. Of these, 4 cases had higher levels of the 3 markers and were on-therapy at progression. Lower levels of PD-1, TIM-3, and LAG-3 were found on acquired resistance in 5 (45%), 6 (55%), and 4 (36%) cases, respectively. Four of these cases showed lower levels of all inhibitory receptors, 3 of which were off-therapy at progression. Only one case had no change in LAG-3 levels. Conclusions: PD-1, TIM-3 and LAG-3 were expressed in the majority of NSCLCs with signal predominantly located in T-lymphocytes. Among acquired resistance cases, higher levels of PD-1, TIM-3 and LAG-3 were associated with progression on-treatment. Lower levels of the markers were associated with progression off-therapy. Although multiple mechanisms may exist, up-regulation of alternative immune inhibitory receptors such as TIM-3 and LAG-3 could mediate acquired resistance to PD-1 axis blockers in a proportion of NSCLCs.

Immune marker profiling and PD-L1, PD-L2 expression mechanisms across non-small cell lung cancer mutations

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Background: PD-1/PD-L1 axis inhibitors have been proven effective, especially in patients expressing Programmed Death Ligand 1 (PD-L1). Their clinical efficacy in patients with epidermal growth factor receptor (EGFR) activating mutations is still unclear, while KRAS mutations seem to be associated with high response rates. In this study we investigated the expression of PD-L1, PD-L2 and Tumor Infiltrating Lymphocyte (TIL) status as a function of mutation status in Non-Small Cell Lung Cancer (NSCLC). Methods: We used the AQUA method of quantitative fluorescence (QIF) to compare PD-L1 and PD-L2 expression and to characterize TILs populations and their activation status in over 150 NSCLC patient tumors with known mutation status. EGFR activation was assessed in situ using the proximity ligation assay (PLA) for EGFR and GRB2 and T cell activation was assessed using a novel multiplexed QIF assay including CD3, Granzyme B and Ki67. Results: PD-L1 tumor and stroma expression was significantly lower in EGFR mutant compared to KRAS mutant (p = 0.009) and EGFR/KRAS Wild Type (p < 0.0001) tumors, while they had a higher frequency of PD-L2 expression. Conversely, KRAS mutants had significantly lower PD-L2 tumor and stroma expression but they were also more inflamed with higher CD4+, CD8+ and CD20+ TILs. Subgroup analysis of patients by their TILs activation status revealed that EGFR mutants had a very high frequency of inactive TILs even though lymphocytes were present in the tumor microenvironment. In contrast, in KRAS mutants, when TILs were present, they were almost always active. Finally, we find that PLA-defined activated EGFR correlated with increased PD-L1 expression in EGFR mutants but not in EGFR WT, while TIL activation was associated with higher PD-L1 in EGFR/KRAS WT. Conclusions: Our findings are consistent with the unique biology of EGFR mutant tumors. The high frequency of inactive TILs could explain the low immune therapy response rates in this patient group. Similarly, in this group, the reason PD-L1 expression fails to predict response may be due to expression as a result of constitutive oncogenic signaling rather than immune signaling, which would be associated with high PD-L1 levels and TILs activation.

Effects of neoadjuvant chemotherapy (NAC) on tumor infiltrating lymphocytes (TIL) and PD-L1 expression in the SWOG S0800 clinical trial

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Background: Higher baseline TILs and PD-L1 expression are associated with greater pathologic complete response (pCR) rates, but how chemotherapy affects these immune parameters is unknown. The goal of this study was to examine TIL and PD-L1 expression in pre- and post-NAC tumor specimens from the S0800 clinical trial that compared weekly nab-paclitaxel/bevacizumab + dose-dense doxorubicin and cyclophosphamide (AC) with nab-paclitaxel + AC as NAC for HER2-negative cases. Association between immune parameters, pCR and NAC-induced changes were tested using ER and NAC-arm adjusted logistic regression. Methods: TILs were assessed on H&E stained full sections of 120 pre- and 62 post-NAC tissues (tumor bed of pCR) including 59 matched samples. PD-L1 immunohistochemistry was performed using the FDA cleared 22C3 assay and results were available for 121 baseline and 43 matched post-NAC samples. Results: At baseline, the mean TIL count was 18%; 16% had no TILs and 9% had > 50% TILs. Higher baseline TILs were associated with higher pCR rate (p = 0.043, trend test p = 0.014) but there was no interaction with NAC arm. Post-NAC, the mean TIL counts was 11%; 5% had no TILs and 1.6% had > 50% TILs. In the matching post-NAC samples, the mean change was 15% decrease in TILs, but in 32% of cases TILs increased. Cases with residual disease (n=44) had lesser average decrease (p=0.029) than cases with pCR (n=15). The post-NAC decrease in TILs was also observed after excluding cases with pCR. At baseline, PD-L1 expression either in the stroma or on epithelial cells or in both was detected in 52 (43%) of 121 cases (5 tumor only, 29 stroma only, 18 tumor + stroma). Those with baseline PD-L1 expression had higher pCR (63% vs. 37%; p=0.008). Post-NAC, PD-L1 expression was seen in 14 of 43 (33%) cases (7 stroma only, 7 tumor + stroma). In the 39 matching pre- and post-NAC samples, PD-L1 expression was negative in both in 20, positive in both in 10 cases and 6 patients had PD-L1 expression at baseline but not in the post-NAC sample. Conclusions: TIL counts and PD-L1 expression generallydecreased, but in a minority of cases increased after NAC. The decrease in TIL was significantly greater in cases achieving pCR. Clinical trial information: NCT00856492.

Nuclear IRF-1 expression as a mechanism to assess "Capability" to express PD-L1 and response to PD-1 therapy in metastatic melanoma

Background

Predictive biomarkers for antibodies against programmed death 1 (PD-1) remain a major unmet need in metastatic melanoma. Specifically, response is seen in tumors that do not express programmed death ligand 1 (PD-L1), highlighting the need for a more sensitive biomarker. We hypothesize that capacity to express PD-L1, as assessed by an assay for a PD-L1 transcription factor, interferon regulatory factor 1 (IRF-1), may better distinguish patients likely to benefit from anti-PD-1 immunotherapy.

Methods

Samples from 47 melanoma patients that received nivolumab, pembrolizumab, or combination ipilimumab/nivolumab at Yale New Haven Hospital from May 2013 to March 2016 were collected. Expression of IRF-1 and PD-L1 in archival pre-treatment formalin-fixed, paraffin-embedded tumor samples were assessed by the AQUA method of quantitative immunofluorescence. Objective radiographic response (ORR) and progression-free survival (PFS) were assessed using modified RECIST v1.1 criteria.

Results

Nuclear IRF-1 expression was higher in patients with partial or complete response (PR/CR) than in patients with stable or progressive disease (SD/PD) (p = 0.044). There was an insignificant trend toward higher PD-L1 expression in patients with PR/CR (p = 0.085). PFS was higher in the IRF-1-high group than the IRF-1-low group (p = 0.017), while PD-L1 expression had no effect on PFS (p = 0.83). In a subset analysis, a strong association with PFS is seen in patients treated with combination ipilimumab and nivolumab (p = 0.0051).

Conclusions

As a measure of PD-L1 expression capability, IRF-1 expression may be a more valuable predictive biomarker for anti-PD-1 therapy than PD-L1 itself.

Electronic supplementary material

The online version of this article (doi:10.1186/s40425-017-0229-2) contains supplementary material, which is available to authorized users.