Abstract P5-05-09: Systemic perturbations induced by all-trans retinoic acid in the gene-expression profiles of sixteen breast cancer cell lines characterized by sensitivity and resistance to the anti-proliferative effects of the retinoid
Authors: Garattini E , Bolis M , Vallerga A , Fratelli M , Paroni G , Zanetti A , Kurosaki M , Gianni' M , Celestini V , Terao M 
Published: May 2019

Abstract
Background: All-trans retinoic acid (ATRA) is a promising agent in the treatment of breast cancer. In view of ATRA-based therapeutic strategies aimed at the personalized treatment of mammary tumors, we recently demonstrated that approximately 70% of estrogen-receptor-positive (ER+) breast cancer is sensitive to the anti-proliferative effects of ATRA (1). In contrast only 10-20% of the HER2-positive and triple-negative counterparts respond to the retinoid. On the basis of these data and the available basal gene-expression profiles of breast cancer cell lines and primary tumors, we developed a model consisting of 21 genes (ATRA-21) which correctly predicts ATRA-sensitivity in the context of breast cancer (2).
Aims and Approach: The present study is aimed at getting insights into the molecular mechanisms underlying the anti-tumor action of ATRA in the specific subsets of breast cancer identified. In addition, we intend to determine specific genes and gene-networks modulated by ATRA which may represent pharmacological targets for the design of rational combinations between the retinoid and unrelated therapeutic agents to be used in the personalized treatment of breast cancer. A final goal is the identification of potential bio-markers of the anti-tumor response to ATRA to be used in the clinics. To address all these points, we performed deep-sequencing experiments on a panel of sixteen cell lines recapitulating the heterogeneity of the breast cancer phenotype and characterized for their anti-proliferative response to ATRA.
Panel of Breast cancer cell lines and characteristicsCell linePhenotypeClassATRA-scoreATRA-sensitivitySKBR3LUMINALHER2+1.0yesHCC1500LUMINALER+0.7yesCAMA1LUMINALER+0.7yesMDAMB361LUMINALHER2+0.6yesHCC202LUMINALHER2+0.2noMDAMB175VIILUMINALER+0.2noZR751LUMINALER+0.1noHCC1419LUMINALHER2+0.1noHCC1599BASALTN1.0yesMB157BASALTN0.3yesMDAMB157BASALTN0.2yesHS578TBASALTN0.2yesMDAMB231BASALTN0.0noCAL851BASALTN0.0noHCC1187BASALTN0.0noMDAMB436BASALTN0.0noATRA-score = ATRA sensitivity index, the higher the score the higher is the sensitivity to ATRA. ER+ = estrogen-receptor-positive cell line. HER2+ = Her2-positive cell line.
Results: We exposed each cell line to ATRA (1 μM) for 24 hours and extracted total RNA which was subjected to deep sequencing. The global gene-expression data were analyzed with a number of complementary bio-informatic tools which resulted in the identification of approximately 100 genes whose expression is up- or down-regulated specifically in ATRA-sensitive luminal and/or basal cell lines. Pathway and gene-network analysis indicate a strong enrichment in the up-regulation of genes involved in the pathways modulated by interferons. These last results are consistent with the idea that ATRA exerts a strong immuno-modulatory action in breast cancer cells and represents proof of principle for the evaluation of combinations between the retinoid and check-point inhibitors in the treatment of breast cancer.
References: 1) Centritto F. et al. EMBO Mol Med. 2015 Jul;7(7):950-7. 2) Bolis M et al.. Ann Oncol. 2017 Mar 1;28(3):611-621.
Citation Format: Garattini E, Bolis M, Vallerga A, Fratelli M, Paroni G, Zanetti A, Kurosaki M, Gianni' M, Celestini V, Terao M. Systemic perturbations induced by all-trans retinoic acid in the gene-expression profiles of sixteen breast cancer cell lines characterized by sensitivity and resistance to the anti-proliferative effects of the retinoid [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-09.