Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer

Biomarkers of response are needed in breast cancer to stratify patients to appropriate therapies and avoid unnecessary toxicity. We used peripheral blood gene expression and cell type abundance to identify biomarkers of response and recurrence in neoadjuvant chemotherapy treated breast cancer patients. We identified a signature of interferon and complement response that was higher in the blood of patients with pathologic complete response. This signature was preferentially expressed by monocytes in single cell RNA sequencing. Monocytes are routinely measured clinically, enabling examination of clinically measured monocytes in multiple independent cohorts. We found that peripheral monocytes were higher in patients with good outcomes in four cohorts of breast cancer patients. Blood gene expression and cell type abundance biomarkers may be useful for prognostication in breast cancer.

Significance

Biomarkers are needed in breast cancer to identify patients at risk for recurrence. Blood is an attractive site for biomarker identification due to the relative ease of longitudinal sampling. Our study suggests that blood-based gene expression and cell type abundance biomarkers may have clinical utility in breast cancer.

Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer

Using an ORF kinome screen in MCF-7 cells treated with the CDK4/6 inhibitor ribociclib plus fulvestrant, we identified FGFR1 as a mechanism of drug resistance. FGFR1-amplified/ER+ breast cancer cells and MCF-7 cells transduced with FGFR1 were resistant to fulvestrant ± ribociclib or palbociclib. This resistance was abrogated by treatment with the FGFR tyrosine kinase inhibitor (TKI) lucitanib. Addition of the FGFR TKI erdafitinib to palbociclib/fulvestrant induced complete responses of FGFR1-amplified/ER+ patient-derived-xenografts. Next generation sequencing of circulating tumor DNA (ctDNA) in 34 patients after progression on CDK4/6 inhibitors identified FGFR1/2 amplification or activating mutations in 14/34 (41%) post-progression specimens. Finally, ctDNA from patients enrolled in MONALEESA-2, the registration trial of ribociclib, showed that patients with FGFR1 amplification exhibited a shorter progression-free survival compared to patients with wild type FGFR1. Thus, we propose breast cancers with FGFR pathway alterations should be considered for trials using combinations of ER, CDK4/6 and FGFR antagonists.

Era+ breast cancer patients often develop resistance to endocrine therapy. Here, the authors show that FGFR1 amplification is a resistance mechanism to CDK4/6 inhibitor and endocrine therapy and that combined treatment with FGFR, CDK4/6, and anti-estrogens is a potential therapeutic strategy in Era+ breast cancer tumors.

ER+ Breast Cancers Resistant to Prolonged Neoadjuvant Letrozole Exhibit an E2F4 Transcriptional Program Sensitive to CDK4/6 Inhibitors

Purpose: This study aimed to identify biomarkers of resistance to endocrine therapy in estrogen receptor-positive (ER⁺) breast cancers treated with prolonged neoadjuvant letrozole.Experimental Design: We performed targeted DNA and RNA sequencing in 68 ER⁺ breast cancers from patients treated with preoperative letrozole (median, 7 months).Results: Twenty-four tumors (35%) exhibited a PEPI score ≥4 and/or recurred after a median of 58 months and were considered endocrine resistant. Integration of the 47 most upregulated genes (log FC > 1, FDR < 0.03) in letrozole-resistant tumors with transcription-binding data showed significant overlap with 20 E2F4-regulated genes (P = 2.56E-15). In patients treated with the CDK4/6 inhibitor palbociclib before surgery, treatment significantly decreased expression of 24 of the 47 most upregulated genes in letrozole-resistant tumors, including 18 of the 20 E2F4 target genes. In long-term estrogen-deprived ER⁺ breast cancer cells, palbociclib also downregulated all 20 E2F4 target genes and P-RB levels, whereas the ER downregulator fulvestrant or paclitaxel only partially suppressed expression of this set of genes and had no effect on P-RB. Finally, an E2F4 activation signature was strongly associated with resistance to aromatase inhibitors in the ACOSOG Z1031B neoadjuvant trial and with an increased risk of relapse in adjuvant-treated ER⁺ tumors in METABRIC.Conclusions: In tumors resistant to prolonged neoadjuvant letrozole, we identified a gene expression signature of E2F4 target activation. CDK4/6 inhibition suppressed E2F4 target gene expression in estrogen-deprived ER⁺ breast cancer cells and in patients' ER⁺ tumors, suggesting a potential benefit of adjuvant CDK4/6 inhibitors in patients with ER⁺ breast cancer who fail to respond to preoperative estrogen deprivation. Clin Cancer Res; 24(11); 2517-29. ©2018 AACR.

Abstract P1-13-08: Extended adjuvant neratinib/fulvestrant blocks ER/HER2 crosstalk and maintains complete responses of ER+/HER2+ tumors following treatment with chemotherapy and anti-HER2 therapy

Background: Neratinib is a potent, irreversible pan-HER tyrosine kinase inhibitor. The phase III trial ExteNET showed improved disease-free survival in patients (pts) with HER2+ breast cancer treated with neratinib vs placebo after trastuzumab-based adjuvant therapy. The benefit from neratinib appeared to be greater in pts with ER+ tumors. Thus, we sought to elucidate mechanisms that may explain the benefit from extended adjuvant therapy with neratinib in pts with ER+/HER2+ breast cancer using a human-in-mouse model that simulates the clinical outcomes seen in ExteNET.

Results: Mice with established ER+/HER2 amplified MDA-361 tumors were treated with trastuzumab (tz) + paclitaxel (pac) for 4 weeks, and then randomized to fulvestrant (fulv) ± neratinib for 4 weeks. All MDA-361 tumors exhibited a prompt and marked reduction in volume after tz/pac treatment; 10 mice achieved a complete response (CR) before receiving 'extended adjuvant' therapy with fulv (n=5) or neratinib/fulv (n=5). A CR was maintained with neratinib/fulv following tz/pac. However, mice treated with fulv alone, relapsed rapidly (p&lt;0.05 at week 8) despite of a complete downregulation of tumor ER levels. In a second experiment, nude mice with established MDA-361 xenografts were treated with pertuzumab/tz/pac for 4 weeks. Following a CR, mice were randomized to neratinib/fulv vs. fulv. Again, mice treated with neratinib/fulv maintained a CR, while mice in the fulv alone arm exhibited tumor progressions within a week. In three ER+/HER2+ cell lines (MDA-361, BT474 and UACC893) but not in ER+/HER– MCF7 cells, treatment with neratinib induced ER reporter transcriptional activity whereas treatment with fulv resulted in an increase in HER2 phosphorylation, suggesting compensatory crosstalk between the ER and HER2 pathways. To further understand the molecular basis of this crosstalk, MDA-361 tumor-bearing mice were treated with either fulv, neratinib or the combination for 7 days, after which tumors were harvested and analyzed using a Nanostring breast cancer ER panel consisting of 196 ER-regulated genes. Compared to vehicle or fulv-treated tumors, tumors treated with neratinib alone and neratinib/fulv showed marked downregulation of cyclin D1 mRNA expression. Similarly, in MDA-361, BT474 and UACC893 cells but not in MCF7 cells, only neratinib/fulv downregulated cyclin D1, P-AKT and P-ERK. Finally, treatment with neratinib/fulv but not fulv alone reduced cyclin D1 transcriptional reporter activity and cyclin D1 protein levels, and induced cell cycle arrest, suggesting double blockade is required to overcome compensatory crosstalk between ER and amplified HER2.

Conclusions: Neratinib/fulv but not fulv alone maintained complete responses of ER+/HER+ tumors following treatment with tz/pac or pertuzumab/tz/pac, reminiscent of the results in ExteNET. Neratinib treatment promoted ER transcriptional activity whereas ER downregulation with fulv was associated with increased HER2 signaling. In ER+/HER2+ breast cancer cells and tumors, neratinib/fulv synergistically inhibited growth, cyclin D1 expression, and AKT and MAPK activation, thus providing a plausible mechanism to explain the results in the ExteNET trial.

Citation Format: Sudhan DR, Schwarz LJ, Guerrero-Zotano AL, Nixon M, Formisano L, Croessmann S, Gonzalez Ericsson PI, Sanders ME, Balko JM, Avogadri-Connors F, Cutler RE, Lalani AS, Bryce R, Auerbach A, Arteaga CL. Extended adjuvant neratinib/fulvestrant blocks ER/HER2 crosstalk and maintains complete responses of ER+/HER2+ tumors following treatment with chemotherapy and anti-HER2 therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-13-08.

Abstract GS6-05: Gain-of-function kinase library screen identifies FGFR1 amplification as a mechanism of resistance to antiestrogens and CDK4/6 inhibitors in ER+ breast cancer

Background: CDK4/6 inhibitors have been approved in combination with endocrine therapy for treatment of ER+ metastatic breast cancer. The goal of this study was to discover mechanisms of resistance to ER antagonists alone and in combination with CDK4/6 inhibitors.

Results: To achieve this goal, we used lentiviral vectors to individually express 559 human kinase open reading frames (ORFs) in ER+ MCF7 human breast cancer cells treated with fulvestrant ± the CDK4/6 inhibitor ribociclib. In MCF7 cells treated with fulvestrant alone or with ribociclib, we identified 15 and 17 kinases associated with resistance, respectively. Ten of these kinases overlapped in both groups. In a secondary screen, MCF7 cells were stably transduced with V5-tagged lentiviruses expressing the positive 'hits' for treatment with fulvestrant/ribociclib. Five of 17 kinases (FGFR1, FRK, HCK, FGR, CRKL) were confirmed to induce resistance to fulvestrant/palbociclib and fulvestrant/ribociblib. Survey of TCGA for copy number alterations and/or expression of these 5 genes showed only FGFR1 to be amplified/overexpressed in ˜15% of ER+ breast cancers. Experiments in vitro showed that ER+/FGFR1-amplified (amp) MDA-134, CAMA-1 and HCC1500 human breast cancer cells and MCF7 cells stably transduced with FGFR1 were relatively resistant to estrogen deprivation, fulvestrant and fulvestrant/palbociclib compared to non-FGFR1 amp MCF7 cells. This resistance was abrogated by treatment with the FGFR tyrosine kinase inhibitor (TKI) lucitanib. Treatment with fulvestrant or palbociclib alone modestly delayed growth of ER+/FGFR1-amp breast cancer patient-derived xenografts (PDX) established in nude mice. However, addition of the FGFR TKI erdafitinib to fulvestrant/palbociclib resulted in marked PDX regression in all mice without associated toxicity and a complete cell cycle arrest measured by Ki67. Treatment of FGFR-amp cells with FGF-2 strongly induced CCND1 (cyclin D1) expression. Downregulation of CCND1 with CCND1 RNAi oligonucleotides restored sensitivity of FGFR1-amp cells to fulvestrant/palbociclib, thus phenocopying the effect of FGFR TKIs. Conversely, overexpression of CCND1 in MCF7 cells induced resistance to estrogen deprivation and to fulvestrant ± palbociclib. Finally, we examined next gen sequencing of cell free tumor DNA by Guardant360 in 34 patients before and after progression on CDK4/6 inhibitor. In 10/34 (29%) post-progression specimens, we detected alterations in the FGFR pathway: FGFR1 amplification (n=7), FGFR1 N546K (n=1), FGFR2 N549K (n=1), and FGFR2 V395D (n=1) activating mutations.

Conclusions: These data suggest aberrant FGFR signaling is a mechanism of resistance to anti-ER therapies ± CDK4/6 inhibitors. We posit overexpression of cyclin D1 induced by both FGFR signaling and ER transcription plays a role in drug resistance. Based on these findings we propose ER+/FGFR1 amplified breast cancers are endocrine resistant and should be candidates for treatment with combinations of ER and FGFR antagonists. Accordingly, we have initiated a phase Ib trial of fulvestrant, palbociclib and erdafitinib in patients with antiestrogen resistant ER+/HER2-negative breast cancer with FGFR1-4 amplification.

Citation Format: Formisano L, Lu Y, Jansen VM, Bauer JA, Hanker A, Gonzalez Ericsson P, Lee K-M, Nixon MJ, Guerrero-Zotano AL, Schwarz LJ, Sanders M, Sudhan D, Dugger TC, Cruz MR, Behdad A, Cristofanilli M, Bardia A, O'Shaughnessy J, Mayer IA, Arteaga CL. Gain-of-function kinase library screen identifies FGFR1 amplification as a mechanism of resistance to antiestrogens and CDK4/6 inhibitors in ER+ breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS6-05.

Association of FGFR1 with ERα Maintains Ligand-Independent ER Transcription and Mediates Resistance to Estrogen Deprivation in ER+ Breast Cancer

Purpose:FGFR1 amplification occurs in approximately 15% of estrogen receptor-positive (ER⁺) human breast cancers. We investigated mechanisms by which FGFR1 amplification confers antiestrogen resistance to ER⁺ breast cancer.Experimental Design: ER⁺ tumors from patients treated with letrozole before surgery were subjected to Ki67 IHC, FGFR1 FISH, and RNA sequencing (RNA-seq). ER⁺/FGFR1-amplified breast cancer cells, and patient-derived xenografts (PDX) were treated with FGFR1 siRNA or the FGFR tyrosine kinase inhibitor lucitanib. Endpoints were cell/xenograft growth, FGFR1/ERα association by coimmunoprecipitation and proximity ligation, ER genomic activity by ChIP sequencing, and gene expression by RT-PCR.Results: ER⁺/FGFR1-amplified tumors in patients treated with letrozole maintained cell proliferation (Ki67). Estrogen deprivation increased total and nuclear FGFR1 and FGF ligands expression in ER⁺/FGFR1-amplified primary tumors and breast cancer cells. In estrogen-free conditions, FGFR1 associated with ERα in tumor cell nuclei and regulated the transcription of ER-dependent genes. This association was inhibited by a kinase-dead FGFR1 mutant and by treatment with lucitanib. ChIP-seq analysis of estrogen-deprived ER⁺/FGFR1-amplified cells showed binding of FGFR1 and ERα to DNA. Treatment with fulvestrant and/or lucitanib reduced FGFR1 and ERα binding to DNA. RNA-seq data from FGFR1-amplified patients' tumors treated with letrozole showed enrichment of estrogen response and E2F target genes. Finally, growth of ER⁺/FGFR1-amplified cells and PDXs was more potently inhibited by fulvestrant and lucitanib combined than each drug alone.Conclusions: These data suggest the ERα pathway remains active in estrogen-deprived ER⁺/FGFR1-amplified breast cancers. Therefore, these tumors are endocrine resistant and should be candidates for treatment with combinations of ER and FGFR antagonists. Clin Cancer Res; 23(20); 6138-50. ©2017 AACR.

Neoadjuvant Trials in ER+ Breast Cancer: A Tool for Acceleration of Drug Development and Discovery

Neoadjuvant therapy trials offer an excellent strategy for drug development and discovery in breast cancer, particularly in triple-negative and HER2-overexpressing subtypes, where pathologic complete response is a good surrogate of long-term patient benefit. For estrogen receptor-positive (ER+) breast cancers, however, use of this strategy has been challenging because of the lack of validated surrogates of long-term efficacy and the overall good prognosis of the majority of patients with this cancer subtype. We review below the clinical benefits of neoadjuvant endocrine therapy for ER+/HER2-negative breast cancer, its use and limitations for drug development, prioritization of adjuvant and metastatic trials, and biomarker discovery.Significance: Neoadjuvant endocrine therapy is an excellent platform for the development of investigational drugs, triaging of novel combinations, biomarker validation, and discovery of mechanisms of drug resistance. This review summarizes the clinical and investigational benefits of this approach, with a focus on how to best integrate predictive biomarkers into novel clinical trial designs. Cancer Discov; 7(6); 561-74. ©2017 AACR.