Activation of the IFN Signaling Pathway is Associated with Resistance to CDK4/6 Inhibitors and Immune Checkpoint Activation in ER-Positive Breast Cancer

PURPOSE

Cyclin-dependent kinase 4 (CDK4) and CDK6 inhibitors (CDK4/6i) are highly effective against estrogen receptor-positive (ER⁺)/HER2^- breast cancer; however, intrinsic and acquired resistance is common. Elucidating the molecular features of sensitivity and resistance to CDK4/6i may lead to identification of predictive biomarkers and novel therapeutic targets, paving the way toward improving patient outcomes.

EXPERIMENTAL DESIGN

Parental breast cancer cells and their endocrine-resistant derivatives (EndoR) were used. Derivatives with acquired resistance to palbociclib (PalboR) were generated from parental and estrogen deprivation-resistant MCF7 and T47D cells. Transcriptomic and proteomic analyses were performed in palbociclib-sensitive and PalboR lines. Gene expression data from CDK4/6i neoadjuvant trials and publicly available datasets were interrogated for correlations of gene signatures and patient outcomes.

RESULTS

Parental and EndoR breast cancer lines showed varying degrees of sensitivity to palbociclib. Transcriptomic analysis of these cell lines identified an association between high IFN signaling and reduced CDK4/6i sensitivity; thus an "IFN-related palbociclib-resistance Signature" (IRPS) was derived. In two neoadjuvant trials of CDK4/6i plus endocrine therapy, IRPS and other IFN-related signatures were highly enriched in patients with tumors exhibiting intrinsic resistance to CDK4/6i. PalboR derivatives displayed dramatic activation of IFN/STAT1 signaling compared with their short-term treated or untreated counterparts. In primary ER⁺/HER2^- tumors, the IRPS score was significantly higher in lumB than lumA subtype and correlated with increased gene expression of immune checkpoints, endocrine resistance, and poor prognosis.

CONCLUSIONS

Aberrant IFN signaling is associated with intrinsic resistance to CDK4/6i. Experimentally, acquired resistance to palbociclib is associated with activation of the IFN pathway, warranting additional studies to clarify its involvement in resistance to CDK4/6i.

Abstract CT256: A prospective, randomized, multicenter, double-blinded, placebo-controlled phase III trial of the HER2/neu peptide GP2 + GM-CSF versus bacteriostatic saline/WFI placebo as adjuvant therapy after any trastuzumab-based therapy in HER2-positive women with operable breast cancer

Background: GP2 is a biologic nine amino acid peptide of the HER2/neu protein delivered in combination with an FDA-approved immunoadjuvant Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF, Sargramostim, Leukine) that stimulates an immune response targeting HER2/neu expressing cancers. In a prospective, randomized, single-blinded, placebo-controlled, multicenter Phase IIb clinical trial completed in 2018, no recurrences were observed in the HER2/neu positive adjuvant setting after median 5 years of follow-up, if the HLA 2+ patient received the 6 primary intradermal injections over the first 6 months (p = 0.0338) in a pre-specified subgroup analysis. Furthermore, the GP2 immunotherapy elicited a potent immune response measured by local skin tests and immunological assays. Of the 138 patients that have been treated with GP2 to date over 4 clinical trials, GP2 treatment was well tolerated and no serious adverse events were observed related to the GP2 immunotherapy. This Phase III trial aims to reproduce the Phase IIb study and will explore the use of GP2 + GM-CSF as adjuvant therapy to prevent the recurrence of breast cancer in HER2/neu positive and HLA 2+ patients, post-surgery and following the first year treatment with any trastuzumab-based therapy.

Trial Design: This Phase III trial is a prospective, randomized, double-blinded, multi-center study. After 1 year of trastuzumab-based therapy or an approved biosimilar, treatment with GP2 + GM-CSF or placebo (Bacteriostatic Saline/WFI ) will be administered intradermally for the 6 primary immunization series over the first 6 months and 5 subsequent boosters over the next 2.5 years for a total of 11 injections over 3 years of treatment. The participant duration of the trial will be 3 years treatment plus 2 years follow-up for a total of 5 years following the first year treatment with trastuzumab-based therapy or approved biosimilar. An interim analysis is planned and patients will be stratified based on prior and current treatments, among other factors.

Eligibility Criteria: The majority of breast cancer patients will be HER2/neu positive and HLA 2+, disease-free, conventionally treated node-positive, post breast tumor removal surgery and following the first year treatment with trastuzumab-based therapy.

Trial Objectives:To determine if GP2 therapy reduces recurrence in HER2/neu positive breast cancer patients.

To monitor the in vitro and in vivo immunologic responses to GP2 therapy and correlate these responses with the clinical outcomes.To monitor for any unexpected adverse events and toxicities related to GP2 therapy.

Accrual: The target enrollment is up to approximately 500 patients.

Contact information: snehal.patel@greenwichlifesciences.com

Funding: This trial is supported by Greenwich LifeSciences.

Citation Format: Snehal S. Patel, David B. McWilliams, Christine T. Fischette, Jaye Thompson, F Joseph Daugherty, C Kent Osborne, Mothaffar F. Rimawi. A prospective, randomized, multicenter, double-blinded, placebo-controlled phase III trial of the HER2/neu peptide GP2 + GM-CSF versus bacteriostatic saline/WFI placebo as adjuvant therapy after any trastuzumab-based therapy in HER2-positive women with operable breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT256.

Abstract 2992: Proteogenomic characterization of triple-negative breast cancer patient-derived xenografts reveals molecular correlates of differential chemotherapy response and potential therapeutic targets to overcome resistance

Background: Chemotherapy is essential for the management of patients with triple-negative breast cancer (TNBC). Identification of biomarkers that may indicate treatment efficacy will be critical to improve patient stratification prior to treatment. To elucidate molecular determinants underlying chemotherapy response, we conducted a proteogenomic study using TNBC patient-derived xenografts (PDXs) treated with chemotherapy.

Approach: 50 TNBC PDXs were treated with either docetaxel or carboplatin. Changes in tumor volume after 4 weeks from baseline were evaluated. Genomic, transcriptomic, and mass-spectrometry-based proteomic profiling were performed on baseline tumors prior to treatment to identify associations with chemotherapy response. Fisher's exact tests were used to test for significant enrichment of mutation and copy number events (p<0.05). Gene Set Enrichment Analysis was performed for pathway analyses.

Results: At the DNA level, genomic aberrations in BRCA2 and BCL2 were enriched in carboplatin-responsive PDXs, while ARID1B aberrations were enriched in docetaxel-responsive PDXs. Gene-drug response correlations supported by both mRNA and protein-based measurements, but not mRNA or protein alone, for both carboplatin and docetaxel treatment in PDXs were associated with prognosis from basal and claudin-low human breast tumors in receipt of any chemotherapy from the METABRIC dataset. These data suggest that the combination of mRNA and protein data increased power to identify genes related to clinical outcome in TNBC. Some of the top genes overexpressed at both mRNA and protein levels in chemoresistant PDXs are targets of approved drugs, many of which have not been evaluated for their ability to augment response to taxane- or platinum-based chemotherapies. These genes are being investigated as therapeutic targets as well as markers of chemotherapy response. At the pathway level, both RNA and protein data associated models resistant to both agents with enhanced oxidative phosphorylation and translation regulation. Protein data further associated resistant models with elevated cytoplasmic ribosomal proteins. In contrast, both RNA and protein data associated tumors sensitive to both agents with genes involved in the E2F-Rb axis and cell cycle progression. Moreover, DNA mismatch repair and mRNA processing pathways were uniquely associated with carboplatin and docetaxel sensitivity, respectively, while amino acid metabolism and MAPK signaling pathways were uniquely associated with carboplatin and docetaxel resistance, respectively.

Conclusion: Taken together, proteogenomic analysis of PDX tumors identifies diverse genes and pathways associated with chemotherapy response and further suggests potential therapeutic opportunities in TNBC.

Citation Format: Jonathan T. Lei, Chen Huang, Ramakrishnan R. Srinivasan, Suhas Vasaikar, Lacey E. Dobrolecki, Alaina N. Lewis, Christina Sallas, Susan G. Hilsenbeck, C Kent Osborne, Mothaffar F. Rimawi, Matthew J. Ellis, Varduhi Petrosyan, Alexander B. Saltzman, Anna Malovannaya, Gerburg Wulf, Daniel C. Kraushaar, Tao Wang, Gloria V. Echeverria, Bing Zhang, Michael T. Lewis. Proteogenomic characterization of triple-negative breast cancer patient-derived xenografts reveals molecular correlates of differential chemotherapy response and potential therapeutic targets to overcome resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2992.

Abstract 1077: Acquired neratinib resistance is associated with acquisition of HER2 and PIK3CA mutations and can be overcome using potent drug combinations in HER2-positive breast cancer models

The role of HER2 and PIK3CA mutations in anti-HER2 resistance is gaining more importance in HER2-positive (+) breast cancer. We recently reported that acquired resistance to lapatinib (Lap)-containing regimens is mediated by HER2 L755S, which could be overcome using the irreversible pan-HER tyrosine kinase inhibitor (TKI) neratinib (Nrb). However, less is known about the role of L755S in resistance to next-generation TKIs, particularly when co-occurring with PIK3CA mutations. HER2+ BT474 cell models with primary or sequential acquired resistance (R) to Lap (LapR) or Nrb (NrbR) and their parental (P) counterparts were profiled for alterations in signaling and gene expression by RPPA, western blot, and RNA-seq. For drug efficacy studies, change in cell growth was assessed using imaging-based high-throughput system. Proteomic profiling revealed partial restoration of HER2 phosphorylation and downstream signaling in the LapR and NrbR derivatives. RNA-seq analysis showed that the LapR and NrbR models, but not P cells, harbor HER2 L755S mutation. Importantly, the NrbR but not LapR cells also co-acquire a PIK3CA pathogenic mutation. GSEA analysis of RNA-seq data showed significant downregulation of G2/M checkpoint in the R derivatives compared to P cells, suggesting genetic instability. In line with the presence of HER2 and PIK3CA activating mutations and HER pathway reactivation in the R models, GSEA revealed an enrichment of mTORC1 and KRAS signaling in the R cells. Furthermore, enrichment of epithelial mesenchymal transition signature and downregulation of apical surface genes was observed in the R models compared to P cells, suggestive of their aggressive phenotype. Interestingly, the LapR cells remained sensitive to Nrb, though a higher dose (IC50: ~50nM) was required compared to P cells (IC50: ~2nM). The LapR and NrbR cells were cross-resistant to the HER2-selective TKI tucatinib, and trastuzumab. We recently showed that the NrbR cells were either partially or completely sensitive to poziotinib or TDM1, respectively, suggesting their therapeutic promise against HER2- and PIK3CA-mutant tumors. Of note, our studies using small molecule agents targeting HER and its downstream pathway to facilitate treatment of CNS lesions suggest that AKT or mutant PIK3CA inhibitors are effective only when combined with either neratinib or poziotinib, but not tucatinib, findings which we are currently expanding to xenograft-derived organoids. Overall, our findings suggest a complex disease evolution upon resistance to neratinib but indicate their potentially continued efficacy in overcoming resistance through drug combinations. Ongoing integrative omics analysis to determine the genomic and mutational complexity and landscape will uncover additional mechanistic insights and guide the discovery of other actionable targets.

Citation Format: Jamunarani Veeraraghavan, Ragini Mistry, Sarmistha Nanda, Sreyashree Bose, Chia Chia Liu, Vidyalakshmi Sethunath, Martin J. Shea, Tamika Mitchell, Meenakshi Anurag, Michael A. Mancini, Irmina Diala, Alshad S. Lalani, Fabio Stossi, C. Kent Osborne, Mothaffar F. Rimawi, Rachel Schiff. Acquired neratinib resistance is associated with acquisition of HER2 and PIK3CA mutations and can be overcome using potent drug combinations in HER2-positive breast cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1077.

Neratinib plus trastuzumab is superior to pertuzumab plus trastuzumab in HER2-positive breast cancer xenograft models

Lapatinib (L) plus trastuzumab (T), with endocrine therapy for estrogen receptor (ER)+ tumors, but without chemotherapy, yielded meaningful response in HER2+ breast cancer (BC) neoadjuvant trials. The irreversible/pan-HER inhibitor neratinib (N) has proven more potent than L. However, the efficacy of N+T in comparison to pertuzumab (P) + T or L + T (without chemotherapy) remains less studied. To address this, mice bearing HER2+ BT474-AZ (ER+) cell and BCM-3963 patient-derived BC xenografts were randomized to vehicle, N, T, P, N+T, or P+T, with simultaneous estrogen deprivation for BT474-AZ. Time to tumor regression/progression and incidence/time to complete response (CR) were determined. Changes in key HER pathway and proliferative markers were assessed by immunohistochemistry and western blot of short-term-treated tumors. In the BT474-AZ model, while all N, P, T, N + T, and P + T treated tumors regressed, N + T-treated tumors regressed faster than P, T, and P + T. Further, N + T was superior to N and T alone in accelerating CR. In the BCM-3963 model, which was refractory to T, P, and P + T, while N and N + T yielded 100% CR, N + T accelerated the CR compared to N. Ki67, phosphorylated (p) AKT, pS6, and pERK levels were largely inhibited by N and N + T, but not by T, P, or P + T. Phosphorylated HER receptor levels were also markedly inhibited by N and N + T, but not by P + T or L + T. Our findings establish the efficacy of combining N with T and support clinical testing to investigate the efficacy of N + T with or without chemotherapy in the neoadjuvant setting for HER2+ BC.

A prospective, randomized, multicenter, double-blinded, placebo-controlled phase III trial of the HER2/neu peptide GP2 + GM-CSF versus bacteriostatic saline/WFI placebo as adjuvant therapy after any trastuzumab-based therapy in HER2-positive women with operable breast cancer

TPS604

Background: GP2 is a biologic nine amino acid peptide of the HER2/ neu protein delivered in combination with an FDA-approved immunoadjuvant Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF, sargramostim, leukine) that stimulates an immune response targeting HER2/neu expressing cancers. In a prospective, randomized, single-blinded, placebo-controlled, multicenter Phase IIb clinical trial completed in 2018, no recurrences were observed in the HER2/neu positive adjuvant setting after median 5 years of follow-up, if the HLA 2+ patient received the 6 primary intradermal injections over the first 6 months ( p = 0.0338) in a pre-specified subgroup analysis. Furthermore, the GP2 immunotherapy elicited a potent immune response measured by local skin tests and immunological assays. Of the 138 patients that have been treated with GP2 to date over 4 clinical trials, GP2 treatment was well tolerated and no serious adverse events were observed related to the GP2 immunotherapy. This Phase III trial aims to reproduce the Phase IIb study and will explore the use of GP2 + GM-CSF as adjuvant therapy to prevent the recurrence of breast cancer in HER2/neu positive and HLA 2+ patients, post-surgery and following the first year treatment with any trastuzumab-based therapy. Methods: This phase III trial is a prospective, randomized, double-blinded, multi-center study. After 1 year of trastuzumab-based therapy or an approved biosimilar, treatment with GP2 + GM-CSF or placebo (bacteriostatic saline/WFI ) will be administered intradermally for the 6 primary immunization series over the first 6 months and 5 subsequent boosters over the next 2.5 years for a total of 11 injections over 3 years of treatment. The participant duration of the trial will be 3 years treatment plus 2 years follow-up for a total of 5 years following enrollment. An interim analysis is planned and patients will be stratified based on prior and current treatments, among other factors. Eligibility Criteria: The majority of breast cancer patients will be HER2/ neu positive and HLA 2+, disease-free, conventionally treated node-positive, post breast tumor removal surgery and following the first year treatment with trastuzumab-based therapy. Trial Objectives: 1. To determine if GP2 therapy reduces recurrence in HER2/ neu positive breast cancer patients. 2. To monitor the in vitro and in vivo immunologic responses to GP2 therapy and correlate these responses with the clinical outcomes. 3. To monitor for any unexpected adverse events and toxicities related to GP2 therapy. Accrual: The target enrollment is up to approximately 500 patients. Contact information: snehal.patel@greenwichlifesciences.com Funding: This trial is supported by Greenwich LifeSciences.

Change in management based on actionable mutations in metastatic breast cancer in an ethnically diverse cohort: Single institution experience

e13067

Background: Recently, next generation sequencing (NGS) has been used with increasing frequency to guide therapy decisions for patients with metastatic solid tumors. NGS is a DNA sequencing technology that detects somatically acquired mutations. If an actionable mutation is identified, it may affect prognosis and guide therapy. At our institution we serve a large proportion of minority and underserved patients and analyzed their NGS results to determine if there was a change in management. Methods: Patients with metastatic breast cancer treated at one of two sites at Baylor College of Medicine who underwent NGS via Tempus between 2018-2020 were included. Tempus provided access to the variant database for these patients. We analyzed the charts of 43 patients who underwent NGS via Tempus on tissue, blood or both. In those patients with clinically actionable mutations, we noted if there was a change in management. Utilizing Redcap, we extracted demographics, sites of metastasis, biomarker activity and site, genomic sequencing, and duration and sequencing of therapies given along with clinical trial information. Results: Of the 43 patients included in this analysis, the mean age was 55 years, 33% were African American, 30% were Hispanic, 21% were white/non-Hispanic, 12% were Asian, 4% were other. Two thirds of patients were treated in the Harris Health System (a safety net hospital with a unique and diverse population) while one third was treated at the Baylor St. Luke’s Medical Center (a private academically affiliated institution). Of the 43 patients, 14 had PIK3CA mutations and 3 had a change in management. 2 patients had microsatellite instability (MSI) and received immunotherapy, and 1 patient had a HER2 mutation and entered a clinical trial with Neratinib. Additionally, 2 patients were incidentally found to have MUTYH germline mutation which is associated with polyposis. Conclusions: With increasing frequency, patients with metastatic malignancy undergo NGS in order to determine if there is an actionable mutation that can guide their next line of treatment. However, this technology could be cost prohibitive for many underserved patients. Our study analyzes a unique and diverse population of patients, many of whom are underserved. We were able conduct this testing in our cohort, study the frequency of somatic mutations and monitor for change in treatment. Of the variants analyzed, PIK3CA mutations are actionable and patients can receive Alpelisib + Fulvestrant- however many did not. There was not a large shift in management based on the incorporation of this DNA sequencing technology which suggests that, unlike the case of other solid tumors, there aren’t yet as many actionable targets for patients with metastatic breast cancer. Shared decision making along with consideration of cost is paramount for these patients as we shift into an era of highly personalized medicine.

Genetic assessment of hereditary breast and ovarian cancer in the Harris Health System: A five-year, single-center experience

10587

Background: Identifying patients with hereditary breast cancer is critical since lifetime breast cancer risk is as high as 85% for those with germline BRCA1/2 mutations and preventive interventions can reduce that risk. However, genetic assessments and counseling are often underutilized among racial/ethnic minority populations. Reducing this genetic testing gap is important since hereditary breast/ovarian cancer syndromes occur among racial/ethnic minorities at least as frequently as non-Ashkenazi Jewish, non-Hispanic White populations. More information on variants in these populations is also needed to better define their genetic susceptibility. Methods: We conducted a retrospective study of adult patients evaluated for genetic testing for hereditary breast/ovarian cancer by a genetic counselor between October 1, 2009 and September 30, 2014 in Harris Health System which is a large, county health system composed mostly of underserved and minority patients. Data from 2015-2019 is currently being extracted and we are reporting the first 5 years of data. Descriptive statistics were used to summarize patient data. Results: 659 patients underwent genetic counseling (10.5% non-Hispanic White, 24.4% Black, 56.9% Hispanic, 5.9% Asian, and 2.3% other). Five patients had Ashkenazi Jewish ancestry. The majority of patients completed testing (87.4%) with 72.7% receiving financial assistance. Among those who did not complete testing, only 12.0% declined, while 66.3% did not meet guideline-based criteria or were recommended to have an affected relative tested. Multigene panel testing was not available until April 2014, so most underwent BRCA sequencing (75.0%) and/or a BRCA large rearrangement test (61.0%). 36.1% received multigene panel testing, 4.6% single site analysis, and 4.4% p53 sequencing. Deleterious mutations occurred in 98 (14.9%) patients: BRCA1 (n = 60), BRCA2 (n = 25), PALB2 (n = 7), ATM (n = 3), and other (n = 3). The distribution of races/ethnicities among those with deleterious mutations was similar to the overall population (7.1% non-Hispanic White, 18.4% Black, 69.4% Hispanic, 3.1% Asian, and 2.0% other). 80.6% of those with deleterious mutations had breast cancer. High rates of bilateral mastectomies were performed in patients with deleterious mutations: BRCA1 60%, BRCA2 55%, PALB2 57.1%, and ATM 33%. Risk-reducing salpingectomy or salpingo-oophorectomy was performed in 56.7% BRCA1, 60% BRCA2, 28.5% PALB2, and 33.3% other mutation carriers. Conclusions: We demonstrate that with the support of financial assistance programs, most patients who receive genetic counseling will accept genetic testing in a socioeconomically underserved, racially/ethnically diverse population. Identification of high-risk patients in these groups is critical since pathogenic variants in this population were common and more than half underwent risk-reducing procedures.

Abstract PS5-29: Insights into the molecular underpinnings of the mevalonate pathway-YAP/TAZ-driven anti-HER2 therapy resistance in HER2+ breast cancer (BC)

Background. We recently reported that the biosynthetic mevalonate (MVA) pathway that produces cholesterol and isoprenoid intermediates, regulates the YAP/TAZ (Y/T) transcriptional co-activators to promote resistance to treatment regimens that effectively inhibit HER2 signaling in HER2+ BC. We further showed that the mTORC1 complex and survivin protein, which contribute to HER2-elicited oncogenic signaling in HER2-driven BC cells, are alternatively activated by the MVA pathway-Y/T axis in anti-HER2 therapy resistant cell models. Of note, other recent reports also showed that increased Y/T activity enables resistant cells to proliferate when other oncogenic pathways (e.g., RAS, EGFR, and FGFR) were effectively inhibited. Here, we sought to further determine the molecular underpinnings of MVA-Y/T axis-driven anti-HER2 therapy resistance to discover novel therapeutic targets and predictive biomarkers for HER2+ BC.Methods. SKBR3 HER2+ BC parental (P) cells and their lapatinib plus trastuzumab (LT) resistant (LTR) derivatives with sustained HER2 inhibition were treated with the MVA pathway inhibitor simvastatin (Sim), with or without the MVA metabolite to rescue Sim’s inhibitory effects. P and LTR cells were also transfected with control or combined Y/T siRNAs. The transcriptomes of all treatment groups were assessed by RNA-seq. Integrative bioinformatics analyses were used to identify differentially expressed (DE) genes and gene sets with functional annotations in LTR vs. P cells upon different interventions.Results. We found that cell cycle and cell proliferation processes were among the top common DE molecular signatures preferentially downregulated (DN) in LTR vs. P cells by both Sim and Y/T knockdown (KD). The top common genes preferentially DN in LTR vs. P cells include the cell cycle regulatory genes CDCA3 and ERCC6L, and the nucleotide metabolism genes TYMS and RRM2. Interestingly, 20% of the genes preferentially DN in LTR vs. P cells by Sim or Y/T KD were predicted to be direct Y/T transcriptional targets based on previously reported ChIP-seq data (PMID: 26258633). Of the Y/T-dependent genes, a significant enrichment of Sim-repressed genes was observed in both P and LTR cells (P = 1.2e-115 and P = 5.5e-138, respectively). The proportion of these enriched genes was higher in LTR vs. P cells (61% vs. 29%). Of note, we found that the global inhibited genes in LTR cells upon Sim or Y/T KD were significantly enriched for the genes DN by short-term LT treatment in P cells (P < 2.2e-16). Likewise, of the genes nominated as putative molecular players in the MVA pathway-Y/T-mediated resistance, BIRC5 (survivin), CDC6, KIF2C, RRM2, and TYMS were recently also reported to be DN in HER2+ tumors treated with neo-adjuvant LT in the PAMELA trial (NCT01973660), a finding that is in line with what we observed in our P cells treated with short-term LT. Conclusions. Upon acquisition of resistance to sustained HER2 inhibition, the MVA pathway-Y/T axis takes over the regulation of pro-proliferative transcriptional programs that are generally downstream of HER2 signaling in treatment-naïve HER2+ BC. The MVA pathway-Y/T axis leads to Y/T-driven transcriptional reprogramming, an emerging mechanism of therapy resistance to anti-HER2 and other targeted therapies that warrants further investigation. The identification of multiple cell cycle related processes as putative targets of the MVA pathway-Y/T axis presents additional targetable vulnerabilities and implies that inhibitors of Y/T and cell cycle checkpoints may help circumvent anti-HER2 resistance in the clinical setting.

Citation Format: Vidyalakshmi Sethunath, Xiaoyong Fu, Pamela L Luna, Sarmistha Nanda, Martin Shea, Jamunarani Veeraraghavan, Carmine De Angelis, Huizhong Hu, Chad Shaw, Mothaffar Rimawi, C. Kent Osborne, Rachel Schiff. Insights into the molecular underpinnings of the mevalonate pathway-YAP/TAZ-driven anti-HER2 therapy resistance in HER2+ breast cancer (BC) [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 PS5-29.

Abstract PD8-03: A FOXA1/FRA1-centered transcriptional axis regulates interferon signaling in high FOXA1-associated endocrine-resistant and metastatic breast cancer

Background: Forkhead box A1 (FOXA1) is an essential pioneer transcription factor (TF) evoking other key TFs-mediated lineage-specific transcriptional programs in several endoderm-derived organs. Aberrant FOXA1 augmentation, via genetic alterations, occurs in 10-15% of ER+ primary and metastatic breast cancer (BC). We have recently shown that high levels of FOXA1 (H-FOXA1) induces enhancer and transcriptional reprogramming to promote endocrine-resistant (EndoR) and pro-metastatic phenotypes. Using the core transcriptional regulatory circuitry (CRC) mapping method, we identified the AP-1 TF JUNB as a key CRC component in BC cells expressing H-FOXA1. In this study, we aimed to further characterize key AP-1 components that play a role in mediating H-FOXA1-induced transcriptional reprogramming in EndoR and metastatic BC. Methods: The ROSE and HOMER tools were used to identify super-enhancers (SEs) and the predicted SE-harboring TFs in MCF7-parental (P) cells with ectopic FOXA1 overexpression (OE), and in MCF7 tamoxifen-resistant (TamR) cells with endogenous FOXA1 amplification and OE. Cell growth, migration, and co-immunoprecipitation assays, were performed using ER+ BC P cells with ectopic FRA1 OE. A FOXA1 core gene signature (GS) was deduced using the BETA.plus algorithm to analyze our previously reported RNA-seq and ChIP-seq data derived from MCF7-P cells with ectopic FOXA1 OE. Additional RNA-seq analyses include MCF7-P cells with ectopic FRA1 OE, FOXA1 OE and simultaneous FRA1 siRNA knockdown (KD), and MCF7-TamR cells with FRA1 KD. We identified a FOXA1/FRA1-centered GS and its clinical relevance was examined using expression profiles of TCGA, METABRIC, and a metastatic biopsy study from cohort of patients with ER+ metastatic BC from Dana-Farber Cancer Institute.Results: We identified FRA1 as one of the top TFs selectively harboring SEs at their gene loci in MCF7-TamR vs. P cells. Both FRA1 and JUNB expression was elevated in TamR vs. P cells and altered concordantly with FOXA1 in P and TamR cells upon FOXA1 OE or KD, respectively. As we identified JUNB as a CRC component with binding sites enriched at the SEs in BC cells expressing H-FOXA1, we hypothesized that FRA1 and JUNB form a feed-forward transcriptional axis amplifying H-FOXA1-induced enhancer reprogramming. We found that JUNB co-immunoprecipitated with FRA1 in MCF7-TamR and MCF7-P cells with ectopic FRA1 OE, suggesting that FRA1 forms a heterodimer with JUNB to exert AP-1 activity. Ectopic FRA1 OE reduced P cell endocrine sensitivity, increased cell migration, and elicited a transcriptome enriched for the FOXA1-induced core GS. In P cells with ectopic FOXA1 OE, we identified a FRA1-dependent GS (n = 27) that is highly enriched for interferon signaling. This FOXA1/FRA1 GS was highly expressed in luminal B vs. A subtype of primary tumors, further elevated in ER+ metastases, where its expression was positively correlated with FRA1 mRNA levels. Notably, this FOXA1/FRA1 GS was not dependent on FRA1 in P cells without FOXA1 OE, suggesting its relevance in the context of H-FOXA1.Conclusions: Here we show that a FOXA1/FRA1-centered transcriptional axis induces an interferon signaling-enriched GS associated with poor outcome of ER+ BC and metastasis. A FRA1/JUNB AP-1 complex may form a feed-forward transcriptional axis to amplify H-FOXA1 signaling. The FOXA1/FRA1-centered GS could be used to stratify patients with ER+ BC who may need additional targeted therapies. Further studies are warranted to elucidate the interplay between FOXA1 and FRA1/JUNB in regulating interferon signaling, which may guide approaches to improve patient outcomes, possibly with immunotherapy using immune checkpoint inhibitors.

Citation Format: Xiaoyong Fu, Resel Pereira, Lanfang Qin, Carmine De Angelis, Sarmistha Nanda, Martin Shea, Agostina Nardone, Rinath Jeselsohn, Ofir Cohen, Nikhil Wagle, Mothaffar Rimawi, C Kent Osborne, Rachel Schiff. A FOXA1/FRA1-centered transcriptional axis regulates interferon signaling in high FOXA1-associated endocrine-resistant and metastatic breast cancer [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 PD8-03.

Abstract PD3-09: HER2 L755S mutation is acquired upon resistance to lapatinib and neratinib and confers cross-resistance to tucatinib and trastuzumab in HER2-positive breast cancer cell models

Background: The role of HER2 mutations in anti-HER2 resistance is gaining more importance in HER2-positive (+) breast cancer (BC). The common HER2 L755S mutation is further enriched in metastatic lesions compared to primary tumors. Despite their mounting significance, effective therapies for HER2-amplified/mutant tumors are lacking. We recently reported that acquired resistance to lapatinib (Lap)-containing regimens is mediated by HER2 L755S, which could be overcome by the irreversible pan-HER tyrosine kinase inhibitor (TKI) neratinib (Nrb). However, less is known about the role of L755S in resistance to new generation TKIs, and the clinically implementable therapeutic strategies to overcome it. Materials and Methods: Our recently developed HER2+ BT474 cell models with acquired resistance to Lap (LapR) or Nrb (NrbR), developed through long-term exposure to increasing doses of the respective drug, and their naïve parental (P) counterparts were used. The resistant derivatives and their cognate P cells were subjected to proteomic (Reverse phase protein array (RPPA) and western blot) and transcriptomic (RNA-seq) characterization. For drug efficacy studies, change in cell growth was assessed using the in situ imaging-based high-throughput IncuCyte system. Results: Proteomic profiling of the resistant models and their P equivalents revealed partial restoration of HER2 phosphorylation and downstream signaling in the LapR and NrbR derivatives. Consistent with activated mTOR signaling observed in the resistant cells, we detected reduced levels of phospho (p)-RAPTOR S792, which is otherwise essential to inhibit the mTOR complex 1 (mTORC1). In addition, p-P38MAPK T180/Y182 levels were reduced. RNA-seq analysis revealed the presence of HER2 L755S mutation in the LapR and NrbR derivatives, but not in P cells, suggesting that the HER signaling reactivation could be attributed to acquisition of HER2 L755S. Interestingly, the NrbR cells co-harbor other pathogenic mutations in key BC related genes, the therapeutic and functional significance of which is being investigated. Importantly, the NrbR derivatives were cross-resistant to Lap and the monoclonal antibody trastuzumab (T). Next, we determined the efficacy of Nrb and the HER2-selective TKI tucatinib (Tuca), both recently approved for metastatic HER2+ BC, either alone or in combination with T. Nrb effectively inhibited the growth of LapR cells, although a higher dose (IC50: ~50nM) was required to inhibit the growth compared to that needed for naïve P cells (~IC50: ~2nM). When combined with T, Nrb was effective in inhibiting the LapR cell growth, though the inhibitory effect may very well be driven entirely by Nrb. On the other hand, the resistant derivatives were cross-resistant to Tuca, both as a single-agent and in combination with T. We then evaluated the efficacy of the antibody drug conjugate TDM1 and the irreversible pan-HER TKI poziotinib. In contrast to the high sensitivity of P cells to both these agents, a spectrum of effect was observed in the NrbR derivatives, with responses ranging from partial growth inhibition by poziotinib to complete response with TDM1, suggesting their therapeutic potential against tumors harboring HER2 mutations. Conclusions: Our findings suggest that HER2 mutations, particularly HER2 L755S, that emerge under the pressure of potent HER2-targeted therapy may confer cross-resistance to other single agent or combination HER2-targeted therapy. This holds important therapeutic implications in light of current treatment landscape. An in-depth molecular characterization of our resistant models to determine the differential gene expression and mutational profile is ongoing to gain additional mechanistic insights and to guide discovery of other actionable targets.

Citation Format: Jamunarani Veeraraghavan, Ragini Mistry, Sarmistha Nanda, Vidyalakshmi Sethunath, Martin Shea, Tamika Mitchell, Meenakshi Anurag, Michael A. Mancini, Fabio Stossi, C. Kent Osborne, Mothaffar F. Rimawi, Rachel Schiff. HER2 L755S mutation is acquired upon resistance to lapatinib and neratinib and confers cross-resistance to tucatinib and trastuzumab in HER2-positive breast cancer cell models [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 PD3-09.

Abstract OT-13-03: A prospective, randomized, multicenter, double-blinded, placebo-controlled phase III trial of the HER2/neupeptide GP2 + GM-CSF versus bacteriostatic saline/WFI placebo as adjuvant therapy after any trastuzumab-based therapy in HER2-positive women with operable breast cancer

Background: GP2 is a biologic nine amino acid peptide of the HER2/neu protein delivered in combination with an FDA-approved immunoadjuvant Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF, Sargramostim, Leukine) that stimulates an immune response targeting HER2/neu expressing cancers. In a prospective, randomized, single-blinded, placebo-controlled, multicenter Phase IIb clinical trial completed in 2018, no recurrences were observed in the HER2/neu positive adjuvant setting after median 5 years of follow-up, if the HLA 2+ patient received the 6 primary intradermal injections over the first 6 months (p = 0.0338) in a pre-specified subgroup analysis. Furthermore, the GP2 immunotherapy elicited a potent immune response measured by local skin tests and immunological assays. Of the 138 patients that have been treated with GP2 to date over 4 clinical trials, GP2 treatment was well tolerated and no serious adverse events were observed related to the GP2 immunotherapy. This Phase III trial aims to reproduce the Phase IIb study and will explore the use of GP2 + GM-CSF as adjuvant therapy to prevent the recurrence of breast cancer in HER2/neu positive and HLA 2+ patients, post-surgery and following the first year treatment with any trastuzumab-based therapy.

Trial Design: This Phase III trial is a prospective, randomized, double-blinded, multi-center study. After 1 year of trastuzumab-based therapy or an approved biosimilar, treatment with GP2 + GM-CSF or placebo (Bacteriostatic Saline/WFI ) will be administered intradermally for the 6 primary immunization series over the first 6 months and 5 subsequent boosters over the next 2.5 years for a total of 11 injections over 3 years of treatment. The participant duration of the trial will be 3 years treatment plus 2 years follow-up for a total of 5 years following the first year treatment with trastuzumab-based therapy or approved biosimilar. An interim analysis is planned and patients will be stratified based on prior and current treatments, among other factors.

Eligibility Criteria: The majority of breast cancer patients will be HER2/neu positive and HLA 2+, disease-free, conventionally treated node-positive, post breast tumor removal surgery and following the first year treatment with trastuzumab-based therapy.

Trial Objectives:To determine if GP2 therapy reduces recurrence in HER2/neu positive breast cancer patients.To monitor the in vitro and in vivo immunologic responses to GP2 therapy and correlate these responses with the clinical outcomes.To monitor for any unexpected adverse events and toxicities related to GP2 therapy.

Accrual: The target enrollment is up to approximately 500 patients.

Contact information: snehal.patel@greenwichlifesciences.com

Funding: This trial is supported by Greenwich LifeSciences.

Citation Format: Snehal S Patel, David B McWilliams, Christine T Fischette, Jaye Thompson, F Joseph Daugherty, C Kent Osborne, Mothaffar F Rimawi. A prospective, randomized, multicenter, double-blinded, placebo-controlled phase III trial of the HER2/neupeptide GP2 + GM-CSF versus bacteriostatic saline/WFI placebo as adjuvant therapy after any trastuzumab-based therapy in HER2-positive women with operable breast cancer [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 OT-13-03.

Association Between 21-Gene Assay Recurrence Score and Locoregional Recurrence Rates in Patients With Node-Positive Breast Cancer

Importance

The 21-gene assay recurrence score is increasingly used to personalize treatment recommendations for systemic therapy in postmenopausal women with estrogen receptor (ER)- or progesterone receptor (PR)-positive, node-positive breast cancer; however, the relevance of the 21-gene assay to radiotherapy decisions remains uncertain.

Objective

To examine the association between recurrence score and locoregional recurrence (LRR) in a postmenopausal patient population treated with adjuvant chemotherapy followed by tamoxifen or tamoxifen alone.

Design, Setting, and Participants

This cohort study was a retrospective analysis of the Southwest Oncology Group S8814, a phase 3 randomized clinical trial of postmenopausal women with ER/PR-positive, node-positive breast cancer treated with tamoxifen alone, chemotherapy followed by tamoxifen, or concurrent tamoxifen and chemotherapy. Patients at North American clinical centers were enrolled from June 1989 to July 1995. Medical records from patients with recurrence score information were reviewed for LRR and radiotherapy use. Primary analysis included 316 patients and excluded 37 who received both mastectomy and radiotherapy, 9 who received breast-conserving surgery without documented radiotherapy, and 5 with unknown surgical type. All analyses were performed from January 22, 2016, to August 9, 2019.

Main Outcomes and Measures

The LRR was defined as a recurrence in the breast; chest wall; or axillary, infraclavicular, supraclavicular, or internal mammary lymph nodes. Time to LRR was tested with log-rank tests and Cox proportional hazards regression for multivariate models.

Results

The final cohort of this study comprised 316 women with a mean (range) age of 60.4 (44-81) years. Median (interquartile range) follow-up for those without LRR was 8.7 (7.0-10.2) years. Seven LRR events (5.8%) among 121 patients with low recurrence score and 27 LRR events (13.8%) among 195 patients with intermediate or high recurrence score occurred. The estimated 10-year cumulative incidence rates were 9.7% for those with a low recurrence score and 16.5% for the group with intermediate or high recurrence score (P = .02). Among patients who had a mastectomy without radiotherapy (n = 252), the differences in the 10-year actuarial LRR rates remained significant: 7.7 % for the low recurrence score group vs 16.8% for the intermediate or high recurrence score group (P = .03). A multivariable model controlling for randomized treatment, number of positive nodes, and surgical type showed that a higher recurrence score was prognostic for LRR (hazard ratio [HR], 2.36; 95% CI, 1.02-5.45; P = .04). In a subset analysis of patients with a mastectomy and 1 to 3 involved nodes who did not receive radiation therapy, the group with a low recurrence score had a 1.5% rate of LRR, whereas the group with an intermediate or high recurrence score had a 11.1% LRR (P = .051).

Conclusions and Relevance

This study found that higher recurrence scores were associated with increased LRR after adjustment for treatment, type of surgical procedure, and number of positive nodes. This finding suggests that the recurrence score may be used, along with accepted clinical variables, to assess the risk of LRR during radiotherapy decision-making.

Abstract 1911: HER2 L755S mutation is associated with acquired resistance to lapatinib and neratinib, and confers cross-resistance to tucatinib in HER2-positive breast cancer models

Despite the availability of potent HER-targeted agents, de novo and acquired resistance is common and continues to pose a major challenge, especially in the advanced setting. Amassing evidence point to the importance of HER2 mutations, including the most common HER2 L755S mutation, in mediating anti-HER2 resistance. The HER2 L755S mutation, in particular, is observed to be enriched in metastatic lesions compared to primary breast tumors. The need for effective therapy to treat tumors harboring HER2 mutations prevails. We have previously reported that acquired resistance to lapatinib (L)-containing treatments, mediated by HER2 L755S, could be overcome by the recently FDA-approved irreversible pan-HER tyrosine kinase inhibitor (TKI) neratinib (N). While N has shown great promise in patients with HER2-mutant metastatic breast cancer, its efficacy is somewhat limited. More recently, tucatinib, a HER2-selective TKI, has been shown to be effective in HER2-positive (+) brain metastases. Its potency in the context of HER2 mutations, however, has not yet been fully studied. In this study, we used the HER2+ BT474-L resistant (LR) cells, harboring endogenous HER2 L755S mutation, and parental (P) cells to first determine whether tucatinib may be effective in overcoming resistance mediated by HER2 mutations. Our results showed that while N effectively inhibited the growth of LR cells, although at a dose higher than that needed to inhibit the growth of naïve P cells, tucatinib failed to inhibit the growth of LR cells. Our results suggest that HER2 L755S mutation may confer cross-resistance to tucatinib. To further study mechanisms of resistance to 2nd generation anti-HER2 agents, we recently developed cell models with acquired resistance to N, through long-term exposure of the BT474-P and LR cells to increasing doses of N. These cells were profiled by reverse phase protein array (RPPA) and western blot analysis, which revealed restoration of HER2 phosphorylation in the NR derivatives, despite being cultured in the continuous presence of N. Interestingly, RNA-seq analysis revealed the presence of HER2 L755S mutation in all the NR derivatives, but not in the P cells, suggesting that the reactivated HER2 signaling observed in NR cells could be attributed to the emergence/acquisition of HER2 L755S mutation. Furthermore, while the P cells were highly sensitive to tucatinib, L, and the monoclonal antibody trastuzumab (T), the NR derivatives were totally resistant to these agents, suggesting that N resistance may also confer cross-resistance to tucatinib, L, and T. Additional molecular characterization to examine differential gene expression and mutational profile of the resistant derivatives, as well as testing of novel anti-HER2 regimens and drug combinations targeting downstream mediators to overcome resistance, both in vitro and in vivo, is ongoing.

Citation Format: Jamunarani Veeraraghavan, Ragini Mistry, Sarmistha Nanda, Vidyalakshmi Sethunath, Martin Shea, Tamika Mitchell, Meenakshi Anurag, Michael A. Mancini, Fabio Stossi, C. Kent Osborne, Mothaffar F. Rimawi, Rachel Schiff. HER2 L755S mutation is associated with acquired resistance to lapatinib and neratinib, and confers cross-resistance to tucatinib in HER2-positive breast cancer models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1911.

A multiparameter classifier to predict response to lapatinib plus trastuzumab (LT) without chemotherapy in HER2+ breast cancer (BC)

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Background: Several trials have shown 25-30% pathologic complete response (pCR) rates in patients with HER2+ BC treated with LT therapy (+ endocrine therapy if ER+), but no chemotherapy (CTX). We hypothesize that a multiparameter classifier, comprised of HER2 gene and protein levels, intratumor heterogeneity (ITH), HER2-enriched (E) subtype, and PIK3CA mutation status can identify patients whose tumors are “addicted” to HER2 signaling and are likely to achieve pCR from a CTX-sparing de-escalation strategy. Methods: Baseline specimens from 2 trials (TBCRC023 [NCT00999804] and PAMELA [NCT01973660]) of neoadjuvant CTX-sparing LT (+ endocrine therapy if ER+) in HER2+ BC were used. HER2 protein and ITH (scored for % 3+ by IHC), and gene amplification (HER2:CEP17 ratio and copy number (CN) by CISH) were measured on the same slide by the dual gene protein assay (GPA). HER2-E and PIK3CA mutation status were assessed by research-based PAM50 and MSK-IMPACT platforms, respectively. A decision tree algorithm was used to determine the GPA cutoffs and to construct the classifier of response (by pCR) in TBCRC023, which was then validated in PAMELA. Results: Of the evaluable patients from TBCRC023 (N = 130) and PAMELA (N = 151), GPA data were available for 121 and 94 cases, respectively. Both cohorts exhibited similar distributions for HER2 ratio, CN, and % 3+, and a strong correlation between HER2 ratio and CN (R > 0.92). In TBCRC023, 73 cases had data from GPA, PAM50, and IMPACT, of which 15 had pCR. Recursive partitioning identified cutoffs of HER2 ratio > 4.6 and % 3+ > 97.5% in both the GPA data cohort (N = 121) and complete data cohort (N = 73). With PAM50 and IMPACT data, the model added HER2-E and PIK3CA wild-type (wt). For practical reasons, the classifier was locked as HER2 ratio ≥ 4.5 AND % 3+ ≥ 90% AND PIK3CA-wt AND HER2-E, which yielded a PPV of 55% and NPV of 94%. Validation in PAMELA using 45 cases with data for all 3 assays yielded PPV of 44% and NPV of 82%. 29 TBCRC023 cases without IMPACT data could be predicted to be non-pCR, of which 26 were correct (NPV = 89%). In PAMELA, 66 additional cases could be predicted to be non-pCR, of which 54 were correct (NPV = 81%). Conclusions: We have constructed a multiparameter classifier that can predict pCR with targeted therapy alone that compare to pCR rates of CTX + dual anti-HER2 in unselected patients. Prospective validation in a clinical trial is warranted. [Table: see text]

Towards personalized treatment for early stage HER2-positive breast cancer

Advances in HER2-targeted therapies have improved the survival of patients with HER2-positive breast cancer. The standard-of-care treatment for localized disease has been chemotherapy and 1 year of adjuvant HER2-targeted therapy, typically with the anti-HER2 antibody trastuzumab. Despite the effectiveness of this treatment, disease relapse occurs in a subset of patients; thus, focus has been placed on escalating treatment by either combining different HER2-targeted agents or extending the duration of HER2-targeted therapy. Indeed, dual HER2-targeted therapies and extended-duration anti-HER2 therapy, as well as adjuvant therapy with the anti-HER2 antibody-drug conjugate T-DM1, have all been approved for clinical use. Emerging evidence suggests, however, that some patients do not derive sufficient benefit from these additional therapies to offset the associated toxicities and/or costs. Similarly, the universal use of chemotherapy might not benefit all patients, and treatment de-escalation through omission of chemotherapy has shown promise in clinical trials and is currently being explored further. The future of precision medicine should therefore involve tailoring of therapy based on the genetics and biology of each tumour and the clinical characteristics of each patient. Predictive biomarkers that enable the identification of patients who will benefit from either escalated or de-escalated treatment will be crucial to this approach. In this Review, we summarize the available HER2-targeted agents and associated mechanisms of resistance, and describe the current therapeutic landscape of early stage HER2-positive breast cancer, focusing on strategies for treatment escalation or de-escalation.

Abstract PD7-01: Identification of a high FOXA1-induced pro-metastatic enhancer signature in endocrine-resistant and metastatic breast cancer

Background: Forkhead box A1 (FOXA1) is a pioneer transcription factor (TF) for chromatin binding and function of other lineage-specific TFs essential for the normal development of endoderm-derived organs. Aberrant FOXA1 signaling, due to genetic amplification or mutations and/or overexpression, has been frequently detected in metastatic tumors of the breast, prostate, pancreas, bladder and thyroid, suggesting a general role and mechanism of FOXA1-driven tumorigenesis and disease progression. We recently reported that high levels of FOXA1 (H-FOXA1) promote endocrine-resistant (EndoR) and metastatic phenotypes in estrogen receptor (ER)+ breast cancer (BC) cells. Here we sought to uncover the role and the mechanisms by which H-FOXA1 promotes EndoR metastatic BC.

Methods: Genomic sequencing data from an ER+/HER2- metastatic BC cohort (n=781, MSK-IMPACT; cBioportal) were used to compare mutations and copy number alterations of FOXA1 and ESR1. Genome-wide FOXA1-chromatin binding (cistrome) and distribution of the enhancer marks histone H3 lysine 27 acetylation (H3K27ac) and lysine 4 mono-methylation (H3K4me1) were analyzed by ChIP-seq in MCF7 cell model with inducible H-FOXA1. FOXA1 cistrome, H3K27ac distribution, and transcriptome of a FOXA1-overexpressing pancreatic ductal adenocarcinoma cell model (PDA-hT2) were obtained from NCBI GEO (GSE99311). The core regulatory circuitry (CRC) Mapper was used to identify auto-regulatory loop of TFs induced by H-FOXA1. Gene Ontology was used for gene set functional annotation. FOXA1-associated enhancers of ER+ metastatic vs. primary tumors were analyzed using the H3K27ac epigenome data (European Nucleotide Archive, PRJEB22757).

Results: The FOXA1 and ESR1 genetic amplification and mutations displayed a largely mutually exclusive pattern in ER+/HER2- metastatic BC, suggesting a role of hyperactive FOXA1 signaling in promoting EndoR and metastatic BC distinct from that of the ESR1 mutations. FOXA1 overexpression in BC cells resulted in increased FOXA1 DNA binding and the establishment of more regions with gained H3K27ac and/or H3K4me1, suggesting a more accessible and active chromatin state. H-FOXA1-induced upregulated genes were enriched for the gained H3K27ac or H3K4me1, especially for the enhancers with both marks. An enhancer signature with gained and overlapped H3K27ac and H3K4me1 predicts genes enriched for proliferation, anti-apoptosis and developmental signaling. Upregulated genes induced by H-FOXA1 with gained enhancers were further enriched for pro-metastatic processes, sharing the same characteristics of cellular morphogenesis during embryonic development. Similar results were obtained using integrated data from the PDA-hT2 cell model, sharing enriched pro-metastatic genes predicted by the H-FOXA1-induced enhancer signature. A CRC auto-regulatory TF loop, comprising components of the AP-1 and SMAD families, was predicted to amplify the impact of this enhancer signature on activation of the pro-metastatic transcriptional programs. In line with our preclinical findings, epigenetic changes of active enhancers in ER+ metastatic vs. primary BC were associated with the H-FOXA1-induced enhancer signature.

Conclusions: Our study suggests that in ER+ metastatic BC, genetic alterations of FOXA1 leading to hyperactive FOXA1 signaling involves epigenetic evolution to promote a pro-metastatic enhancer signature. This genome-wide H-FOXA1-induced enhancer signature supports the role of H-FOXA1 in unleashing oncogenic activities of lineage-specific TFs in many types of metastatic tumors. Developing therapeutics targeting FOXA1 itself or key components of the H-FOXA1-induced CRC is warranted to treat or prevent EndoR and metastatic BC effectively via targeting the entire aberrant transcriptional programs.

Citation Format: Xiaoyong Fu, Resel Pereira, Carmine De Angelis, Sarmistha Nanda, Lanfang Qin, Jamunarani Veeraraghavan, Pier Selenica, Britta Weigelt, Jorge S Reis-Filho, Agostina Nardone, Rinath Jeselsohn, Myles Brown, Mothaffar F Rimawi, C Kent Osborne, Rachel Schiff. Identification of a high FOXA1-induced pro-metastatic enhancer signature in endocrine-resistant and metastatic breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD7-01.

Abstract P5-02-01: Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study

Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but has unacceptable between-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) Assess inter-laboratory reproducibility of automated Ki67 measurement among 17 participating labs and compare those with standardized pathologist-based visual scoring. (ii) Investigate the comparability of Ki67 measurement across corresponding core biopsy and whole section cases. (iii) Test prognostic potential of the built Ki67 scoring algorithms on an independent cohort.

Methods: Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding whole tumor sections from 30 ER+ breast cancer cases were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and stained for Ki67 using the Mib-1 antibody. The QuPath (open-source software) DIA platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed in our previous study (Acs et al, Lab Invest 2019). A detailed guideline for building an automated Ki67 scoring algorithm was sent to the participating labs. Visual scoring of average Ki67 expression was performed by pathologists according to published standardized methods (Leung et al, NPJ Br Cancer 2016; Leung et al, Histopath 2019). Locked down DIA Ki67 scoring algorithms were applied to a validation cohort: 222 breast cancer cases from the Karolinska University Hospital in whole section format. Sufficient reproducibility to declare analytical validity was defined as an Intra Class Correlation (ICC) with lower limit of 95% credible interval (CI) >0.80. Markov Chain Monte Carlo routines for generalized linear mixed models were used to estimate ICCs and calculate corresponding CIs.

Results: The same-section ICC was 0.902 (CI: 0.852-0.949) across 17 labs using calibrated DIA platform on core biopsy slides and 0.845 (CI: 0.778-0.912) on whole sections. The different-section ICC across the 17 labs was 0.873 (CI: 0.806-0.932) scoring on core biopsy slides and 0.777 (CI: 0.670-0.874) on whole sections. The pathologist-based visual Ki67 scoring showed ICC of 0.860 for all comparisons, respectively (CI: 0.795-0.927). Similar to what was observed for visual Ki67 scoring, the DIA scores are higher for core biopsy slides compared to paired whole sections (p≤0.001; median difference: 5.31%; IQR: 11.50%). Ki67 scores of all locked down DIA algorithms correlates significantly (p≤0.023) with outcome on the validation cohort (observed hazard ratios range: 2.518-2.922).

Conclusions: Automated Ki67 evaluation using a calibrated, open-source DIA platform (QuPath) met the pre-specified criterion of success on core biopsies but not on whole sections in the multi-institutional setting. The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation) and intratumor heterogeneity. We found that different algorithms built according to calibrated DIA methods had similar prognostic potential. Assessment of clinical utility is planned.

Citation Format: Balazs Acs, Samuel C.Y. Leung, Kelley M. Kidwell, Indu Arun, Renaldas Augulis, Sunil S. Badve, Yalai Bai, Anita L. Bane, John M.S. Bartlett, Jane Bayani, Gilbert Bigras, Annika Blank, Signe Borgquist, Henk Buikema, Martin C. Chang, Robin L. Dietz, Andrew Dodson, Anna Ehinger, Susan Fineberg, Cornelia M. Focke, Dongxia Gao, Allen M. Gown, Carolina Gutierrez, Johan Hartman, Judith C. Hugh, Zuzana Kos, Anne-Vibeke Lænkholm, Arvydas Laurinavicius, Richard M. Levenson, Rustin Mahboubi-Ardakani, Mauro G. Mastropasqua, Takuya Moriya, Sharon Nofech-Mozes, C. Kent Osborne, Liron Pantanowitz, Frédérique M. Penault-Llorca, Tammy Piper, Mary Anne Quintayo, Tilman T. Rau, Stefan Reinhard, Stephanie Robertson, Takashi Sakatani, Roberto Salgado, Melanie Spears, Jane Starczynski, Tomoharu Sugie, Bert van der Vegt, Giuseppe Viale, Shakeel Virk, Lila A. Zabaglo, Daniel F. Hayes, Mitch Dowsett, Torsten O. Nielsen, David L. Rimm, International Ki67 in Breast Cancer Working Group, BIG-NABCG. Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-02-01.

Abstract P6-04-02: Integrative cistromic/transcriptomic profiling identifies a high FOXA1/ER-activated pro-metastatic secretome in endocrine-resistant breast cancer

Background: The estrogen receptor (ER) plays an evolving role in conferring endocrine resistance (EndoR) via altering chromatin binding and transcriptional reprogramming in ER+ metastatic breast cancer (BC). We have recently reported that high levels of FOXA1 (H-FOXA1), a pioneer factor for ER-chromatin binding and function, promote EndoR and metastatic phenotypes in ER+ BC cells. Here we further investigated the interplay between FOXA1 and ER by cistromic and transcriptomic profiling of ER+ BC cells expressing H-FOXA1 and a consequential pro-metastatic secretome associated with poor outcome of ER+ BC.

Methods: FOXA1 and ER cistromes were analyzed by ChIP-seq in MCF7 cells expressing ectopic H-FOXA1 or treated with estrogen or the growth factor EGF. Transcriptomes of ER+ BC cells (MCF7, ZR75-1, and T47D) expressing ectopic H-FOXA1 and our established EndoR cell models (MCF7, ZR75-1, T47D, and 600MPE) were analyzed by RNA-seq. A core gene signature (CGS) and secretome gene sets induced by H-FOXA1 were identified by integrative analyses of cistromic/transcriptomic data and public secretory protein databases. Multivariant proportional hazards modeling and Kaplan-Meier log-rank test were performed to assess prognostic significance of the secretome gene sets using the METABRIC and KMplotter datasets. A transcriptomic dataset of ER+ primary and metastatic BC (The Metastatic Breast Cancer Project) was used to determine secretome expression changes in metastatic vs. primary tumors and the correlation with FOXA1 levels. A tamoxifen-resistant ER+ metastatic mouse model we previously established was used to determine pro-metastatic secretome gene expression.

Results: Ectopic H-FOXA1 expanded and reprogramed the FOXA1 cistrome in ER+ BC cells and induced a CGS shared by multiple H-FOXA1-expressing cancer cell models, including prostate and pancreatic cancer cells. H-FOXA1 redirected an estrogen-independent ER cistrome in ER+ BC cells, but had no effect on the FOXA1 cistrome under short-term treatment with estrogen or EGF. Upregulated CGS was enriched for secretome-encoding genes with variance in ER dependency across multiple EndoR cell models. The H-FOXA1/ER-activated (n=10), but not the ER-repressed or -independent secretome, predicted poor disease-free survival in ER+ BC treated with endocrine therapy (METABRIC, n=1,103). Multivariate analyses further identified each of four secretome genes (ST6GALNAC2, SERPINI1, S100P, and CD55) significantly contributing to overall survival of ER+ BC. The prognostic significance of this secretome signature was also observed in relapse-free survival and distant metastasis-free survival of ER+, but not ER- BC, using the KMplotter dataset. The expression levels of the identified secretome were significantly increased in ER+ metastatic (n=147) vs. primary (n=48) tumors (including 31 pairs) and positively correlated with FOXA1 mRNA levels in metastases. Notably, there was no association between the H-FOXA1/ER-regulated pro-metastatic secretome and the ESR1 mutations. Finally, H-FOXA1-induced EndoR metastatic xenograft tumors were associated with elevated secretome gene expression.

Conclusions: We identified an H-FOXA1/ER-activated pro-metastatic secretome via integrative analyses of the FOXA1/ER cistromes and transcriptomes of our preclinical models expressing H-FOXA1. This secretome signature predicts poor outcome of ER+ BC treated with endocrine therapy and has no correlation with the ESR1 mutations in ER+ metastatic BC. The increased expression of these secretome genes in ER+ metastatic vs. primary tumors suggests continuing interplay of FOXA1 and ER in promoting pro-metastatic transcriptional programs during ER+ disease progression, which warrants further investigation.

Citation Format: Xiaoyong Fu, Resel Pereira, Carmine De Angelis, Sarmistha Nanda, Lanfang Qin, Martin J Shea, Tamika Mitchell, Jamunarani Veeraraghavan, Vidyalakshmi Sethunath, Carolina Gutierrez, Balázs Győrffy, Ofir Cohen, Nikhil Wagle, Agostina Nardone, Rinath Jeselsohn, Myles Brown, Mothaffar F Rimawi, C Kent Osborne, Rachel Schiff. Integrative cistromic/transcriptomic profiling identifies a high FOXA1/ER-activated pro-metastatic secretome in endocrine-resistant breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-04-02.

Abstract P3-06-12: Autophagy-mediated survival mechanism to c-Src inhibitor therapy in triple negative breast cancer

c-Src (Src) is a proto-oncogene involved in signaling that culminates in the control of multiple biological functions. Src is also one of the most frequently upregulated pathways in triple negative breast cancer (TNBC). Dysregulation of Src has been detected in TNBC and is strongly associated with tumor metastasis and poor prognosis. However, even after promising preclinical studies, Src inhibitors did not show major clinical advantage in unselected TNBC populations. We have previously published that metastatic TNBC has high energy-dependency to mitochondrial fatty acid beta-oxidation (FAO) and FAO activates Src by inducing autophosphorylation at Y419. However, our recent analysis suggests that as observed with the Src inhibitors, TNBC tumors treated with FAO inhibitors also develop drug-resistance and exhibit continuous tumor growth. Evaluation of their drug resistance mechanism revealed that while short-term inhibition of FAO or Src induces autophagic and apoptotic cell deaths, long-term inhibition results in autophagy-mediated drug resistance and survival. Further analyses suggest that FAO/Src inhibitors promote interferon regulatory factor 1 (IRF1) expression and activate mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway via the induction of cellular reactive oxygen species (ROS) in TNBC. Activated MEK/ERK then suppresses IRF1 expression and induces survival pathways for drug resistance and tumor survival. Validation of in vitro findings using in vivo TNBC models confirmed that combination of FAO/Src inhibitors with MEK/ERK inhibitor or ROS scavenger provide significant benefit to overcome the therapeutic resistance of TNBC. These findings open-up new therapeutic opportunities to manage TNBC patients with currently non-targetable metastatic tumors.

Citation Format: Kwanghwa Jung, Junhyoung Park, Tirupataiah Sirupangi, Dongya Jia, Nishant Gandhi, Shivanand Pudakalakatti, Jessica Elswood, Weston Porter, Nagireddy Putluri, Xiang H.-F Zhang, Xi Chen, Pratip K. Bhattacharya, Chad J. Creighton, Michael T. Lewis, Jeffrey M. Rosen, Lee-Jun C. Wong, Gokul M. Das, C. Kent Osborne, Mothaffar F Rimawi, Benny Abraham Kaipparettu. Autophagy-mediated survival mechanism to c-Src inhibitor therapy in triple negative breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-06-12.

HER2-enriched subtype and pathological complete response in HER2-positive breast cancer: A systematic review and meta-analysis

BACKGROUND

HER2-positive (HER2+) breast cancer (BC) comprises all the four PAM50 molecular subtypes. Among these, the HER2-Enriched (HER2-E) appear to be associated with higher pathological complete response (pCR) rates following anti-HER2-based regimens. Here, we present a meta-analysis to validate the association of the HER2-E subtype with pCR following anti-HER2-based neoadjuvant treatments with or without chemotherapy (CT).

METHODS

A systematic literature search was performed in February 2019. The primary objective was to compare the association between HER2-E subtype (versus others) and pCR. Selected secondary objectives were to compare the association between 1) HER2-E subtype and pCR in CT-free studies, 2) HER2-E subtype within hormone receptor (HR)-negative and HR+ disease and 3) HR-negative disease (versus HR+) and pCR in all patients and within HER2-E subtype. A random-effect model was applied. The Higgins' I² was used to quantify heterogeneity.

RESULTS

Sixteen studies were included, 5 of which tested CT-free regimens. HER2-E subtype was significantly associated with pCR in all patients (odds ratio [OR] = 3.50, p < 0.001, I² = 33%), in HR+ (OR = 3.61, p < 0.001, I² = 1%) and HR-negative tumors (OR = 2.28, p = 0.01, I² = 47%). In CT-free studies, HER2-E subtype was associated with pCR in all patients (OR = 5.52, p < 0.001, I² = 0%) and in HR + disease (OR = 4.08, p = 0.001, I² = 0%). HR-negative status was significantly associated with pCR compared to HR + status in all patients (OR = 2.41, p < 0.001, I² = 30%) and within the HER2-E subtype (OR = 1.76, p < 0.001, I² = 0%).

CONCLUSIONS

The HER2-E biomarker identifies patients with a higher likelihood of achieving a pCR following neoadjuvant anti-HER2-based therapy beyond HR status and CT use. Future trial designs to escalate or de-escalate systemic therapy in HER2+ disease should consider this genomic biomarker.

HER2-Enriched Subtype and ERBB2 Expression in HER2-Positive Breast Cancer Treated with Dual HER2 Blockade

BACKGROUND

Identification of HER2-positive breast cancers with high anti-HER2 sensitivity could help de-escalate chemotherapy. Here, we tested a clinically applicable RNA-based assay that combines ERBB2 and the HER2-enriched (HER2-E) intrinsic subtype in HER2-positive disease treated with dual HER2-blockade without chemotherapy.

METHODS

A research-based PAM50 assay was applied in 422 HER2-positive tumors from five II-III clinical trials (SOLTI-PAMELA, TBCRC023, TBCRC006, PER-ELISA, EGF104090). In SOLTI-PAMELA, TBCRC023, TBCRC006, and PER-ELISA, all patients had early disease and were treated with neoadjuvant lapatinib or pertuzumab plus trastuzumab for 12-24 weeks. Primary outcome was pathological complete response (pCR). In EGF104900, 296 women with advanced disease were randomized to receive either lapatinib alone or lapatinib plus trastuzumab. Progression-free survival (PFS), overall response rate (ORR), and overall survival (OS) were evaluated.

RESULTS

A total of 305 patients with early and 117 patients with advanced HER2-positive disease were analyzed. In early disease, HER2-E represented 83.8% and 44.7% of ERBB2-high and ERBB2-low tumors, respectively. Following lapatinib and trastuzumab, the HER2-E and ERBB2 (HER2-E/ERBB2)-high group showed a higher pCR rate compared to the rest (44.5%, 95% confidence interval [CI] = 35.4% to 53.9% vs 11.6%, 95% CI = 6.9% to 18.0%; adjusted odds ratio [OR] = 6.05, 95% CI = 3.10 to 11.80, P < .001). Similar findings were observed with neoadjuvant trastuzumab and pertuzumab (pCR rate of 66.7% in HER2-E/ERBB2-high, 95% CI = 22.3% to 95.7% vs 14.7% in others, 95% CI = 4.9% to 31.1%; adjusted OR = 11.60, 95% CI = 1.66 to 81.10, P = .01). In the advanced setting, the HER2-E/ERBB2-high group was independently associated with longer PFS (hazard ratio [HR] = 0.52, 95% CI = 0.35 to 0.79, P < .001); higher ORR (16.3%, 95% CI = 8.9% to 26.2% vs 3.7%, 95% CI = 0.8% to 10.3%, P = .02); and longer OS (HR = 0.66, 95% CI = 0.44 to 0.97, P = .01).

CONCLUSIONS

Combining HER2-E subtype and ERBB2 mRNA into a single assay identifies tumors with high responsiveness to HER2-targeted therapy. This biomarker could help de-escalate chemotherapy in approximately 40% of patients with HER2-positive breast cancer.

TBCRC023: A Randomized Phase II Neoadjuvant Trial of Lapatinib Plus Trastuzumab Without Chemotherapy for 12 versus 24 Weeks in Patients with HER2-Positive Breast Cancer

PURPOSE

Prior neoadjuvant trials with 12 weeks of dual anti-HER2 therapy without chemotherapy demonstrated a meaningful pathologic complete response (pCR) in patients with HER2-positive breast cancer. In this trial, we sought to determine whether longer treatment would increase the rate of pCR.

PATIENTS AND METHODS

TBCRC023 (NCT00999804) is a randomized phase II trial combining a Simon phase II design in the experimental arm with a pick-the-winner design, not powered for direct comparison. Women with HER2-positive breast tumors measuring ≥2 cm (median = 5 cm) were randomized in a 1:2 ratio to 12 versus 24 weeks of lapatinib and trastuzumab. Letrozole (along with ovarian suppression if premenopausal) was administered in patients whose tumors were also estrogen receptor (ER) positive. All evaluable patients were assessed for in-breast pCR.

RESULTS

Ninety-seven patients were enrolled (33 in 12-week arm and 64 in 24-week arm), of whom 94 were evaluable. Median age was 51 years, and 55% were postmenopausal. Median tumor size was 5 cm, and 65% were ER-positive. The rate of pCR in the 24-week arm was 28% and numerically superior to the 12-week arm (12%). This was driven by increased pCR in the ER-positive subgroup (33% vs. 9%). Study treatment was well tolerated, with grade 1-2 diarrhea and acneiform rash being the most common toxicities.

CONCLUSIONS

Treatment with dual anti-HER2 therapy for 24 weeks led to a numeric increase in pCR rate in women with HER2-positive breast cancer, without using chemotherapy. If validated, this approach may help identify patients who may benefit from deescalation of therapy.

Targeting the Mevalonate Pathway to Overcome Acquired Anti-HER2 Treatment Resistance in Breast Cancer

Despite effective strategies, resistance in HER2⁺ breast cancer remains a challenge. While the mevalonate pathway (MVA) is suggested to promote cell growth and survival, including in HER2⁺ models, its potential role in resistance to HER2-targeted therapy is unknown. Parental HER2⁺ breast cancer cells and their lapatinib-resistant and lapatinib + trastuzumab-resistant derivatives were used for this study. MVA activity was found to be increased in lapatinib-resistant and lapatinib + trastuzumab-resistant cells. Specific blockade of this pathway with lipophilic but not hydrophilic statins and with the N-bisphosphonate zoledronic acid led to apoptosis and substantial growth inhibition of R cells. Inhibition was rescued by mevalonate or the intermediate metabolites farnesyl pyrophosphate or geranylgeranyl pyrophosphate, but not cholesterol. Activated Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ) and mTORC1 signaling, and their downstream target gene product Survivin, were inhibited by MVA blockade, especially in the lapatinib-resistant/lapatinib + trastuzumab-resistant models. Overexpression of constitutively active YAP rescued Survivin and phosphorylated-S6 levels, despite blockade of the MVA. These results suggest that the MVA provides alternative signaling leading to cell survival and resistance by activating YAP/TAZ-mTORC1-Survivin signaling when HER2 is blocked, suggesting novel therapeutic targets. MVA inhibitors including lipophilic statins and N-bisphosphonates may circumvent resistance to anti-HER2 therapy warranting further clinical investigation. IMPLICATIONS: The MVA was found to constitute an escape mechanism of survival and growth in HER2⁺ breast cancer models resistant to anti-HER2 therapies. MVA inhibitors such as simvastatin and zoledronic acid are potential therapeutic agents to resensitize the tumors that depend on the MVA to progress on anti-HER2 therapies.