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Purpose:Preclinical data suggest that antiprogestins inhibit the growth of luminal breast carcinomas that express higher levels of progesterone receptor isoform A (PRA) than isoform B (PRB). Thus, we designed a presurgical window of opportunity trial to determine the therapeutic effects of mifepristone in patients with breast cancer, based on their high PRA/PRB isoform ratio (MIPRA; NCT02651844).Patients and Methods:Twenty patients with luminal breast carcinomas with PRA/PRB > 1.5 (determined by Western blots), and PR ≥ 50%, naïve from previous treatment, were included for mifepristone treatment (200 mg/day orally; 14 days). Core needle biopsies and surgical samples were formalin fixed for IHC studies, while others were snap-frozen to perform RNA sequencing (RNA-seq), proteomics, and/or Western blot studies. Plasma mifepristone levels were determined using mass spectrometry. The primary endpoint was the comparison of Ki67 expression pretreatment and posttreatment.Results:A 49.62% decrease in Ki67 staining was observed in all surgical specimens compared with baseline (P = 0.0003). Using the prespecified response parameter (30% relative reduction), we identified 14 of 20 responders. Mifepristone induced an increase in tumor-infiltrating lymphocytes; a decrease in hormone receptor and pSer118ER expression; and an increase in calregulin, p21, p15, and activated caspase 3 expression. RNA-seq and proteomic studies identified downregulated pathways related to cell proliferation and upregulated pathways related to immune bioprocesses and extracellular matrix remodeling.Conclusions:Our results support the use of mifepristone in patients with luminal breast cancer with high PRA/PRB ratios. The combined effects of mifepristone and estrogen receptor modulators warrant clinical evaluation to improve endocrine treatment responsiveness in these patients.See related commentary by Ronchi and Brisken, p. 833

DOC- 25K, Supplementary Tables 1-6

Supplementary Figure Legends

Supplementary Figure 1. "Phase 2-Eligible" Population. Supplementary Figure 2. ALKA-372-001 and STARTRK-1 Dosing Regimens.

RNA-Seq and Proteomics analysis. A and B, Dot plot of relevant enriched pathways from GSEA results (Reactome and Hallmark databases) separating responsive (A) and unresponsive tumors (B). C, Immune cell deconvolution (xcell) in the different tumors analyzed by RNA-Seq. Plots with significant p values analyzed by Wilcoxon test and the T cell CD8+ plot are shown. D, Kegg diagram of the Cell cycle pathway, that may explain mifepristone therapeutics effects. A colored code was used: the first half of the box is colored according to the RNA-Seq data (8 tumors) and the last half of the box is colored according to the proteomic data (n=10 tumors; nuclear fraction).

RNA-Seq Variant calling

Purpose:Preclinical data suggest that antiprogestins inhibit the growth of luminal breast carcinomas that express higher levels of progesterone receptor isoform A (PRA) than isoform B (PRB). Thus, we designed a presurgical window of opportunity trial to determine the therapeutic effects of mifepristone in patients with breast cancer, based on their high PRA/PRB isoform ratio (MIPRA; NCT02651844).Patients and Methods:Twenty patients with luminal breast carcinomas with PRA/PRB > 1.5 (determined by Western blots), and PR ≥ 50%, naïve from previous treatment, were included for mifepristone treatment (200 mg/day orally; 14 days). Core needle biopsies and surgical samples were formalin fixed for IHC studies, while others were snap-frozen to perform RNA sequencing (RNA-seq), proteomics, and/or Western blot studies. Plasma mifepristone levels were determined using mass spectrometry. The primary endpoint was the comparison of Ki67 expression pretreatment and posttreatment.Results:A 49.62% decrease in Ki67 staining was observed in all surgical specimens compared with baseline (P = 0.0003). Using the prespecified response parameter (30% relative reduction), we identified 14 of 20 responders. Mifepristone induced an increase in tumor-infiltrating lymphocytes; a decrease in hormone receptor and pSer118ER expression; and an increase in calregulin, p21, p15, and activated caspase 3 expression. RNA-seq and proteomic studies identified downregulated pathways related to cell proliferation and upregulated pathways related to immune bioprocesses and extracellular matrix remodeling.Conclusions:Our results support the use of mifepristone in patients with luminal breast cancer with high PRA/PRB ratios. The combined effects of mifepristone and estrogen receptor modulators warrant clinical evaluation to improve endocrine treatment responsiveness in these patients.See related commentary by Ronchi and Brisken, p. 833

Morphological evaluation of CNBs and matched surgical samples; RNA-Seq analysis; Proteomics

TS1: List of upregulated Gene Ontology biological processes, TS2: List of downregulated Gene Ontology biological processes, TS3: List of normalized differential expressed genes with MFP, TS4: Gene Ontology Biological processes from differential expressed genes, TS5: Upregulated genes implicated in the Inflammatory response.

The role of active antitumor immunity in hormone receptor–positive (HR+) breast cancer has been historically underlooked. The aim of this study was to determine the contribution of the immune system to antiprogestin-induced tumor growth inhibition using a hormone-dependent breast cancer model. BALB/c-GFP+ bone marrow (BM) cells were transplanted into immunodeficient NSG mice to generate an immunocompetent NSG/BM-GFP+ (NSG-R) mouse model. Treatment with the antiprogestin mifepristone (MFP) inhibited growth of 59–2-HI tumors with similar kinetics in both animal models. Interestingly, MFP treatment reshaped the tumor microenvironment, enhancing the production of proinflammatory cytokines and chemokines. Tumors in MFP-treated immunocompetent mice showed increased infiltration of F4/80+ macrophages, natural killer, and CD8 T cells, displaying a central memory phenotype. Mechanistically, MFP induced immunogenic cell death (ICD) in vivo and in vitro, as depicted by the expression and subcellular localization of the alarmins calreticulin and HMGB-1 and the induction of an ICD gene program. Moreover, MFP-treated tumor cells efficiently activated immature dendritic cells, evidenced by enhanced expression of MHC-II and CD86, and induced a memory T-cell response, attenuating tumor onset and growth after re-challenge. Finally, MFP treatment increased the sensitivity of HR+ 59–2-HI tumor to PD-L1 blockade, suggesting that antiprogestins may improve immunotherapy response rates. These results contribute to a better understanding of the mechanisms underlying the antitumor effect of hormonal treatment and the rational design of therapeutic combinations based on endocrine and immunomodulatory agents in HR+ breast cancer.Significance:Antiprogestin therapy induces immunogenic tumor cell death in PRA-overexpressing tumors, eliciting an adaptive immune memory response that protects mice from future tumor recurrence and increases sensitivity to PD-L1 blockade.

Supplementary Figure 1: The NSG-R mouse model mimics an immunocompetent host.

PDF file - 160K, ER� increase PR activity. MDA-MB-231 cells were stably transfected with human PRB (pSG5-PRB) or with the empty vector (pSG5) and different clones were obtained. The expression of PRB was evaluated by Western blot (A), using T47D cells as a positive control of hormone receptors, or by immunofluorescence (B, bar: 30�m). (C) MDA-MB-231 pSG5 clone (3) and pSG5-PRB clone (1) cells were transiently transfected with human ER� (pSG5-HEGO) and its expression was evaluated by immnunofluorescence. Bar: 15�m. (D) MDA-MB-231 pSG5 clone (3) and pSG5-PRB clone (1) cells were co-transfected with ER� and PRE-Luc vectors. After 24 h starvation in 1% chFCS, cells were incubated with MPA for another 24 h and the activity of luciferase was evaluated.

PDF file - 177K, T47D cells were starved and then treated or not with MPA for 10 min, and processed for immunofluorescence and confocal microscopy using specific antibodies to detect pSer162 PRB and ER� (SP1, A) or pSer294 PR and ER� (M7047, B). Bar: 15�m. Co-localization between nuclear receptors was quantified using the quantitative statistical analysis for nuclear pixel overlap after 10 min of MPA treatment and was estimated using the Pearson's correlation coefficient. (C) Cellular fractionation of T47D cells was controlled by Western blot using anti-tubulin (cytoplasmatic marker, Ab4 from Thermo) or anti-Sp1 (nuclear marker, from Thermo) antibodies. Erk1/2 was used as a loading control. (D) T47D cells were starved and then treated with ICI during 3, 6, 12, 24 and 48 h. ER� (SP1) and PR (Ab7) expression was analyzed by Western blot. Erk1/2 was used as a loading control.

PDF file - 3.3MB, Expression of CCND1 and MYC proteins after MPA treatment. T47D cells were starved in 1% chFCS and incubated with MPA (10nM) for different times. Total protein extracts were used in Western blot assays to evaluate the expression of CCND1 and MYC. Erk1/2 was used as loading control. A representative experiment of three (left) is shown together with the quantification of the bands respect to the loading control (right).

PDF file - 133K

PDF file - 138K, (A) Left. Purified C4-HD cells were cultured in chamber slides. After attachment, the medium was replaced and the cells starved in 1% chFCS for 24 h. Cells were untreated or treated with MPA (10 nM) and/or ICI (1 �M) during 6 h in the presence of BrdU and processed for immunofluorescence and confocal microscopy with specific antibodies: anti-BrdU (green) and cytokeratin (CK, red). Right. Quantification of BrdU+/CK+ cells (mean � SEM) after treatment. (B) Left. 3H-thymidine uptake assays: C4-HD cells were transfected with siRNAs for mouse ER� or a control siRNA, starved, treated for 48 h with MPA and the 3H-thymidine uptake index calculated as described previously. A representative experiment (mean � SEM) of three is shown. Right. Western blots: Protein extracts of C4-HD cells transfected for 48 h with siRNAs for mouse ER� as described previously were used to evaluate the expression of ER� (MC-20) in transfected cells. Erk1/2 was used as a loading control. Cell extracts from C4-HD cells treated with ICI for 24 hs were used as a control. (C) C4-HD cells were starved and then treated with ICI during 6, 12 and 24 h. ER� (MC-20) and PR (C-19) expression was analyzed by Western blot. �-actin (I-19, Santa Cruz) was used as a loading control.

Supplementary Figures 1-5 from Interaction between FGFR-2, STAT5, and Progesterone Receptors in Breast Cancer

Supplementary Table 1 from Interaction between FGFR-2, STAT5, and Progesterone Receptors in Breast Cancer

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. Citation Format: Andres Elia, Martin Abba, Hugo Gass, Caroline A Lamb, Victoria T Fabris, Paula Martinez Vazquez, Javier Burruchaga, Eunice Spengler, Ines Caillet Bois, Alejandra Castets, Silvia Lovisi, Marcos Liguori, Gabriela Pataccini, Maria Florencia Abascal, Virginia Novaro, Alfredo Molinolo, Silvia I Vanzulli, Paola Rojas, Claudia Lanari. Transcriptome modulation by mifepristone treatment in breast cancer patients with higher levels of progesterone receptor A than B [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-16-09.

The role of active antitumor immunity in hormone receptor–positive (HR+) breast cancer has been historically underlooked. The aim of this study was to determine the contribution of the immune system to antiprogestin-induced tumor growth inhibition using a hormone-dependent breast cancer model. BALB/c-GFP+ bone marrow (BM) cells were transplanted into immunodeficient NSG mice to generate an immunocompetent NSG/BM-GFP+ (NSG-R) mouse model. Treatment with the antiprogestin mifepristone (MFP) inhibited growth of 59–2-HI tumors with similar kinetics in both animal models. Interestingly, MFP treatment reshaped the tumor microenvironment, enhancing the production of proinflammatory cytokines and chemokines. Tumors in MFP-treated immunocompetent mice showed increased infiltration of F4/80+ macrophages, natural killer, and CD8 T cells, displaying a central memory phenotype. Mechanistically, MFP induced immunogenic cell death (ICD) in vivo and in vitro, as depicted by the expression and subcellular localization of the alarmins calreticulin and HMGB-1 and the induction of an ICD gene program. Moreover, MFP-treated tumor cells efficiently activated immature dendritic cells, evidenced by enhanced expression of MHC-II and CD86, and induced a memory T-cell response, attenuating tumor onset and growth after re-challenge. Finally, MFP treatment increased the sensitivity of HR+ 59–2-HI tumor to PD-L1 blockade, suggesting that antiprogestins may improve immunotherapy response rates. These results contribute to a better understanding of the mechanisms underlying the antitumor effect of hormonal treatment and the rational design of therapeutic combinations based on endocrine and immunomodulatory agents in HR+ breast cancer. Significance: Antiprogestin therapy induces immunogenic tumor cell death in PRA-overexpressing tumors, eliciting an adaptive immune memory response that protects mice from future tumor recurrence and increases sensitivity to PD-L1 blockade.

Background: Different antiprogestins have been clinically evaluated in gynecological andbreast cancers. Mifepristone (MFP), as well as onapristone and telapristone acetate, showedpartial responses in breast cancer clinical trials. Preclinical data indicates that antiprogestinsinhibit cell proliferation of luminal breast carcinomas expressing higher levels of progesteronereceptor isoform A (PRA) than those of isoform B (PRB) evaluated by western blots (WB). Thus,we designed a pre-surgical window trial to determine the therapeutic effects of oral MFP oncell proliferation and on differential gene expression in 20 breast cancer patients selected bytheir high PRA/PRB isoform ratio.Methods. MIPRA is an open-label, one-arm, prospective interventional study (NCT02651844).We interviewed 140 naive breast cancer patients and 133 accepted to participate. Four coreultrasound-guided biopsies were performed, two were formalin-fixed for diagnosis, ER, PR,HER2, and Ki67 evaluation and two were snap-frozen for WB and molecular studies. Patientsthat met the inclusion criteria, with ER+, PRA/PRB>1.5 and total PR ≥50% determined by WBand immunohistochemistry (IHC), respectively, were included for MFP treatment. Plasma wasobtained before and after treatment for future studies. Patients were treated with oral MFP(200 mg/day) for 14 days before surgery which was performed on day 15. Clinical examinationwas performed at days 7 and 14 to register possible adverse effects and to measure tumorsize. During surgery, samples were formalin-fixed for IHC studies, and others were snap-frozenfor further molecular studies. One patient had a bilateral breast cancer, and both tumorsmatched with the inclusion criteria and were included. The primary endpoint was Ki67labeling, comparing diagnostic core needle biopsy to post-therapy surgical specimens.Considering previous studies performed with tamoxifen, we pre-specified that 30% of relativereduction in Ki67 would be considered as a positive response. Differences in Ki67 expressionwere quantitated by an expert pathologist counting at least ten 40x fields per slide. Theseresults are currently being validated by a second pathologist. One patient, with a core biopsywith less than 500 total cells, was excluded. Ongoing experiments include secondary and otherendpoints: comparison of apoptotic, proliferative and hormone receptor markers by IHC,measurement of MFP plasma levels and, RNAseq analysis in samples pre- and post-treatment. Ki67 changes from baseline were tested with paired Wilcoxon matched-pairssigned-rank test.Results: The median (range) Ki67 value of biopsies was 11.87% (2.70- 34.56) and for surgicalspecimens was 6.45% (0.48-23.77). A 45.67% of decrease in the median % Ki67 (41.63%comparing the arithmetic mean values and 50.83% comparing the geometric mean values) wasregistered in all surgical specimens compared to baseline (p= 0.003). Using the pre-specifiedresponse parameter (30% relative reduction in Ki67), we identified 15/20 (75%) responders.Considering only responsive tumors, a 49.87% decrease in the median % Ki67 (50.83%,arithmetic mean; 62.34% geometric mean) was observed (p Citation Format: Andres Elia, Silvia I Vanzulli, Hugo Gass, Caroline A Lamb, Victoria T Fabris, Paula Martinez Vazquez, Javier Burruchaga, Eunice Spengler, Ines Caillet Bois, Alejandra Castets, Silvia Lovisi, Marcos Liguori, Gabriela Pataccini, M Florencia Abascal, Virginia Novaro, Gabriela Acosta Haab, Alfredo Molinolo, Paola Rojas, Claudia Lanari. Mipra, a window of opportunity study evaluating mifepristone treatment for postmenopausal breast cancer patients with higher levels of progesterone receptor isoform a than b [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS11-35.

Entrectinib, a potent oral inhibitor of the tyrosine kinases TRKA/B/C, ROS1, and ALK, was evaluated in two phase I studies in patients with advanced or metastatic solid tumors, including patients with active central nervous system (CNS) disease. Here, we summarize the overall safety and report the antitumor activity of entrectinib in a cohort of patients with tumors harboring NTRK1/2/3, ROS1, or ALK gene fusions, naïve to prior TKI treatment targeting the specific gene, and who were treated at doses that achieved therapeutic exposures consistent with the recommended phase II dose. Entrectinib was well tolerated, with predominantly Grades 1/2 adverse events that were reversible with dose modification. Responses were observed in non–small cell lung cancer, colorectal cancer, mammary analogue secretory carcinoma, melanoma, and renal cell carcinoma, as early as 4 weeks after starting treatment and lasting as long as >2 years. Notably, a complete CNS response was achieved in a patient with SQSTM1–NTRK1-rearranged lung cancer.Significance: Gene fusions of NTRK1/2/3, ROS1, and ALK (encoding TRKA/B/C, ROS1, and ALK, respectively) lead to constitutive activation of oncogenic pathways. Entrectinib was shown to be well tolerated and active against those gene fusions in solid tumors, including in patients with primary or secondary CNS disease. Cancer Discov; 7(4); 400–9. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 339