Abstract PO2-15-08: Exploring Essential Immune Genes Linked to Pathological Complete Response and Survival in Early-Stage Triple-Negative Breast Cancer (TNBC) after Chemotherapy Treatment
Authors: Fara Brasó-Maristany, Laia Paré, Benedetta Conte, Laura Angelats, Ana Vivancos, Joel S Parker, Charles M. Perou, Patricia Villagrasa, Aleix Prat
Journal: Cancer Research (2024)

Abstract Background: De-escalation and escalation of systemic therapy in early-stage TNBC will require the implementation of biomarkers to guide therapy. To date, high expression of a variety of immune genes has been associated with higher pathological complete response (pCR) rates following neoadjuvant chemotherapy or with improved survival, or both, in early-stage TNBC. However, it is currently unknown which are the key genes influencing survival (i.e., the Core Immune Genes [CIG]) and if combinations of these genes can improve their association with both clinical endpoints. Methods: The expression of up to 185 genes was evaluated on pre-treatment tumor biopsies from 3 independent publicly available datasets of early-stage TNBC: CALGB40603 (n=388) (NCT00861705), BrighTNess (n=482) (NCT02032277), and SCAN-B (n=498). Patients in CALGB40603 and BrighTNess were treated with neoadjuvant chemotherapy-based therapy and had response data. Patients in CALGB40603 and SCAN-B had survival outcome data (event-free survival [EFS] or relapse-free interval [RFi]). Each individual gene was associated with each clinical endpoint within each dataset using Cox model and logistic regression analyses, adjusting for treatment arm. Genes found in common across datasets were selected as CIG, except for PDCD1, which was not available in BrighTNess. Using the CIGs, we evaluated whether combinations of 2 genes enhance their association with each clinical endpoint using different methods: adding, subtracting, multiplying, and ratio. Likelihood ratio testing was used to evaluate the added contribution of each gene in 2 combined cohorts evaluating pCR (i.e., CALGB40603 and BrighTNess) and survival (i.e., CALGB40603 and SCAN-B). Results: 10 CIGs related to B-cells and T-cells (i.e., IRF4, LAX1, POU2AF1, CD274, CD79A, TNFRSF17, PIM2, PDCD1, CXCR6, and SLAMF1) were associated with higher pCR rates and improved survival outcome across datasets. Of note, 5 (50%) genes are known components of the 14-gene immunoglobulin/B-cell (IGG) signature. The correlation coefficient among the 10 CIG genes was 0.63 (moderate). In general, the sum of 2 CIGs provided more prognostic information than a single gene (p&amp;lt; 0.001). Specifically, the sum of 2 CIGs provides more prognostic information than a single gene in 30 of 45 (66.6%) cases. Two-gene subtraction, multiplication or ratio decreased the amount of prognostic information (p&amp;lt; 0.001). The top 10 2-gene CIGs associated with prognosis (p&amp;lt; 0.001) were CD274_TNFRSF17, IRF4_CD274, PDCD1_TNFRSF17, CD79A_CD274, CD274_POU2AF1, CXCR6_TNFRSF17, LAX1_TNFRSF17, SLAMF1_TNFRSF17, CD274_LAX1 and CD79A_CXCR6. In general, the sum of 2 CIGs provided more information about pCR than a single gene (p&amp;lt; 0.001). Specifically, the sum of 2 CIGs provided numerically more information about pCR than 1 gene in 17 of 36 (47.2%) cases. Two-gene subtraction, multiplication or ratio decreased the amount of information about pCR (p&amp;lt; 0.001). The top 10 2-gene CIGs associated with pCR were CD274_PIM2, CD274_POU2AF1, CXCR6_PIM2, CD274_CXCR6, IRF4_CD274, CXCR6_POU2AF1, CD274_LAX1, IRF4_CXCR6, CXCR6_LAX1, and POU2AF1_SLAMF1. Conclusion: The expression of CIGs associated with B-cell and T-cell adaptive immune response is closely linked to pCR and survival outcomes following (neo)adjuvant chemotherapy. When combining the expression of 2 specific CIGs through addition, we found that this method provides more informative insights into pCR and survival outcomes compared to other combination methods. This approach enhances the predictive power of CIGs, enabling a better understanding of treatment response and patient prognosis, ultimately contributing to improved clinical decision-making and patient outcomes. Citation Format: Fara Brasó-Maristany, Laia Paré, Benedetta Conte, Laura Angelats, Ana Vivancos, Joel S Parker, Charles M. Perou, Patricia Villagrasa, Aleix Prat. Exploring Essential Immune Genes Linked to Pathological Complete Response and Survival in Early-Stage Triple-Negative Breast Cancer (TNBC) after Chemotherapy Treatment [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-15-08.