Abstract P1-08-34: Peripheral immunity predicts therapeutic outcomes in breast cancer patients
Authors: Axelrod Margaret L , Wang Yu , Xu Yaomin , Bejan Cosmin A. , Sun Xiaopeng , Gonzalez-Ericsson Paula I , Bergman Riley E , Donaldson Joshua , Nunnery Sara , Sanders Melinda , Massa Chiara , Seliger Barbara , Mayer Ingrid A , Balko Justin M 
Published: March 2022

Abstract
Purpose: Neoadjuvant chemotherapy (NAC), the standard of care for many breast cancer patients, is known to have systemic immunologic effects and is increasingly being used in clinical trials in combination with immunotherapeutics. Currently, there are few biomarkers to predict NAC or immunotherapy response. Biomarkers are needed to identify patients who will benefit from combination therapy compared to those who are likely to respond to NAC alone, and thus avoid the added risk of toxicity and financial burden. Peripheral blood is an attractive site of biomarker development due to the relative ease of longitudinal sampling. We have previously shown that high expression of a cytotoxicity gene signature in the blood following NAC is associated with presence of residual disease (RD) and future breast cancer recurrence, demonstrating the feasibility of using blood-based transcriptional biomarkers. Methods: We used RNA sequencing to profile the peripheral blood of 53 breast cancer patients prior to definitive surgery (n=23 RD; 9 pathologic complete response (pCR); 21 no NAC). DESeq was used to identify differentially expressed genes and gene set enrichment analysis to identify differentially expressed pathways using the Molecular Signatures Database hallmark gene sets. CIBERSORTx was used to deconvolute cell type abundance. To extend the cell type abundance data to a larger cohort, we used a de-identified electronic medical record to collect clinically measured cell type abundance data on breast cancer patients treated with NAC (n=110; 35 pCR; 75 RD). Results: We identified 1,238 (FDR corrected q-value &lt;0.1) differentially expressed genes between pCR and RD samples. Interferon (IFN)-γ Response (q-value &lt;0.0001; normalized enrichment score (NES)=3.32), IFNα Response (q-value &lt;0.0001; NES=3.14), and Complement (q-value&lt;0.001; NES=2.29) pathways were significantly enriched in the blood of patients experiencing pCR vs. RD. We combined expression of the unique leading-edge genes from each pathway into a 60-gene IFN/Complement score. Interestingly, expression of the IFN/Complement score was independent of expression of our previously published cytotoxicity score. Using single cell RNA sequencing on peripheral blood mononuclear cells, we localized expression of the IFN/Complement genes to monocytes whereas the cytotoxicity score was confined to CD8+ T cells and natural killer cells. A combination peripheral immunologic response score (PIRS; IFN/Complement score - Cytotoxic score) had improved predictive power compared to either signature alone. PIRS was highest in patients with pCR and lowest in patients with RD who experienced a breast cancer recurrence with 3 years. Using CIBERSORTx, we further identified relative monocyte abundance as higher in samples with pCR compared to those with RD. Clinically measured post-NAC, but not pre-NAC, monocytes were significantly higher in patients with pCR compared to those with RD. Using the synthetic derivative medical record, we further identified 110 breast cancer patients treated with NAC. In this cohort, relative monocytes were also statistically significantly higher in patients with pCR compared to those with RD (p=0.0367). Conclusions: Peripheral blood gene expression scores and cell type abundance may be useful biomarkers of NAC response and outcome in breast cancer. We identified an immunologic gene signature that was highest in patients with the best outcomes (pCR) and lowest in those with the worst outcome (RD with recurrence). We further identified monocyte abundance, which is routinely measured clinically, as highest in patients with pCR. Taken together, these results suggest that peripheral blood biomarkers following NAC may be useful in predicting long-term outcome. Future work will explore the utility of peripheral blood biomarkers in predicting immunotherapy response.
Citation Format: Margaret L Axelrod, Yu Wang, Yaomin Xu, Cosmin A. Bejan, Xiaopeng Sun, Paula I Gonzalez-Ericsson, Riley E Bergman, Joshua Donaldson, Sara Nunnery, Melinda Sanders, Chiara Massa, Barbara Seliger, Ingrid A Mayer, Justin M Balko. Peripheral immunity predicts therapeutic outcomes in breast cancer patients [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-34.