Abstract 4346: TFF1 and TFF3 predict response to CDK4/6 inhibitors in breast cancer patients
Authors: Luo Linjie , Wang Yan , Mastoraki Sophia , Raghavendra Akshara Singareeka , Navarro-Yepes Juliana , Kettner Nicole M. , Kim Serena , Tripathy Debasish , Hunt Kelly , Keyomarsi Khandan 
Published: April 2023

Abstract
Background: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) in combination with endocrine therapy (ET) have become the mainstay treatment for patients with hormone receptor (ER)-positive, HER2-negative metastatic breast cancer (BC). However, one-third of patients do not respond to the treatment (intrinsic resistance), leading to early tumor progression and treatment failure, and most patients eventually acquire resistance to therapy. The exact mechanisms of resistance to CDK4/6i are yet to be elucidated, and due to subsequent early (intrinsic) or late progression on CDK4/6i, long-term cures are not achieved.
Methods: Transcriptomic profiles of BC cell lines that were sensitive or resistant to approved CDK4/6i, independent of subtype, were downloaded from the Cancer Cell Line Encyclopedia database. Bioinformatics analysis was performed by integrated Differential Expression and Pathway (iDEP) workflow. In parallel, transcriptomic profiles of metastatic biopsies from pre-CDK4/6i-treated BC patients (n = 54) were generated using RNA-Access technology. Key common biomarkers identified from the BC cell lines and patient tumor samples were validated by immunohistochemistry in formalin-fixed paraffin-embedded (FFPE) metastatic specimens from 73 patients prior to CDK4/6i therapy.
Results: Transcriptomic profile comparisons of BC cell lines (n = 35) that were sensitive versus resistant to CDK4/6is identified Trefoil Factor 1 and 3 (TFF1 and TFF3) secretory proteins as top predictors of response. Correlation analysis showed a strong negative correlation between TFF1 and TFF3 levels to IC50 values of palbociclib and abemaciclib. Knockdown of TFF3 in CDK4/6i-sensitive BT20 cells with shRNA induced drug resistance in the cells. Transcriptomic data from 54 BC patients pre-treated with CDK4/6i showed the expression levels of TFF1 and TFF1/3 receptors (CCR4 and CCR7) were significantly increased in patients who developed late progression (&gt; 6 months) compared to early progressors (&lt; 3 months). In addition, IHC analysis of TFF1 and TFF3 expressions in 73 pre-treated BC patient samples showed significantly higher protein expression levels in late progressors than in early progressors.
Conclusions: Our results identified and validated the common biomarkers, TFF1 and TFF3, as predictors of CDK4/6i response efficacy in ER-positive, HER2-negative BC patients. These findings provide a predictive tool capable of selecting de novo metastatic BC patients who will have the greatest benefit from the combination of CDK4/6i with endocrine treatment. Furthermore, our discovery of biomarkers in early versus late progression on CDK4/6i therapy will enable new therapeutic avenues and provide the rationale for future large-scale clinical trials.
Citation Format: Linjie Luo, Yan Wang, Sophia Mastoraki, Akshara Singareeka Raghavendra, Juliana Navarro-Yepes, Nicole M. Kettner, Serena Kim, Debasish Tripathy, Kelly Hunt, Khandan Keyomarsi. TFF1 and TFF3 predict response to CDK4/6 inhibitors in breast cancer patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4346.