Abstract LB-359: Gene expression profile and tumor infiltrating lymphocytes in Hispanic women with breast cancer
Authors: Encarnacion Jarline , Ortiz-Sanchez Carmen , Dutil Julie , Torres-Gracia Wandaliz , Eschrich Steven , Pilon-Thomas Shari , Matta Jaime L. 
Published: September 2020

Abstract
Breast cancer (BC) is the most commonly diagnosed cancer among women and is currently classified into four molecular subtypes. These subtypes have been characterized by their distinct immune gene profiles, where only triple-negative (TN) and HER2+ subtypes are recognized for being tumor immunogenic cancers. The main objective of this pilot study is to understand whether the immune gene expression profile from breast tumors can be associated with tumor infiltrating lymphocytes (TILs) levels in Hispanic women. Breast tumors were obtained through the Puerto Rico Biobank at Ponce Health Sciences University and in collaboration with Moffitt Cancer Center. Pathology reports were also obtained to collect information about tumor characteristics and molecular subtype classification. Fresh frozen (FF) (n=40) and FFPE (n=27) breast tumors were cut into slide sections and stained with H&E to confirm the presence of tumor cells. The percentage of TILs was measured by staining additional tumor sections for CD3+ T cells. TILs levels were scored by analyzing the infiltration of CD3+ T cells and were further classified into: low (≤40%) or high (&gt;40%). After microdissection of the breast tumors by a pathologist, total RNA was extracted to assess the expression changes of 770 immune genes (Pancancer Immune Panel, NanoString Technologies). The RNA quality was tested to ensure that it met the required specification for genomic analysis. Data was analyzed using the “randomForest” R package followed by proportion tests of the clinical data using contingency table analysis. All the samples were infiltrating ductal carcinomas with BC subtype distribution as follows: luminal A (n=50), luminal B (n=8), HER2+ (n=4), and TN (n=5). No significant differences were found after comparing the proportions of TILs between FF and FFPE tumor samples (p=1.00). Differentially expressed genes (DEGs) were obtained separately for FF and FFPE tumor with high and low TIL levels. The random forest analyses showed high predictive performance (~80% accuracy) to classify samples stratified by TIL levels in terms of these DEGs expressions. Sixteen (16) DEGs were found consistenly in FF and FFPE samples when stratifiying by TIL levels. The expression profiles of these DEGs show consistently higher expression in samples with high TILs levels. Among those DEGs are CLTA4 (p&lt;0.01, adj: FF 0.2030, FF: 0.0206), CXCL9 (p&lt;0.01, adj: FF: 0.203, FFPE: 0.229), CCL17 (p&lt;0.01, adj: FF: 0.151, FFPE: 0.203), and TIGIT (p&lt;0.01, adj: FF: 0.157, FFPE: 0.203). CLTA4 codifies for an immune checkpoint receptor while CXCL9 and CCL17 are known enhancers of antitumor immunity in BC. Another immune checkpoint molecule, was recently reported to be produced by BC cells to suppress the TH1 response. Our results suggest that the tumor cells can activate transcription factors that can affect the immune response in Hispanic women. Supported by grant: #4U54CA163071-05.
Citation Format: Jarline Encarnacion, Carmen Ortiz-Sanchez, Julie Dutil, Wandaliz Torres-Gracia, Steven Eschrich, Shari Pilon-Thomas, Jaime L. Matta. Gene expression profile and tumor infiltrating lymphocytes in Hispanic women with breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-359.