Abstract PD5-08: Tumor immune-cell activity assessed by RNAseq is an independent predictor of therapy response and prognosis after neoadjuvant chemotherapy in HER2 negative breast cancer patients - An analysis of the GeparSepto trial
Authors: Fasching Peter A , Denkert Carsten , Benz Stephen , Weber Karsten E , Szeto Christopher , Budczies Jan , Schneeweiss Andreas , Stickeler Elmar , Schmatloch Sabine , Jackisch Christian , Karn Thomas , Sinn Hans Peter , Warm Mathias , van Mackelenbergh Marion , Rabizadeh Sharooz , Schem Christian , Heinmöller Ernst , Müller Volkmar , Marmé Frederik , Soon-Shiong Patrick , Nekljudova Valentina , Untch Michael , Loibl Sibylle 
Published: March 2020

Abstract
Background: Tumor immune markers such as tumor infiltrating lymphocytes (TILs) or expression-based profiles have been correlated with both response to neoadjuvant chemotherapy and prognosis in early breast cancer (BC) patients. Some chemotherapies, such as paclitaxel, lead to the development of TILs and in some cases, suppression of regulatory T-cells. Therefore, assessment of the tumor microenvironment (TME) could provide important information for clinical decision-making. The aim of this study was to test if RNAseq-based TME classification of BC tumors is predictive of pathological complete Response (pCR) and prognosis in the neoadjuvant GeparSepto (G7) trial (NCT01583426). Methods: We performed a retrospective-prospective analysis of a subset of 810 subjects of the total of 1207 patients of the G7 trial. In G7 HER2-negative early high-risk BC patients were studied to determine if nab-paclitaxel is superior to solvent-based paclitaxel. In addition to the taxane paclitaxel, both treatment arms received epirubicin plus cyclophosphamide before surgery. For this analysis, a subset of 279 HER2 negative patients with sufficient quality of pretherapeutic core biopsies to perform whole-transcriptome RNAseq (~200x106 reads per tumor) was used. Based on RNAseq data, immune activity classification was provided by ImmunityBio (Culver City, CA) by comparison of expression of 23 immune-cell-specific gene signatures as described by Bindea et al. (Immunity, 2013) to those from a reference population of 1467 similarly-profiled unselected tumor samples from a large tumor database (NantOmics, Culver City, CA). Unsupervised hierarchical clustering of inferred immune activities revealed 3 distinct groups termed “hot”, “warm”, and “cold” clusters. Logistic regression analysis based on age, trial arm, tumor size, nodal status, Ki-67, hormone-receptor (HR) status and immune activity cluster (hot/warm vs. cold) as independent variables was performed to predict pCR (ypT0/ypN0). Cox regression analysis with the same covariates was also performed to predict disease-free survival (DFS) and overall survival (OS). Results: Of the 279 patients, 67 had a pCR (24%). The analyzed subset was similar to the main HER2 negative population (pCR-rate: 22%). Patients with a “hot/warm” or “cold” immune activity assessment had a pCR in 30% and 13% of the cases, respectively. The odds-ratio of the multivariate logistic regression analysis was 2.17 (95% CI: 1.00-4.71, p=0.0512). With regard to DFS and OS, T follicular helper cell B-cell, and T-cell signatures seemed to play a prominent role, and the hazard ratios (also “hot/warm” vs. “cold”) for the multivariate analyses were 0.38 (95% CI: 0.21-0.66; p=0.0007) and 0.34 (95%CI: 0.16-0.72, p= 0.0045), respectively. Within the 23 individual immune-cell-specific gene signatures, CD56dimNatural Killer (NK), type 1 helper T-cells, and CD8+ T-cell signatures seemed to be closely associated with achievement of a pCR. RNAseq-based deconvolution of immune-cell activity was corroborated by IHC-based TIL scoring. Immune-hot/warm patients had more intratumoral lymphocytes compared to cold tumors (mean: 11.6% vs. 4.9%, p&lt;0.0001). Specifically, adaptive immunity gene signatures (i.e. CD8+ T-cell signature, CD56dim NK, and Th1) were moderately correlated with the percentage of TILs (rho correlation coefficients from 0.42 to 0.53). Conclusion: TME profiling by RNAseq may be an independent biomarker useful for predicting response to and prognosis after neoadjuvant chemotherapy including taxanes and anthracyclines in early HER2 negative high-risk BC. These results indicate that the further development of this biomarker could be of direct clinical importance.
Citation Format: Peter A Fasching, Carsten Denkert, Stephen Benz, Karsten E Weber, Christopher Szeto, Jan Budczies, Andreas Schneeweiss, Elmar Stickeler, Sabine Schmatloch, Christian Jackisch, Thomas Karn, Hans Peter Sinn, Mathias Warm, Marion van Mackelenbergh, Sharooz Rabizadeh, Christian Schem, Ernst Heinmöller, Volkmar Müller, Frederik Marmé, Patrick Soon-Shiong, Valentina Nekljudova, Michael Untch, Sibylle Loibl. Tumor immune-cell activity assessed by RNAseq is an independent predictor of therapy response and prognosis after neoadjuvant chemotherapy in HER2 negative breast cancer patients - An analysis of the GeparSepto trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD5-08.