Abstract PO4-16-03: Ectopic expression of lineage-specific transcription factors in Breast Cancer
Authors: Badve Sunil , Hu Jian , Zhang Yu , Gokmen-Polar Yesim 
Published: May 2024

Background: Lineage-specific transcription factors (LTFs) are purported to define cellular lineages and their expression could be used to identify subtypes of cancer. In many cancers, tuft cell differentiation appears to have prognostic impact. However, such differentiation has not been documented in breast cancer.

Methods: We sought to study the fidelity of LTFs (MYOG, POU2F3, FOXA1, FOXA2, FOXA3, FOXJ1, HNF4A, HNF4G, SPIB, SOX8, GRHL1, GRHL2, and GRHL3) for their presence and prognostic impact in breast cancer. Single cell RNA data from GSE 161529, which contains 421,761 single cells, was downloaded and analyzed for the expression and co-expression of LTFs. The data was first subdivided based on ER+ and TNBC status. Analysis was performed using cells from 10ER+ samples and 4 TNBC samples. Cell clustering using Louvain’s method was run using all genes. Cell type assignment was then performed using well-known markers for both tumor and lymphocyte marker from existing publications. Further analysis was restricted to keratin expressing cells and to study the presence and co-expression of LTFs in the epithelial cells. KM-Plotter was employed to determine the prognostic value of these LTFs. The analysis was further stratified by expression of estrogen receptor positive and negative status. The endpoint of relapse free survival was used, as it provided data on the largest number of patients.

Results: Single-cell analysis pipeline successfully identified distinct populations of tumor epithelial cells accompanied by various lymphocytes, including B cells, CD8+ T cells, CD4+ T cells, dendritic cells, and macrophages, in both ER+ tumors and TNBC tumor samples. We further confirmed the expression of the LTFs in the epithelial (keratin+) compartment. Expression of all LTFs (except MYOG, and FOXA2) was scattered in the different epithelial clusters. Further analysis of single LTFs showed differentiational co-expression based on ER+ status. POU2F3+/ER+ cells also co-expressed FOXA1 and GRHL1 while POU2F3+/ER- cells were GRHL1+ and (weak) SPIB+. The analysis of LTFs using KM-Plotter tool revealed their expression documenting multiple cell lineages in breast cancer; this was noted in ER+, HER2+ cancers and TNBCs. The directionality of the outcome (good or bad prognosis) varied with the specific TFs and subtype of breast cancer. High expression of POU2F3, and FOXA1, and SPIB were associated with better relapse-free survival (RFS) in ER+ breast cancer. POU2F3, FOXA2, FOXA3 were associated with worse RFS, whereas SPIB was with prognosis in ER- breast cancers.

Conclusions: We for the first time document the expression of LTFs in breast cancer and their prognostic relevance based on ER+ and ERneg status. Expression of POU2F3, a marker of tuft cells which are known to regulate immune response, was noted to be associated with improved outcomes in ER+ tumors. Further characterization of the relevance of LTFs and their co-expression with respect to therapeutic response is ongoing.

Citation Format: Sunil Badve, Jian Hu, Yu Zhang, Yesim Gokmen-Polar. Ectopic expression of lineage-specific transcription factors in Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-16-03.