Identification and Validation of a Novel Theranostic Target in Triple Negative Breast Cancer with Transcriptomics and Protein Analyses

Background: Triple negative breast cancer (TNBC) poses a significant clinical challenge in imaging and therapy due to absence of conventional targets such as estrogen, progesterone, and HER2 receptors. The aim of this study is to identify potential targets for TNBC through comprehensive transcriptomic analyses and validation in TNBC cell lines and tissues. Methods: Single-cell RNA sequencing (scRNA-seq) data obtained from 8 TNBC patients and 11 normal patients were analyzed to identify differentially expressed surface proteins using adjusted p-values based on Bonferroni correction. To verify the validity of potential targets identified through scRNA-seq, expression of selected proteins was evaluated in bulk RNA-seq data from 162 TNBC and 113 normal breast tissues in the TCGA cohort. Finally, expression of selected proteins was examined in representative human TNBC cell lines and xenograft tumors in immunodeficient mice. Results: Nine proteins were revealed to be expressed more than twice as much in TNBC cells compared to normal cells: LY6E, LY6D, LAMP1, EMP2, TTYH1, CD74, BST2, HLA-DRA, and HLA-DRB1 (P < 10 − 10 for all). Among those, LY6E, LY6D, BST2, and TTYH1 were selected as potential target proteins with significantly higher expression in TNBC tissues (P < 0.0001 for LY6E and LY6D; P = 0.007 for BST2; P = 0.002 for TTYH1). Validation experiments revealed that LY6E demonstrated high expression on the membrane of TNBC cell lines, while exhibiting low expression in normal breast epithelial cells. Consistently, Western blot analysis of tumors from an in vivo xenograft model derived from a TNBC cell line confirmed elevated LY6E expression. Conclusion: In conclusion, this study suggests LY6E as a potential target for the selective imaging and therapy of TNBC, identified by transcriptomics analysis and cell line experiments. It lays the groundwork to augment clinical impact of future preclinical studies for the development of diagnostic and treatment approaches for TNBC. Keywords: triple negative breast cancer, diagnosis, therapy, target protein, transcriptomics