Transcriptome modulation by mifepristone treatment in breast cancer patients with higher levels of progesterone receptor A than B

ELIAS, ANDRES; ABBA, MARTIN; GASS, HUGO; LAMB, CAROLINE A.; FABRIS, VICTORIA T.; MARTINEZ VAZQUEZ, PAULA; BURRUCHAGA, JAVIER; SPENGLER, EUNICE; CAILLET BOIS, INES; CASTETS, ALEJANDRA; LIGUORI, MARCOS; PATACCINI, GABRIELA; ABASCAL, MARÍA FLORENCIA; NOVARO, VIRGINIA; MOLINOLO, ALFREDO; VANZULLI, SILVIA; ROJAS, PAOLA; LANARI, CLAUDIA

Congreso; San Antonio Breast Cancer Symposium; 2021

Background: Preclinical data suggests that antiprogestins inhibit the growth of luminal breast carcinomas expressing higher levels of progesterone receptor isoform A (PRA) than isoform B (PRB). Thus, we designed a pre-surgical window of opportunity trial to determine the therapeutic effects of oral mifepristone (MFP) in 20 breast cancer patients selected by their high PRA/PRB isoform ratio (MIPRA; NCT02651844).Methods. MIPRA is an open-label, one-arm, prospective interventional study. After the selection process, 20 patients that met the inclusion criteria, with ER+, PRA/PRB>1.5 determined by Western blots, and total PR ≥50% determined by immunohistochemistry (IHC), were included for daily MFP treatment (200 mg/day p.o., 14 days). Core needle biopsies and surgical samples were formalin-fixed for IHC studies, and others were snap-frozen for further molecular studies. Besides, plasma samples were obtained for MFP dosing by LC-MS/MS. RNA was extracted from frozen tissue with a column-based method. The library for sequencing was constructed using SMART-Seq v4 Ultra Low Input RN from 8 paired samples in which tissue was available and passed the RNA quality control. Sequencing data was aligned with STAR and processed in R/Bioconductor. The counts matrix was obtained with featureCounts and differential expression paired analysis was performed with DESeq2. Gene set enrichment analysis (GSEA) was executed with the MSigDB collection.Results: A 49.62% decrease in Ki-67 staining was registered in all surgical specimens compared to baseline (p = 0.0003). Using the pre-specified response parameter (30% relative reduction) we identified 14/20 responders. Mifepristone was detected in all available plasma samples and the mean concentration was 308.33 ±57.91 ng/ml (716.71 ±134.62 nM). We conducted an RNA-seq analysis to explore changes at the transcript level. First, we conducted the study with all pairs of samples, without considering the response to MFP in Ki-67 studies. Unsupervised analysis showed the paired samples clustered together but neither the principal component analysis, nor the hierarchical clustering, showed any relevant cluster. The differential expression analysis identified 11 and 76 genes down- and up-regulated, respectively. We performed a GSEA based on KEGG databases and determined enriched pathways related to modulation of cell cycle and apoptosis. When the analysis was conducted with the REACTOME up-modulation of immune bioprocess and extracellular matrix re-modeling pathways such as degradation of extracellular matrix, activation of matrix metalloproteinases and collagen formation, were observed in the latter. Additionally, we observed down-modulation of pathways related to cell cycle such as DNA replication and synthesis, APC/C, and phase transition pathways. Interestingly, when we considered the tumors that responded to MFP according to Ki-67 data (n=4) and those that did not respond (n=4), we found that the non-responsive group shared some of the up and down modulated pathways as the responsive group.Conclusion: The results obtained in RNA-Seq data support the findings obtained by IHC indicating that MFP inhibits cell proliferation in luminal breast carcinomas with higher levels of PRA than PRB. The fact that MFP increased immune-related pathways is in line with previous preclinical data from our laboratory suggesting that MFP may prime this group of tumors for further immune therapy. Interestingly, we found that some relevant pathways regarding inhibition of cell proliferation were also modulated in the non-responsive group suggesting that tumors in which a decrease in Ki-67 was not evident, may be still responding to MFP treatment. Ongoing analysis will determine changes in other markers that may help to further define MFP-responsive patients.