Abstract P2-23-06: Estrogen receptor-negative progesterone receptor-positive breast cancer is a molecularly distinct group characterized by the down-regulation of genes controlled by ESR1 and SUZ12
Authors: Kunc Michał , Popęda Marta , Bieńkowski Michał , Braun Marcin , Łacko Aleksandra , Radecka Barbara , Pikiel Joanna , Litwiniuk Maria , Pogoda Katarzyna , Niemira Magdalena , Szałkowska Anna , Iżycka-Świeszewska Ewa , Cserni Gabor , Biernat Wojciech , Senkus Elżbieta 
Published: March 2023

Abstract
Background: Single hormone receptor-positive breast cancers (BCs) display two distinct phenotypes: ER+/PgR– and ER–/PgR+ further stratified by their HER2 status. Their molecular features are not well defined. Our study aimed to identify differentially expressed genes in ER–/PgR+ BCs compared to other phenotypes. Methods: Our cohort comprised 15 ER+/PgR–/HER2–, 11 ER+/PgR–/HER2+, 17 ER–/PgR+/HER2–, 9 ER–/PgR+/HER2+, 5 ER+/PgR+/HER2–, and 5 ER–/PgR–/HER2– invasive BCs collected from 9 Polish and 2 Hungarian centers. The cases were selected from a larger cohort after being matched according to grade, HER2 status, lymph nodes, and distant metastasis status. ER–/PgR+ group was thoroughly validated via immunohistochemistry [Kunc et al. 2022]. The expression of 776 genes was profiled with nCounter® Breast Cancer 360™ Panel in archival formalin-fixed paraffin-embedded tissue samples. A gene was defined as differentially expressed between groups if it met the following criteria: the log2 fold-change in the expression of &gt;1 or ←1 and the p-value &lt; 0.05 (Mann-Whitney U test). Additionally, weighted correlation network analysis (WGCNA) was performed to identify modules of at least 15 highly correlated genes. Subsequently, the association between gene modules and PgR status in ER– subgroup was performed. Identified mRNAs were subjected to functional annotation analysis to determine the top enriched pathways. Results: ER–/PgR+ BCs were characterized by significantly lower expression of ESR1 compared to double-positive (p&lt; 0.001) and ER+/PgR– tumors (p&lt; 0.001), whereas PGR expression was higher compared to ER+/PgR– (p&lt; 0.001), and no significantly different from ER+/PgR+ BCs (p=0.14). Triple-negative BCs had no detectable PGR mRNA. Four genes (MIA, ID4, FOXC1, CDC20) were consistently up-regulated and six genes (FAM214A, MLPH, NFKBIZ, FOS, SLC44A4, SPDEF) were down-regulated in ER–/PgR+/HER2– tumors compared to other HER2– subgroups. Compared to ER+/HER2– BCs, ER–/PgR+/HER2– cases showed up-regulation of 15 genes associated with response to vitamin D, response to ketone, and regulation of transcription, and downregulation of 33 genes involved in response to estrogen, negative regulation of cell population proliferation, regulation of epithelial-mesenchymal transition, and controlled by ESR1 and SUZ12. In WGCNA analysis of the ER– subgroup, PgR status was negatively correlated with 4 gene modules and positively correlated with 1 gene module. In line with differential gene expression analysis, genes negatively correlated with ER–/PgR+ status are regulated by ESR1 and SUZ12 and are involved in the regulation of cell proliferation, extracellular matrix organization, and NOTCH1 signaling. Genes positively correlated with ER–/PgR+ status are regulated by E2F4, FOXM1, SIN3A, NFYB, E2F1, FOS, IRF1, ZMIZ1, and UBTF and participate in cell cycle, regulation of mitosis, and microtubule cytoskeleton regulation. Conclusions: ER–/PgR+ BCs display a distinct mRNA expression profile characterized by the down-regulation of genes controlled by ESR1 and SUZ12. The latter as a part of Polycomb Repressive Complex 2 contributes to chromatin silencing, and some previous studies suggested its role in the regulation of steroid hormone receptors expression. Additionally, ER–/PgR+ BCs overexpress FOXC1 which is linked to more aggressive, high-grade, and treatment-resistant breast cancers. Our data indicate the need to unravel the mechanism of epigenetic regulation of PGR expression, especially its methylation status, in ER–/PgR+ breast cancer.
Citation Format: Michał Kunc, Marta Popęda, Michał Bieńkowski, Marcin Braun, Aleksandra Łacko, Barbara Radecka, Joanna Pikiel, Maria Litwiniuk, Katarzyna Pogoda, Magdalena Niemira, Anna Szałkowska, Ewa Iżycka-Świeszewska, Gabor Cserni, Wojciech Biernat, Elżbieta Senkus. Estrogen receptor-negative progesterone receptor-positive breast cancer is a molecularly distinct group characterized by the down-regulation of genes controlled by ESR1 and SUZ12 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-06.