The long and winding road to biomarkers for immunotherapy: a retrospective analysis of samples from patients with triple-negative breast cancer treated with pembrolizumab

BACKGROUND

Immune checkpoint blockade (ICB) in combination with chemotherapy improves outcome of patients with triple-negative breast cancer (TNBC) in metastatic and early settings. The identification of predictive biomarkers able to guide treatment decisions is challenging and currently limited to programmed death-ligand 1 (PD-L1) expression and high tumor mutational burden (TMB) in the advanced setting, with several limitations.

MATERIALS AND METHODS

We carried out a retrospective analysis of clinical-pathological and molecular characteristics of tumor samples from 11 patients with advanced TNBC treated with single-agent pembrolizumab participating in two early-phase clinical trials: KEYNOTE-012 and KEYNOTE-086. Clinical, imaging, pathological [i.e. tumor-infiltrating lymphocytes (TILs), PD-L1 status], RNA sequencing, and whole-exome sequencing data were analyzed. We compared our results with publicly available transcriptomic data from TNBC cohorts from TCGA and METABRIC.

RESULTS

Response to pembrolizumab was heterogeneous: two patients experienced exceptional long-lasting responses, six rapid progressions, and three relatively slower disease progression. Neither PD-L1 nor stromal TILs were significantly associated with response to treatment. Increased TMB values were observed in tumor samples from exceptional responders compared to the rest of the cohort (P = 3.4 × 10-4). Tumors from exceptional responders were enriched in adaptive and innate immune cell signatures. Expression of regulatory T-cell markers (FOXP3, CCR4, CCR8, TIGIT) was mainly observed in tumors from responders except for glycoprotein-A repetitions predominant (GARP), which was overexpressed in tumors from rapid progressors. GARP RNA expression in primary breast tumors from the public dataset was significantly associated with a worse prognosis.

CONCLUSIONS

The wide spectrum of clinical responses to ICB supports that TNBC is a heterogeneous disease. Tumors with high TMB respond better to ICB. However, the optimal cut-off of 10 mutations (mut)/megabase (Mb) may not reflect the complexity of all tumor subtypes, despite its approval as a tumor-agnostic biomarker. Further studies are required to better elucidate the relevance of the tumor microenvironment and its components as potential predictive biomarkers in the context of ICB.

Homologous Recombination Repair Deficiency and the Immune Response in Breast Cancer: A Literature Review

The success of cancer immunotherapy with immune checkpoint blockade (ICB) has demonstrated the importance of targeting a preexisting immune response in a broad spectrum of tumors. This is particularly novel and relevant for less immunogenic tumors, such as breast cancer (BC), where the efficacy of ICB was more evident in the triple-negative (TNBC) subtype, in earlier stages, and in association with chemotherapy. Tumors harboring homologous recombination DNA repair (HRR) deficiency (HRD) are supposed to have a higher number of mutations, hence a higher tumor mutational burden, which could potentially make them more sensitive to immunotherapy. However, the mechanisms involved in ICB sensitivity and patient selection are still yet to be defined in BC: whether the innate system could play a role and how the adaptive immunity could be linked with HRR pathways are the two key points of debate that we will discuss in this article. The aim of this review was to close the loop between what was found in clinical trial results so far, go back to laboratory theory and preclinical results and point out what needs to be clarified from now on.

Clinical significance of CD73 in triple-negative breast cancer: multiplex analysis of a phase III clinical trial

Background

CD73 is an ecto-enzyme that promotes tumor immune escape through the production of immunosuppressive extracellular adenosine in the tumor microenvironment. Several CD73 inhibitors and adenosine receptor antagonists are being evaluated in phase I clinical trials.

Patients and methods

Full-face sections from formalin-fixed paraffin-embedded primary breast tumors from 122 samples of triple-negative breast cancer (TNBC) from the BIG 02-98 adjuvant phase III clinical trial were included in our analysis. Using multiplex immunofluorescence and image analysis, we assessed CD73 protein expression on tumor cells, tumor-infiltrating leukocytes and stromal cells. We investigated the associations between CD73 protein expression with disease-free survival (DFS), overall survival (OS) and the extent of tumor immune infiltration.

Results

Our results demonstrated that high levels of CD73 expression on epithelial tumor cells were significantly associated with reduced DFS, OS and negatively correlated with tumor immune infiltration (Spearman's R= -0.50, P < 0.0001). Patients with high levels of CD73 and low levels of tumor-infiltrating leukocytes had the worse clinical outcome.

Conclusions

Taken together, our study provides further support that CD73 expression is associated with a poor prognosis and reduced anti-tumor immunity in human TNBC and that targeting CD73 could be a promising strategy to reprogram the tumor microenvironment in this BC subtype.

Abstract P2-08-47: Evaluation of stromal tumor-infiltrating lymphocytes (sTIL) and tertiary lymphoid structures (TLS) in early breast cancer patients with triple negative breast cancer(TNBC) included in a prospective study of neoadjuvant chemotherapy (NAC) with Epirubicin and cyclophosphamide (EC) and carboplatin-paclitaxel (PC) (BSMO 2014-01)

Background: BSMO 2014-01 is a completed prospective phase 2 study evaluating the efficacy of neoadjuvant EC and PC. One of the secondary endpoints was the correlation of sTIL with response, pCR and survival. We also assessed the relationship between sTIL and TLS in the diagnostic biopsies.

Methods: Stromal TIL (sTIL) were evaluated on H&E stained tumor biopsies before the start of the NAC according to the criteria described by Salgado et al(1). Scores were defined as "low" or "high" if lymphocytic infiltration in the stroma around the tumor was ≤ 10% or &gt; 10%. TLS are ectopic lymph node-like structures recently identified in breast cancer. TLS were counted using a dual IHC stain for CD3 (T cells) and CD20 (B cells) and categorized as "little" if the TLS occupied &lt; 10% or "moderate to abundant" if they occupied ≥ 10% of the adjacent tissue. The correlation between sTIL and pathologic parameters was analyzed using the chi-square test; DFS and OS between the groups was estimated by using the log-rank test.

Results: So far we could quantify the number of sTIL in 38 out of 63 TNBC pts treated with neoadjuvant EC-PC. Twenty eight pts had a high sTIL score and 10 pts had a low sTIL score. The high-sTIL group (19/28) achieved a numerical higher pathologic complete remission (pCR) rate than the low-sTIL group (5/10) (p=0.3); both groups had a comparable disease free survival of 28.6 mths and 26.7 mths respectively (p=0.7). The overall survival was similar:29 mths and 27.8 mths respectively (p=0.8). Stromal TLS were identified in 10 out 23 samples available for this analysis and we could demonstrate a positive correlation between high levels of sTIL and high levels of moderate to abundant TLS(CD3) in the adjacent tissue in six out of the ten samples in which TLS were present (p=0.1).

Conclusion: These preliminary results could not confirm the results published by Denkert et al earlier this year(2). A trend for correlation of the presence of high sTIL with moderate to abundant levels of TLS was found. Analysis on the remaining samples of all patients included in the study and correlation with outcome is ongoing and these completed results will be presented.

(1)Assessing Tumor-infiltrating lymphocytes in solid tumors. Hendry S, Salgado R et al. Adv Anat Pathol 2017; 235-251.

(2)Tumour-infiltrating lymphocytes and prognosis in different subtypes of breast cancer. Denkert C et al. Lancet Oncol 2018; 40-50.

Citation Format: Fontaine C, Van den Eynden G, de Wind R, Boisson A, Renard V, Van den Bulck H, Vuylsteke P, Glorieux P, Dopchie C, Decoster L, De Grève J, Awada A, Wildiers H, Willard-Gallo K. Evaluation of stromal tumor-infiltrating lymphocytes (sTIL) and tertiary lymphoid structures (TLS) in early breast cancer patients with triple negative breast cancer(TNBC) included in a prospective study of neoadjuvant chemotherapy (NAC) with Epirubicin and cyclophosphamide (EC) and carboplatin-paclitaxel (PC) (BSMO 2014-01) [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 P2-08-47.

Abstract PD5-10: Immune characterization of matched primary and multiple metastatic samples issued from an institutional autopsy cohort

Introduction

While immune infiltrates have already been extensively characterized in primary tumors (P), data on breast cancer metastases (M) remains limited. To this end we quantified and qualified the immune cells in a unique cohort of multiple matched P and M samples selected from an institutional breast cancer autopsy cohort.

Patients and methods

Twenty-three patients were selected from an institutional autopsy program (Semmelweis University, Budapest, Hungary) based on matched P and M sample availability (124 samples). All samples were centrally characterized for estrogen (ER), progesterone (PR) and HER2 receptors. The primary molecular subtypes were as follows: 9 ER+/PR+/HER2-, 8 triple negative and 6 HER2+. Ten patients relapsed ≤1 year after diagnosis and were further referred to as “early relapsers”, as opposed to the remaining qualified as “late relapsers”. Immunohistochemistry (IHC) was carried out against CD3/CD20 and CD4/CD8 in 21 patients (119 samples). Tumor infiltrating lymphocytes (TILs) were assessed on hematoxylin and eosin (H&E) and CD3-stained slides. Gene expression data were generated using the NanoString nCounter assay (PanCancer Immune Profiling Panel) for 11 patients (35 samples) and analyzedusing the R package NanoStringQCPro. The scores from published immune gene signatures were calculated as a weighted sum of the expressions of their genes. All samples were analyzed for 22 immune cell subtypes relative abundance using CIBERSORT.

Results

TILs assessed on H&E and CD3-stained slides were weakly correlated (Rho= 0.38, p&lt;.001). TIL levels as well as the number of tertiary lymphoid structures (TLS) were significantly lower in Ms as compared to Ps (p&lt;.001). Among the different metastatic sites, the lung was more infiltrated when considering CD3+ and CD4+ cells (p=.01 and .02, respectively). We further observed significantly higher levels of TILs, CD3+, CD4+ and CD8+ cells in the Ms but not in the Ps from late relapsers as opposed to those from early relapsers. Gene expression analyses further confirmed these observations as several immune gene signatures displayed significantly higher scores in the Ms from late compared to early relapsers. An unsupervised analysis identified 13 genes significantly differentially expressed between Ps and Ms: CSF1R, CXCL14, CYBB, IL21R, IL2RB, TNF and TNFSF15 were upregulated in Ps while BCL2L1, C7, HSD11B1, and PSMB7 were upregulated in Ms. The matched P/M CIBERSORT analyses revealed a distinct composition of immune cell types between P and M of a same patient. Apart from a potential increase in M0 macrophages, no common trait was observed in immune cell composition between the Ms from the different patients.

Conclusion

This is to the best of our knowledge the first study characterizing the immune infiltration in patients with multiple matched P and M samples. The results suggest that Ms have not only a globally lower immune infiltration as compared to Ps, but also a different immune composition. Additionally, Ms from late relapsers are more infiltrated as compared to early relapsers. The present data also uncovers not only important inter-patient but also intra-patient immune heterogeneity, which should be taken into consideration for optimal treatment decision.

Citation Format: Szekely B, Bareche Y, Van den Eynden G, Salgado R, Buisseret L, Garaud S, Willard-Gallo K, Hatzis C, Szasz M, Kulka J, Larsimont D, Sotiriou C, Pusztai L, Desmedt C. Immune characterization of matched primary and multiple metastatic samples issued from an institutional autopsy cohort [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 PD5-10.

Abstract PD5-06: The immunomodulatory potential of denosumab in breast cancer: results from D-BEYOND, a window of opportunity trial evaluating a RANK-ligand (RANKL) inhibitor and its biological effects in young pre-menopausal women diagnosed with early breast cancer

Background

Breast cancer (BC) in young women has unique biology and poor prognosis. Previous reports suggest that they often express RANKL, which was also shown to play a role in mammary tumorigenesis and various immune processes. Here, we present the primary results of D-BEYOND, a window study investigating the biological activity of the RANKL inhibitor; denosumab in pre-menopausal BC patients.

Methods

D-BEYOND is a prospective, phase Iia, single-arm, multicenter study assessing the effect of denosumab on BC biology in premenopausal women with early BC (NCT01864798). Patients received two subcutaneous injections of denosumab (120mg), one week apart, followed by breast surgery. The primary endpoint was geometric mean change in tumor Ki67 assessed by immunohistochemistry (IHC). Blood, tumor and normal adjacent breast tissue were collected pre- and post-treatment. Serum levels of RANKL, OPG and CTX were assessed by ELISA. RNA was extracted from fresh-frozen tissue and RNAseq was performed. DESeq2 was used for differential expression analysis, GAGE was used for pathway analysis and CIBERSORT was used to infer immune cell subsets between pre- and post-treatment. Ki67, CD4/Foxp3 and CD4/CD8 IHC were performed on FFPE tissue to further assess the immune microenvironment. The percentage of TILs was independently evaluated by two pathologists on H&E slides. Pre- and post-treatment values were compared using a paired t-test.

Results

A total of 27 patients were enrolled in the study between October 2013 and July 2016. The median age was 45 years (range 35-51 years). Tumors of 21 patients were hormone receptor positive (77.8%), 4 were HER2 positive (14.8%) and 2 were triple negative (7.4%). No serious adverse events were reported, the most frequent non-serious adverse event being arthralgia (14.8%). After treatment, serum levels of CTX and RANKL decreased in all patients (P &lt; 0.001) whereas OPG increased in 76.9% of patients (P = 0.009, 95% CI 0.56-0.91). There was no significant reduction of Ki67 values from baseline (geometric mean [GM] change after treatment; 0.98, 95% CI 0.76-1.26; P = 0.90). Twenty-four pre- and post-treatment tumor pairs were available for RNAseq, IHC and TILs evaluation. There was a significant increase in the percentage of stromal TILs after treatment (GM change of 1.75, 95% CI 1.28–2.39; P = 0.001). 1084 differentially expressed genes were identified and pathway analysis revealed enrichment of several immune processes. CIBERSORT revealed an enrichment of CD8+ T cells (GM change 1.72, 95% CI 1.19–2.48; P = 0.006) and a decrease of Treg cells (0.71, 95% CI 0.52–0.98, P = 0.040). These results were confirmed by IHC of CD8+ and CD4+/Foxp3+ cells (GM change 1.59, 95% CI 1.14–2.21; P = 0.008 and 0.63, 95% CI 0.49–0.83, P = 0.001, respectively).

Conclusion

Short course of denosumab did not reduce tumor proliferation rate. However, it induced a significant increase in TILs and CD8 cytotoxic T cells, while Treg infiltration decreased. These findings suggest an immunomodulatory role for denosumab in young breast cancer and that its use in combination could boost immunotherapy efficacy.

Citation Format: Nguyen B, Marion M, Salgado R, Venet D, Vuylsteke P, Polastro L, Wieldiers H, Simon P, Lindeman G, Larsimont D, Van den Eynden G, Velghe C, Rothe F, Garaud S, Michiels S, Willard-Gallo K, Azim Jr HA, Loi S, Piccart M, Sotiriou C. The immunomodulatory potential of denosumab in breast cancer: results from D-BEYOND, a window of opportunity trial evaluating a RANK-ligand (RANKL) inhibitor and its biological effects in young pre-menopausal women diagnosed with early breast cancer [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 PD5-06.

Abstract PD5-09: Immune parameters associated with survival in triple negative and HER2-positive breast cancer patients with 10 years of follow-up

The clinical utility of tumor-infiltrating lymphocytes (TIL) is actively being investigated in breast cancer (BC). It is unclear whether TIL spatial location and organization in tertiary lymphoid structures (TLS) have an impact on prognosis. Additionally, the significance of PD-1 and PD-L1 expression is being debated due to conflicting data from several studies. We hypothesize that the presence, extent and spatial location of multiple immune biomarkers, reflecting ongoing immune responses, will be consistently associated with a good prognosis in highly infiltrated BC [triple-negative (TNBC) and HER2+].

The relationship between these immune biomarkers and clinical outcome was examined in the TNBC and HER2+ cohorts of node-positive BC patients enrolled in the BIG 02-98 adjuvant phase III trial with available material for immunohistochemical (IHC) labeling (N=113 and N=136, respectively). HER2+ patients did not receive trastuzumab. Dual IHC staining was performed on full-face consecutive tissue sections. Scoring was independently performed by two pathologists, blinded to the clinical data, and included: global, intratumoral and stromal TIL and TLS, assessed on CD3/CD20 slides; the percentage and location of PD-1 and PD-L1 expression, assessed on PD-1/PD-L1 slides. TIL were considered as a categorical variable with different cut-offs used for each parameter and for each cohort (TNBC and HER2+). Invasive disease-free survival (I-DFS) and overall survival (OS) were analyzed (median follow-up: 10 years). Cox proportional hazard models were used for survival analyses.

The TNBC cohort revealed an association between global TIL and outcome [adjusted hazard ratio (HR) for I-DFS: 0.27 (0.15-0.51); OS: 0.26 (0.13-0.53)]. Similar results were observed for stromal and intratumoral TIL. PD-L1 expression within TLS was an independent predictor of OS, after adjustment for tumor size and age [HR: 0.30 (0.09-0.99)]. Multivariate analysis reveals this effect was principally driven by high stromal TIL (&gt;17.5% based on CD3/CD20 assessment) (χ2 OS: p=0.009). In contrast, no significant prognostic associations were found in the overall HER2+ cohort. However high T cell TIL were associated with improved I-DFS and OS in the ER-/HER2+ group [I-DFS: 0.34 (0.14-0.80); OS: 0.32 (0.12-0.86)] and stromal TIL were associated with improved I-DFS in the ER+/HER2+ group [HR: 0.29 (0.09-0.94)] (univariate analyses). No significant associations between the number of TLS nor the expression of PD-1 with outcomes were observed in either cohorts.

The presence of PD-L1+ TLS, driven by high baseline TIL, was associated with an excellent prognosis in node-positive TNBC. This observation might reflect specific immune activities taking place in these mini lymph node-like structures adjacent to the tumor bed where specific antitumor memory immune responses could be generated. No different prognostic impact was observed when analyzing TIL spatial location. Although the statistical power of the study might be limited, in line with previous findings our data reveal that, among the immune parameters evaluated, TIL are the strongest predictor of outcome in TNBC, while PD-L1+ TLS could be a new and important parameter that requires further investigation.

Citation Format: Solinas C, de Wind A, Van den Eynden G, Ameye L, Garaud S, De Silva P, Boisson A, Noel G, Langouo Fontsa M, Buisseret L, de Azambuja E, Francis PA, Di Leo A, Crown JP, Sotiriou C, Larsimont D, Paesmans M, Piccart-Gebhart M, Willard-Gallo K. Immune parameters associated with survival in triple negative and HER2-positive breast cancer patients with 10 years of follow-up [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 PD5-09.

Abstract PD6-07: Clinical significance of CD73 expression in triple-negative breast cancer from the BIG 02-98 adjuvant phase III clinical trial

Background: CD73 is an ecto-enzyme that promotes tumor immune escape through the production of immunosuppressive extracellular adenosine in the tumor microenvironment. Several CD73 inhibitors and adenosine receptor antagonists are being evaluated in phase I clinical trials.

Objective: To investigate the prognosis significance of CD73 in human triple-negative breast cancer.

Design and setting: This is a prospective-retrospective biomarker analysis. Using multiplex immunofluorescence and image analysis, we assessed CD73 protein expression on tumor cells, tumor-infiltrating leukocytes and stromal cells on full-face sections from formalin-fixed paraffin-embedded primary breast tumors.

Participants: 122 samples of triple-negative breast cancer from the BIG 02-98 adjuvant phase III clinical trial were included in our analysis. This trial compared the addition of taxanes to anthracyclines-based chemotherapy in node-positive breast cancer.

Results: Our results demonstrated that high levels of CD73 expression on epithelial tumor cells were significantly associated with reduced disease-free survival (DFS) and overall survival (OS) in patients with triple-negative breast cancer. Using the median as a threshold between low and high levels of CD73 on epithelial cells, hazard ratios (HR) adjusted for grade, number of positive lymph nodes and tumor size, were of 2.21 (95% confidence interval (CI): 1.15-4.25); p=0.02 for DFS and of 2.47 (95%CI: 1.21-5.07); p=0.01 for OS. CD73 expression negatively correlated with tumor immune infiltration (Spearman's R= -0.50, p&lt;0.0001). Patients with high levels of CD73 and low levels of tumor-infiltrating leukocytes had the worse clinical outcome (HR: 4.24 (1.90-9.45), p&lt;0.001 for DFS, HR: 3.91 (1.65-9.31), p=0.002 for OS) compared to patients with low CD73 and high tumor-immune infiltration. Flow cytometric analysis of tumor-infiltrating leukocytes revealed a high frequency of CD73-expressing B cells and higher CD73 expression on tumor-infiltrating myeloid cells and natural killer cells compared to peripheral blood.

Conclusion and relevance: Taken together, our study provides further support that CD73 expression is associated with a poor prognosis and reduced anti-tumor immunity in human triple-negative breast cancer and that targeting CD73 could be a promising strategy to reprogram the tumor microenvironment in this breast cancer subtype.

Citation Format: Buisseret L, Pommey S, Allard B, Garaud S, Bergeron MA, Cousineau I, Ameye L, Paesmans M, Crown JPA, Di Leo A, Piccart-Gebhart M, Willard-Gallo K, Sotiriou C, Stagg J. Clinical significance of CD73 expression in triple-negative breast cancer from the BIG 02-98 adjuvant phase III clinical trial [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 PD6-07.

Abstract P2-04-04: BRCA gene mutations do not shape the extent and organization of tumor infiltrating lymphocytes in triple negative breast cancer

The remarkable responses observed in metastatic cancer patients treated with immunotherapies, including inhibitors directed to the PD-1 and PD-L1 checkpoint molecules, makes it a priority to identify critical variations in pro- and anti-tumor immune responses in breast cancer (BC). In patients with triple negative (TN) BC, an increased presence of tumor infiltrating lymphocytes (TIL) and tertiary lymphoid structures (TLS) have been associated with good clinical outcomes. However, the frequency of specific lymphocyte subpopulations, PD-1 and/or PD-L1 expression and their prognostic significance remains an open question. Our recent work found that PD-1 and PD-L1 expression are specifically associated with higher TIL densities and an increased number of TLS in BC. We further demonstrated that TIL density, TLS and PD-L1 expression were correlated with more aggressive breast tumor characteristics, including higher proliferation and hormone receptor negativity. In this project, we examined the prevalence of TIL, TLS, PD-1 and PD-L1 expression in TNBC and further compared these immune parameters between TNBC patients harboring BRCA1 or BRCA2 germline gene mutations with those carrying the wild-type (wt) genes.

A total of 1402 BC patients whose blood was genetically tested for germline BRCA1 and BRCA2 mutations were examined for inclusion in this study. Ninety-eight chemotherapy-naïve patients with primary invasive ER–, PR– and HER2– BC and demonstrated germline BRCA1 or BRCA2 wt or mutated-gene status were included in this study. Ninety-four tumors were determined to be suitable for evaluating immune cell infiltration (51 BRCA wt and 43 BRCA-mutated). FFPE tumor tissue from the surgical specimens was analyzed by immunohistochemistry (IHC) staining of full-face tissue sections. IHC was performed as a dual label using CD3 plus CD20 for T and B cells, CD4 plus CD8 for the major T cell subpopulations and PD-1 plus PD-L1 for individual or paired expression of these receptors. The stained slides were independently scored by two experienced pathologists for TIL, TIL subpopulations, TLS and checkpoint molecule expression.

These analyses revealed that 87% of our TNBC cohort was TIL-positive (≥10% TIL) with 35% classified as lymphocyte predominant BC (LPBC; ≥50% TIL). T cells were the principal component of the lymphocytic infiltrate with no significant differences between the BRCA wt and BRCA-mutated groups detected in total T cells (CD3+), helper T cells (CD4+), cytotoxic T cells (CD8+) or B cells (CD20+). TLS were identified in 73% of tumors with again no significant differences between the BRCA groups. Examination of checkpoint molecule expression identified 33% tumors as PD-1 positive and 40% as PD-L1 positive. PD-1 expression was correlated with PD-L1 expression and both with TIL positivity and the level of immune infiltration but not BRCA mutational status.

Overall, our analyses revealed that BRCA wt and BRCA-mutated TNBC are remarkably similar in terms of TIL heterogeneity, a TLS presence and checkpoint molecule expression. These data suggest that BRCA gene mutations are not immunogenic nor do they directly drive immune infiltration in TNBC.

Citation Format: Willard-Gallo K, Solinas C, Marcoux D, t'Kint de Roodenbeke D, Garaud S, Van den Eynden G, de Wind A, Boisson A, Larsimont D, Piccart M. BRCA gene mutations do not shape the extent and organization of tumor infiltrating lymphocytes in triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-04-04.

Characterization of human breast cancer tissues by infrared imaging

Fourier Transform InfraRed (FTIR) spectroscopy coupled to microscopy (IR imaging) has shown unique advantages in detecting morphological and molecular pathologic alterations in biological tissues. The aim of this study was to evaluate the potential of IR imaging as a diagnostic tool to identify characteristics of breast epithelial cells and the stroma. In this study a total of 19 breast tissue samples were obtained from 13 patients. For 6 of the patients, we also obtained Non-Adjacent Non-Tumor tissue samples. Infrared images were recorded on the main cell/tissue types identified in all breast tissue samples. Unsupervised Principal Component Analyses and supervised Partial Least Square Discriminant Analyses (PLS-DA) were used to discriminate spectra. Leave-one-out cross-validation was used to evaluate the performance of PLS-DA models. Our results show that IR imaging coupled with PLS-DA can efficiently identify the main cell types present in FFPE breast tissue sections, i.e. epithelial cells, lymphocytes, connective tissue, vascular tissue and erythrocytes. A second PLS-DA model could distinguish normal and tumor breast epithelial cells in the breast tissue sections. A patient-specific model reached particularly high sensitivity, specificity and MCC rates. Finally, we showed that the stroma located close or at distance from the tumor exhibits distinct spectral characteristics. In conclusion FTIR imaging combined with computational algorithms could be an accurate, rapid and objective tool to identify/quantify breast epithelial cells and differentiate tumor from normal breast tissue as well as normal from tumor-associated stroma, paving the way to the establishment of a potential complementary tool to ensure safe tumor margins.

Abstract S1-02: Lymphocytic infiltration in invasive lobular breast cancer

Background: The presence and prognostic value of tumor infiltrating lymphocytes (TILs) in invasive breast carcinoma has been demonstrated in several studies, especially in the triple-negative and HER2-positive subtypes. So far, TILs have not been investigated with sufficient detail in invasive lobular breast cancer (ILBC). Here we therefore aimed at: first, assessing the distribution of stromal TILs in ILBC; second, correlating the presence of TILs with standard clinical and pathological markers; third, exploring associations of TILs with recurrent genomic alterations; and, fourth, comparing the lymphocytic composition of ER-positive/HER2-negative lobular to ER-positive/HER2-negative ductal tumors.

Material and methods: The percentage of stromal TILs was independently assessed according to Salgado et al. (Ann Oncol 2015) by three pathologists on full-face hematoxylin and eosin slides in a well-annotated retrospective series of 614 primary ILBCs previously characterized at the genomic level. The median value of TILs was used for the analyses. For the association analyses, we focused on the more homogeneous group of ER-positive/HER2-negative ILBC (555/614). Breast cancer-free interval was used as survival endpoint and the analyses were censored at 12 years of follow-up. The comparison of the lymphocytic composition (relative percentage of CD45+ TILs which are CD4+, CD8+ or CD19+) was assessed by FACS in a separate prospective cohort of 51 ER-positive/HER2-negative lobular and 112 ER-positive/HER2-negative ductal tumors.

Results: The intraclass correlation coefficient between the three pathologists was 0.71 (95%CI:0.65-0.76). The median percentage of stromal TILs was 5% and the interquartile range 5-10%, with only 9% of the samples having ≥ 20%. Greater numbers of TILs were significantly associated with younger age at diagnosis, axillary lymph node involvement, high proliferative tumors as assessed by Ki67, and with the mixed non-classic ILBC subtypes. Greater numbers of TILs were associated with worse prognosis (HR=1.22; 95%CI:1.07-1.38, p=0.003) only in the unadjusted analysis, as it lost significance after adjustment for standard clinical and pathological variables. Greater numbers of TILs were observed in tumors harboring ARID1A, BRCA2, KMT2C and TP53 mutations, as well as chr3p21.31 and chr8q24.23 (PTK2) loss; whereas lower numbers were observed in tumors with ERBB3 mutations as well as chr7p and chr11q14.1 (PAK1) gains. There were no significant differences in the relative proportion of CD4+, CD8+ or CD19+ lymphocytes between ER-positive/HER2-negative lobular and ductal tumors.

Conclusion: In this work, which reports to our knowledge on the largest series of ILBC ever assessed for TILs, we showed that most ILBCs were characterized by low lymphocytic infiltration. Besides the association of TILs with clinical and pathological features of ILBC patients, we found that higher TIL levels were observed in the presence of specific mutations and copy number alterations. Higher numbers of TILs were associated with worse prognosis at the univariate analysis. Finally, based on the assessed markers, we have no evidence of differential lymphocytic composition between ER-positive/HER2-negative lobular and ductal tumors.

Citation Format: Desmedt C, Salgado R, Buisseret L, Zoppoli G, Fornili M, Van den Eynden G, Garaud S, Gundem G, Rothé F, Brown D, Kheddoumi N, Rouas G, Galant C, Bertucci F, Piccart M, Campbell P, Viale G, Larsimont D, Willard-Gallo K, Biganzoli E, Pruneri G, Sotiriou C. Lymphocytic infiltration in invasive lobular breast cancer. [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 S1-02.

Label-free phenotyping of peripheral blood lymphocytes by infrared imaging

It is now widely accepted that the immune microenvironment of tumors and more precisely Tumor Infiltrating Lymphocytes (TIL) play an important role in cancer development and outcome. TILs are considered to be important prognostic and predictive factors based on a growing body of clinical evidence; however, their presence at the tumor site is not currently assessed routinely. FTIR (Fourier transform infrared) imaging has proven it has value in studying a range of tumors, particularly for characterizing tumor cells. Currently, very little is known about the potential for FTIR imaging to characterize TIL. The present proof of concept study investigates the ability of FTIR imaging to identify the principal lymphocyte subpopulations present in human peripheral blood (PB). A negative cell isolation method was employed to select pure, label-free, helper T cells (CD4(+)), cytotoxic T cells (CD8(+)) and B cells (CD19(+)) from six healthy donors PB by Fluorescence Activated Cell Sorting (FACS). Cells were centrifuged onto Barium Fluoride windows and ten infrared images were recorded for each lymphocyte subpopulation from all six donors. After spectral pre-treatment, statistical analyses were performed. Unsupervised Principal Component Analyses (PCA) revealed that in the absence of donor variability, CD4(+) T cells, CD8(+) T cells and B cells each display distinct IR spectral features. Supervised Partial Least Square Discriminant Analyses (PLS-DA) demonstrated that the differences between the three lymphocyte subpopulations are reflected in their IR spectra, permitting their individual identification even when significant donor variability is present. Our results also show that a distinct spectral signature is associated with antibody binding. To our knowledge this is the first study reporting that FTIR imaging can effectively identify T and B lymphocytes and differentiate helper T cells from cytotoxic T cells. This proof of concept study demonstrates that FTIR imaging is a reliable tool for the identification of lymphocyte subpopulations and has the potential for use in characterizing TIL.

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

BACKGROUND

The morphological evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is gaining momentum as evidence strengthens for the clinical relevance of this immunological biomarker. Accumulating evidence suggests that the extent of lymphocytic infiltration in tumor tissue can be assessed as a major parameter by evaluation of hematoxylin and eosin (H&E)-stained tumor sections. TILs have been shown to provide prognostic and potentially predictive value, particularly in triple-negative and human epidermal growth factor receptor 2-overexpressing BC.

DESIGN

A standardized methodology for evaluating TILs is now needed as a prerequisite for integrating this parameter in standard histopathological practice, in a research setting as well as in clinical trials. This article reviews current data on the clinical validity and utility of TILs in BC in an effort to foster better knowledge and insight in this rapidly evolving field, and to develop a standardized methodology for visual assessment on H&E sections, acknowledging the future potential of molecular/multiplexed approaches.

CONCLUSIONS

The methodology provided is sufficiently detailed to offer a uniformly applied, pragmatic starting point and improve consistency and reproducibility in the measurement of TILs for future studies.

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

BACKGROUND

The morphological evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is gaining momentum as evidence strengthens for the clinical relevance of this immunological biomarker. Accumulating evidence suggests that the extent of lymphocytic infiltration in tumor tissue can be assessed as a major parameter by evaluation of hematoxylin and eosin (H&E)-stained tumor sections. TILs have been shown to provide prognostic and potentially predictive value, particularly in triple-negative and human epidermal growth factor receptor 2-overexpressing BC.

DESIGN

A standardized methodology for evaluating TILs is now needed as a prerequisite for integrating this parameter in standard histopathological practice, in a research setting as well as in clinical trials. This article reviews current data on the clinical validity and utility of TILs in BC in an effort to foster better knowledge and insight in this rapidly evolving field, and to develop a standardized methodology for visual assessment on H&E sections, acknowledging the future potential of molecular/multiplexed approaches.

CONCLUSIONS

The methodology provided is sufficiently detailed to offer a uniformly applied, pragmatic starting point and improve consistency and reproducibility in the measurement of TILs for future studies.

Abstract P5-01-02: Characterization of follicular helper CD4 T cells and B cells resident in peritumoral tertiary lymphocyte structures as specific markers for an immunological grade in breast cancer

Molecular approaches such as gene expression profiling have improved the classification of human breast cancer (BC) by identifying molecular subtypes and demonstrating that the immune infiltrate is an important prognostic or predictive factor. Our prospective study of freshly isolated CD4+ T cells infiltrating (TIL) BC discovered that along with Th1, Th2 and Th17 effector memory and Treg subpopulations the newest CD4+ Th subset, T follicular helper (Tfh) cells, was also present in the tumor. Comparison of extensive versus minimally-infiltrated tumors led to our finding that extensive immune infiltrates are distinguished by Tfh cells located in tertiary lymphoid structures (TLS) next to the tumor bed. TLS are highly organized with a CD3+ T cell zone adjacent to a CD20+ B cell follicle with germinal centers containing Bcl6+ Tfh cells, CD23+ follicular dendritic cells and Ki67+ cells. Tfh cells are known to play a critical role in generating antibody producing plasma cells and memory B cells. We demonstrated that Tfh cells are the principal cellular source of the B cell chemoattractant CXCL13 in BC. Thus, a Tfh presence paralleled the TLS incidence and together they were associated with an increased peritumoral B cell presence and a higher frequency of CD8+ T cells in the tumor bed. Our recent work shows that approximately 50% of the infiltrating B cells are memory cells in contrast to normal and non-tumor non-adjacent breast tissue (controls, less than 15%). A significant B cell presence is found in extensively infiltrated high proliferative BC subtypes with germinal center centroblasts and centrocytes consistently associated with a Tfh cell presence. We assessed immunoglobulin isotypes in supernatants of fresh breast tissue homogenates, detecting decreased IgA and increased IgG and IgM in the tumor tissue compared to controls. Patient sera, particularly from patients with high proliferative BC subtypes, had elevated IgG3 and IgG4 compared to low proliferative tumors and healthy donors. Immunofluorescent analysis found the majority of B cells infiltrating tumors have germinal center characteristics (IgD+Ki67+CD35+CD21+PD-1+) and are clustered with Tfh in the B cell follicles surrounded by a T cell zone, which together create the tumor-associated TLS. Based on their specificity for TLS, we derived a scoring system, referred to as immunological grade, to measure the extent of the lymphocytic infiltrate and the level of immune organization. This system is based on a morphological score (the density of the lymphocyte infiltrate determined by CD3/CD20 immunohistochemistry plus the number and size of peritumoral TLS assessed by two pathologists) together with a molecular score [an 8 gene qRT-PCR Tfh signature that predicts long term survival in an untreated patient cohort with &gt;10-year survival (n = 794) or pathological complete response in patients treated with preoperative chemotherapy (n = 996)]. We are testing this immunological grading system on a large retrospective series of patients to determine its value in evaluating a patient's anti-tumor immune response in pre-operative biopsies and/or the primary tumor at surgery as a new marker for use in treatment decisions.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-01-02.

The role of NPM, p14arf and MDM2 in precursors of bronchial squamous cell carcinoma

Murine double minute clone 2 (MDM2), p14 alternate reading frame (p14arf), and nucleophosmin (NPM) regulate p53 activity. A total of 200 biopsies, including normal bronchial, pre-invasive and invasive tissues, were examined for changes in NPM, p14arf, MDM2 and p53 expression patterns by immunohistochemistry and immunofluorescence with confocal microscopy. NPM and p14arf displayed a diffuse nuclear staining in most normal bronchial tissue. The fraction of biopsies displaying an increased MDM2 staining or a nucleolar relocalisation of NPM increased at mild and moderate dysplasia, respectively. Two different modifications occurred in p14arf expression, i.e. its loss or its nucleolar relocalisation, both increasing at severe dysplasia and both being associated with high MDM2 expression. In addition, the nucleolar relocalisation of p14arf was associated with that of NPM. Immunofluorescence staining indicated that NPM and p14arf either co-localised in the nucleoplasm or in the nucleoli, before and as a result of severe dysplasia, respectively. MDM2 was not detected in the nucleoli. Thus, changes occur in murine double minute clone 2, p14 alternate reading frame and nucleophosmin level of expression and/or cellular distribution during early steps of lung carcinogenesis. Their relative localisation as determined by immunofluorescence, supports the hypothesis that p14 alternate reading frame nucleolar relocalisation impairs p14 alternate reading frame-murine double minute clone 2 complex formation and that nucleophosmin might sequester p14 alternate reading frame. The demonstration of this hypothesis requires further functional studies.

Clonal Th2 lymphocytes in patients with the idiopathic hypereosinophilic syndrome

Idiopathic hypereosinophilic syndrome (HES) and Gleich's syndrome are related disorders characterized by persistent or recurrent hypereosinophilia of unknown origin. Elevated IgE levels and polyclonal hypergammaglobulinaemia are considered as markers of benign outcome in this setting as they are generally associated with predominant cutaneous manifestations and favourable response to glucocorticoid therapy. In a previous study, we identified a clonal population of CD3-CD4+ Th2-like lymphocytes secreting interleukin (IL)-5 and IL-4 in peripheral blood of a patient fulfilling the diagnostic criteria of HES with associated serum hyper-IgE. We now extend this observation by describing identical findings in three additional patients, and we compare their clinical and biological parameters with five other patients with HES. Chromosomal abnormalities were detected in purified CD3-CD4+ Th2 cells from three patients, among whom one developed anaplastic null cell lymphoma. We therefore suggest that a careful search for T-lymphocyte clonality and cytogenetic changes should be included in the work-up of HES for adequate management.

LMP2+ proteasomes are required for the presentation of specific antigens to cytotoxic T lymphocytes

BACKGROUND

Major histocompatibility complex (MHC) class I molecules present short peptides generated by intracellular protein degradation to cytotoxic T lymphocytes (CTL). The multisubunit, non-lysosomal proteinases known as proteasomes have been implicated in the generation of these peptides. Two interferon-gamma (IFN-gamma)-inducible proteasome subunits, LMP2 and LMP7, are encoded within the MHC gene cluster in a region associated with antigen presentation. The incorporation of these LMP subunits into proteasomes may alter their activity so as to favour the generation of peptides able to bind to MHC class I molecules. It has been difficult, however, to demonstrate a specific requirement for LMP2 or LMP7 in the presentation of peptide epitopes to CTL.

RESULTS

We describe a T-cell lymphoma, termed SP3, that displays a novel selective defect in MHC class I-restricted presentation of influenza virus antigens. Of the MHC-encoded genes implicated in the class I pathway, only LMP2 is underexpressed in SP3 cells. Expression of IFN-gamma in transfected SP3 cells simultaneously restores LMP2 expression and antigen presentation to CTL. Expression of antisense-LMP2 mRNA in these IFN-gamma-transfected cells selectively represses antigen recognition and the induction of surface class I MHC expression. Moreover, the expression of this antisense-LMP2 mRNA in L929 fibroblast cells, which constitutively express LMP2 and have no presentation defect, blocks the presentation of the same influenza virus antigens that SP3 cells are defective in presenting.

CONCLUSIONS

Our results show that the LMP2 proteasome subunit can directly influence both MHC class I-restricted antigen presentation and class I surface expression.