Proteome and RNA-Seq changes in breast cancer patients with higher levels of progesterone receptor A than B after mifepristone treatment

ANDRES ELIA; JANA SANCHEZ; PAOLA ROJAS; LEO SALDAIN; PAULA MARTÍNEZ VAZQUEZ; JAVIER BURRUCHAGA; EUNICE SPENGLER; INÉS CAILLET BOIS; MARCOS LIGUORI; HUGO GASS; MARTÍN ABBA; JAVIER MUÑOZ; LUISA HELGUERO; CLAUDIA LANARI

Congreso; ESMO Breast Cancer Congress; 2022

BackgroundAntiprogestins inhibit experimental breast cancer growth when progesterone receptor isoform A (PRA) levels are higher than those of isoform B (PRB). Thus, we conducted a window of opportunity trial to determine the therapeutic effects of oral mifepristone (MFP, 200mg) in 20 breast cancer patients selected by their high PRA/PRB isoform ratio (MIPRA; NCT02651844). We identified 14/20 patients that achieved the pre-specified response parameter (30% relative reduction) showing a 49.62% decrease in Ki67 staining after MFP treatment (p = 0.0003). The aim of the study was to evaluate changes at the genomic and protein levels to reinforce Ki67 findings.MethodsCore needle biopsies and surgical samples were formalin-fixed and snap-frozen. RNA was extracted from frozen tissue. After QC, 8 paired samples were sent for library construction and sequencing (SMART-Seq v4 Ultra Low Input RN). RNA-Seq data was analyzed using a paired analysis (R/Bioconductor packages). Cytosolic (C) and nuclear (N) protein extracts obtained from frozen tissue with commercial kits were sent for proteome analysis through the European Proteomics Infrastructure Consortium - Providing Access (EPIC-XS).ResultsRNA-Seq studies identified 11 and 76 genes down- and up-regulated, respectively by MFP treatment. We observed an up-modulation of immune bioprocess and extracellular matrix re-modeling pathways and a down-modulation of those related to cell cycle such as DNA replication (GESEA analysis). Proteomic analysis of non-paired samples revealed 174 down- and 180 upregulated proteins in N fractions, and 110 down- and 80 upregulated in C fractions. Enrichment analysis showed a modulation in extracellular matrix organization, Wnt signaling and G1/S transition of mitotic cell cycle, among other pathways. When a paired analysis was attempted HLA-C, SRRM2 and MYH11 were highly deregulated in the N fractions and IGHG4 and SMAP1 in the C fractions (paired t-test, FDR