Identification of cell surface targets for CAR-T cell therapies and antibody–drug conjugates in breast cancer

Abstract

Background Two promising therapeutic strategies in oncology are chimeric antigen receptor-T cell (CAR-T) therapies and antibody–drug conjugates (ADCs). To be effective and safe, these immunotherapies require surface antigens to be sufficiently expressed in tumors and less or not expressed in normal tissues. To identify new targets for ADCs and CAR-T specifically targeting breast cancer (BC) molecular and pathology-based subtypes, we propose a novel in silico strategy based on multiple publicly available datasets and provide a comprehensive explanation of the workflow for a further implementation. Methods We carried out differential gene expression analyses on The Cancer Genome Atlas BC RNA-sequencing data to identify BC subtype-specific upregulated genes. To fully explain the proposed target-discovering methodology, as proof of concept, we selected the 200 most upregulated genes for each subtype and undertook a comprehensive analysis of their protein expression in BC and normal tissues through several publicly available databases to identify the potentially safest and viable targets. Results We identified 36 potentially suitable and subtype-specific tumor surface antigens (TSAs), including fibroblast growth factor receptor-4 ( FGFR4 ), carcinoembryonic antigen-related cell adhesion molecule 6 ( CEACAM6 ), GDNF family receptor alpha 1 ( GFRA1 ), integrin beta-6 ( ITGB6 ) and ectonucleotide pyrophosphatase/phosphodiesterase 1 ( ENPP1 ). We also identified 63 potential TSA pairs that might be appropriate for co-targeting strategies. Finally, we validated subtype specificity in a cohort of our patients, multiple BC cell lines and the METABRIC database. Conclusions Overall, our in silico analysis provides a framework to identify novel and specific TSAs for the development of new CAR-T and antibody-based therapies in BC.

Systematic Analysis of an Invasion-Related 3-Gene Signature and Its Validation as a Prognostic Model for Pancreatic Cancer

“…ITGB6, which is highly expressed in colorectal cancer, is associated with a poor prognosis ( 37 ). ITGB6 can also be used as a tumor-specific surface antigen (TSA) to identify cell surface targets of CAR-T cell therapy and antibody-drug conjugates in breast cancer ( 38 ). Studies have shown that ITGB6 was a liver-metastasis-related gene for PAAD patients ( 39 ) and the overexpression of ITGB6 was significantly associated with advanced AJCC stage and histologic grade, and worse prognosis in pancreatic cancer ( 40 ).…”

Antibody–drug conjugates: Smart chemotherapy delivery across tumor histologies

“…Such antigens should have specific characteristics, making them suitable for targeting with ADCs: differential expression between tumor (high expression) and normal tissues (low/no expression), surface location, and internalization after ligand interaction 12 . To identify promising candidate antigens with these features, in silico strategies are being developed using RNA‐sequencing and protein‐expression data to predict the most suitable antigens for targeting 115,116 . These strategies could inform the design of ADCs in the future, allowing the development of antigen maps of cancers and the identification of histologies most likely to benefit from particular conjugates.…”

CAR-T Cell Therapy for Breast Cancer: From Basic Research to Clinical Application

“…In addition to the targets discussed above, other targets have also been explored as potential antigens for CAR-T cell therapy. A in silico analysis compared gene expression patterns to identify potential targets for breast cancer immunotherapy, resulting in 36 potentially tumor-surface antigens being discovered, including integrin beta-6 (ITGB6), fibroblast growth factor receptor-4 (FGFR4), and ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) 168 . Only a few studies focused on those potential targets to clarify their therapeutic effects; therefore, more investigation is needed to estimate their potentiality.…”