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.

Changes in serum interleukin-8 (IL-8) levels reflect and predict response to anti-PD-1 treatment in melanoma and non-small-cell lung cancer patients

Background

Surrogate biomarkers of efficacy are needed for anti-PD1/PD-L1 therapy, given the existence of delayed responses and pseudo-progressions. We evaluated changes in serum IL-8 levels as a biomarker of response to anti-PD-1 blockade in melanoma and non-small-cell lung cancer (NSCLC) patients.

Patients and methods

Metastatic melanoma and NSCLC patients treated with nivolumab or pembrolizumab alone or nivolumab plus ipilimumab were studied. Serum was collected at baseline; at 2-4 weeks after the first dose; and at the time-points of response evaluation. Serum IL-8 levels were determined by sandwich ELISA. Changes in serum IL-8 levels were compared with the Wilcoxon test and their strength of association with response was assessed with the Mann-Whitney test. Accuracy of changes in IL-8 levels to predict response was estimated using receiver operation characteristics curves.

Results

Twenty-nine melanoma patients treated with nivolumab or pembrolizumab were studied. In responding patients, serum IL-8 levels significantly decreased between baseline and best response (P <0.001), and significantly increased upon progression (P =  0.004). In non-responders, IL-8 levels significantly increased between baseline and progression (P =  0.013). Early changes in serum IL-8 levels (2-4 weeks after treatment initiation) were strongly associated with response (P <0.001). These observations were validated in 19 NSCLC patients treated with nivolumab or pembrolizumab (P =  0.001), and in 15 melanoma patients treated with nivolumab plus ipilimumab (P <0.001). Early decreases in serum IL-8 levels were associated with longer overall survival in melanoma (P =  0.001) and NSCLC (P =  0.015) patients. Serum IL-8 levels also correctly reflected true response in three cancer patients presenting pseudoprogression.

Conclusions

Changes in serum IL-8 levels could be used to monitor and predict clinical benefit from immune checkpoint blockade in melanoma and NSCLC patients.

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 P3-07-06: Objective measurement of HER2 (ERBB2) intracellular and extracellular domain spatial co-localization stratifies benefit from adjuvant trastuzumab

Background: The ASCO/CAP guidelines consider chromogen-based immunohistochemistry (IHC) as the primary assay to determine HER2 status in breast cancer. U. S. Food and Drugs Administration (FDA) approved HER2 antibody assays target the protein's intracellular domain (ICD). Studies suggest that quantitative, domain-specific measurement of HER2 might predict benefit from trastuzumab therapy, further classifying traditional HER2-positive breast cancer. Here we define a method of simultaneous, objective measurement of HER2 ICD and extracellular (ECD) domains, and determine its effect on trastuzumab benefit in the adjuvant setting.

Methods: We measured co-expression of HER2 ICD and ECD using a proximity ligation assay (PLA) and quantitative immunofluorescence (QIF) in a HER2 standardization tissue microarray (TMA) with CLIA-lab defined HER2 status. Previously validated, standardized HER2 antibodies were used to detect ICD and ECD (CB11 and SP3, respectively). We determined the relationship between HER2 PLA scores, HER2 clinical status and domain-specific scores. Finally, we measured HER2 ICD/ECD PLA in 180 patients from a clinical trial of adjuvant chemotherapy followed by trastuzumab (HeCOG 10/05). Median cut-point was used to stratify patients according to HER2 PLA scores. Cut-points for HER2 ICD and ECD were obtained using Joinpoint software. All statistical tests were two-sided.

Results: In the standardization TMA, HER2 PLA levels were associated to HER2 CLIA status (P&lt;0.0001). There was a good correlation between HER2 PLA scores and HER2 ICD and ECD (R2=0.57 and R2=0.54, respectively). In trastuzumab-treated patients from HeCOG 10/05, a similarly good correlation was observed between HER2 PLA scores and HER2 ICD and ECD (R2=0.41 and R2=0.3, respectively). In univariate analysis, HER2 PLA-low status was associated with ER-positive status (P=0.005). There was no association with age, histological grade, tumor size, lymph node status and TNM stage. Although all tumors were HER2-positive, HER2 PLA-high status was significantly associated with longer 5-year disease-free survival (DFS) (log-rank P=0.036, HR=0.32, 95% CI: 0.132-0.935). HER2 PLA status was superior to ICD status (log-rank P=0.67) and numerically comparable to ECD status (log-rank P=0.049, HR=0.31, 95% CI: 0.144-0.997) to predict benefit from adjuvant trastuzumab, as previously published by our group. HER2 PLA-high status was independent predictor of better outcome in a Cox proportional hazards model including age, histological grade, ER status, tumor size, lymph node status and TNM stage.

Discussion: Using an objective, quantitative HER2 assay for synchronous, domain-specific measurement, we stratified benefit from adjuvant trastuzumab treatment in patients from a prospective cohort. Our results further support the concept that benefit from HER2 ECD-targeted therapies might be modulated by the presence of truncated HER2 protein variants and that tyrosine kinase inhibitors (ICD-directed) may be advantageous for a subset of HER2-positive patients. Furthermore, this technique that uses two antibodies has the potential to increase both sensitivity and specificity of the IHC assay to predict response to HER2 pathway inhibitors.

Citation Format: Carvajal-Hausdorf DE, Toki M, Schalper KA, Pusztai L, Psyrri A, Kalogeras KT, Kotoula V, Fountzilas G, Rimm DL. Objective measurement of HER2 (ERBB2) intracellular and extracellular domain spatial co-localization stratifies benefit from adjuvant trastuzumab. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-06.

Abstract P5-07-09: Heterogeneity of tumor infiltrating lymphocytes in breast cancer and its impact for use as a biomarker

Background: In breast cancer, elevated tumor infiltrating lymphocytes (TILs) is associated with PD-L1 expression, hormone receptors negativity, and better outcome. The presence of numerous CD8+ cytotoxic T cells in pre-treatment specimens is associated with clinical benefit from PD-1 axis blockade in melanoma and lung cancer, suggesting its predictive value. Despite recent efforts to standardize the pathologist evaluation of TILs in breast cancer, objective determination of lymphocyte subpopulations and their distribution/uniformity within tumor tissues remains largely unexplored. Here, we simultaneously measured diverse TIL subpopulations using quantitative immunofluorescence (QIF) in different areas of breast tumors to determine the heterogeneity of TILs and its possible impact for use as biomarker.

Methods: Using a multiplexed QIF-based assay for simultaneous detection of DAPI (all cells), Cytokeratin (epithelial cells, M3515-DAKO), CD3 (T lymphocytes, E272--Novus), CD8 (cytotoxic T cells, C8/144B--DAKO), and CD20 (B cells, clone L26-DAKO), we measured the levels of TIL subpopulations in whole tissue section slides of 3 tumor cores obtained from different areas of 31 breast carcinomas. The levels of the markers were measured using the AQUA method of QIF and the heterogeneity was studied using numerical correlations of log2 transformed scores and variance component analysis with linear mixed effects (LME). The concordance (kappa index [κ]) between binarized scores obtained measuring 1 vs 3 cores of the same tumor was also evaluated.

Results: As expected, we found a positive correlation between CD3 and CD8 levels across all patients (Pearson correlation coefficient [CC]=0.827). The levels of CD3 and CD8 showed weaker association with CD20 signal (CC=0.446 and 0.363, respectively). For all the TIL markers, the intra-tumor variation was higher than the inter-tumor differences with intraclass correlation coefficients (ICC) of 0.411 for CD3, 0.324 for CD8, and 0.252 for CD20. In the variance component analysis, 66-69% of the variance was attributable to signal differences between areas of the same tumor core and 30-33% was due to differences between cores from different areas. Consistent with this and using the median score as cutpoint to stratify cases in high/low marker levels, the concordance of measuring TILs in 1 vs 3 cores of the same tumor was κ=0.705 for CD3, κ=0.655 for CD8, and κ=0.603 for CD20.

Conclusion: Objective measurement of TIL markers indicates that T and B lymphocytes show heterogeneity in breast cancer. The tumor variation of the markers is driven predominantly by differences within the same tumor core. The data from our study suggests that although a single core biopsy of tumors provides considerable information regarding the degree of lymphocyte infiltration in breast cancer patients, caution should be taken when using this as a clinical biomarker.

Citation Format: Mani NL, Schalper K, Hatzis C, Chagpar A, Pusztai L, Rimm DL. Heterogeneity of tumor infiltrating lymphocytes in breast cancer and its impact for use as a biomarker. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-07-09.

Abstract P1-08-09: EGFR expression is associated with decreased response from HER2 targeted therapeutics in the neo-adjuvant setting in the NeoALTTO trial

Background: Epidermal Growth Factor Receptor (EGFR, HER1) is known to heterodimerize with HER2 and may modulate the effectiveness of trastuzumab or lapatinib. Historically, it has been difficult to measure, but recently we reported a new, standardized, quantitative immunofluorescence assay and a novel EGFR antibody which showed that high levels of EGFR were associated with decreased benefit in the concurrent arm of the North Central Cancer Treatment Group (NCCTG/Alliance) N9831 trial (Rimm et al, SABCS 2012). Here we assess its value in the neo-adjuvant setting in the NeoALTTO trial.

Methods: NeoALTTO randomized 455 breast cancer patients to neoadjuvant trastuzumab, lapatinib or both and showed benefit in both single anti-HER2 therapy arms, and the combination therapy showing about twice as much benefit as either single drug arm. We used the previously described AQUA method of quantitative immunofluorescence to measure EGFR levels using the D38B1 antibody on between 4 and 140 fields of view per slide on 353 specimens. The averaged EGFR score was standardized to the absolute concentration using cell lines and western blots and the 13 ng/ug total protein established in the N9831 trial was tested to determine predictive value for pathological complete response (pCR) defined as ypT0/is.

Results: In NeoALTTO, 19% of the patients had EGFR levels above 13 ng/ug, compared to 16% in NCCTG N9831. The pCR rate was 35.3% in the patients with low EGFR, compared with 29.8% for high EGFR but this difference was not statistically significant. However, when adjusted for treatment and hormone receptor (HR) status, high EGFR is statistically significantly associated with lower response rate(p = 0.038). Continuous analysis measures were not significant. The effect on overall response at 6 weeks was also weakly significant when adjusting for treatment and HR status (p = 0.06). Surprisingly, for HR negative patients in the lapatinib only arm, the pCR rate in the low EGFR group was 47.2% compared with 16.0% in the high group. While this difference is statistically significant (p = 0.014), it should be interpreted cautiously because of the small numbers of patients and the multiple tests performed.

Conclusions: High expression of EGFR by the AQUA platform appears to be associated with decreased pCR rate from HER2 targeted therapy in the neoadjuvant setting. This observation is consistent with NCCTG N9831. Although underpowered, high EGFR levels predicted decreased pCR rate from lapatinib, the opposite of that anticipated for this small molecule dual EGFR/HER2 inhibitor. Further studies are required to determine the clinical utility of this assay and the biological mechanisms underlying these observations.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-09.

Abstract P2-10-02: PD-L1 protein expression is a prognostic biomarker in breast cancer

BACKGROUND: Programmed death ligand 1 (PD-L1) and its receptor, PD1, are involved in limiting immune response. In the context of cancer, tumor cells expressing PD-L1 can suppress the immune response of PD1-expressing tumor infiltrating lymphocytes (TILs). Disruption of this pathway with antibodies to either the ligand or the receptor has shown promise in the treatment of non small cell lung cancer, melanoma and renal cell cancer. Here we investigate the pathway in breast cancer.

METHODS: PD-L1 protein expression was assessed on two Yale TMA breast cancer cohorts with two-fold redundancy by quantitative immunofluorescence (QIF) using AQUA technology. Cohort 1 (YTMA201) consists of 400 patients with has extensive follow-up and adjuvant treatment information. Cohort 2 (YTMA128) consists of 245 patients with limited follow-up and no treatment information. The PD-L1 antibody (Lieping Chen, clone 5H1) has been previously validated for specificity and reproducibility using transfected cell models. TILs were assessed by a pathologist for each cohort using a score from 0-3 based on the amount of TILs within the spot. AQUA scores for PD-L1 were used as a continuous variable and also cut at the median for outcome analysis.

RESULTS: PD-L1 protein is positively correlated with TILs (p&lt;0.0001 on cohort 1 and p = 0.0072 on cohort 2) and inversely correlated with estrogen receptor status (p&lt;0.0001 on cohort 1 and p = 0.0188 on cohort 2) on both breast cancer cohorts examined (total n = 594). On cohort 1, PD-L1 protein expression is a marker of good prognosis as a continuous variable (p = 0.0271) as well as when cut at the median (p = 0.0151), particularly in the estrogen receptor positive subset of patients.

CONCLUSIONS: PD-L1 expression in breast cancer is positively associated with TILs and inversely associated with estrogen receptor status on two independent breast cancer cohorts. PD-L1 protein expression shows prognostic value in breast cancer patients, particularly the ER positive subset of patients. Further assessment of PD-1 axis marker expression may be valuable as the associated therapeutics are being tested in breast cancer patients.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-10-02.

Pin1 modulates ERα levels in breast cancer through inhibition of phosphorylation-dependent ubiquitination and degradation

Estrogen receptor-alpha (ERα) is an important biomarker used to classify and direct therapy decisions in breast cancer (BC). Both ERα protein and its transcript, ESR1, are used to predict response to tamoxifen therapy, yet certain tumors have discordant levels of ERα protein and ESR1, which is currently unexplained. Cellular ERα protein levels can be controlled post-translationally by the ubiquitin-proteasome pathway through a mechanism that depends on phosphorylation at residue S118. Phospho-S118 (pS118-ERα) is a substrate for the peptidyl prolyl isomerase, Pin1, which mediates cis-trans isomerization of the pS118-P119 bond to enhance ERα transcriptional function. Here, we demonstrate that Pin1 can increase ERα protein without affecting ESR1 transcript levels by inhibiting proteasome-dependent receptor degradation. Pin1 disrupts ERα ubiquitination by interfering with receptor interactions with the E3 ligase, E6AP, which also is shown to bind pS118-ERα. Quantitative in situ assessments of ERα protein, ESR1, and Pin1 in human tumors from a retrospective cohort show that Pin1 levels correlate with ERα protein but not to ESR1 levels. These data show that ERα protein is post-translationally regulated by Pin1 in a proportion of breast carcinomas. As Pin1 impacts both ERα protein levels and transactivation function, these data implicate Pin1 as a potential surrogate marker for predicting outcome of ERα-positive BC.