ZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer

Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming, which allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified Zinc Finger Protein 397 (ZNF397) as a bona fide coactivator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a Ten-Eleven Translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that a TET2 inhibitor can eliminate the resistance to AR targeted therapies in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate cancer acquires lineage plasticity via epigenetic rewiring and offer promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity.

PRMT5 is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer

CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with estrogen receptor-positive (ER+) breast cancer. However, patients treated with CDK4/6i eventually develop drug resistance and progress. RB1 loss-of-function alterations confer resistance to CDK4/6i, but the optimal therapy for these patients is unclear. Through a genome-wide CRISPR screen, we identify protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in ER+/RB1-knockout breast cancer cells. Inhibition of PRMT5 blocks the G1-to-S transition in the cell cycle independent of RB, leading to growth arrest in RB1-knockout cells. Proteomics analysis uncovers fused in sarcoma (FUS) as a downstream effector of PRMT5. Inhibition of PRMT5 results in dissociation of FUS from RNA polymerase II, leading to hyperphosphorylation of serine 2 in RNA polymerase II, intron retention, and subsequent downregulation of proteins involved in DNA synthesis. Furthermore, treatment with the PRMT5 inhibitor pemrametostat and a selective ER degrader fulvestrant synergistically inhibits growth of ER+/RB-deficient cell-derived and patient-derived xenografts. These findings highlight dual ER and PRMT5 blockade as a potential therapeutic strategy to overcome resistance to CDK4/6i in ER+/RB-deficient breast cancer.

AXL/WRNIP1 Mediates Replication Stress Response and Promotes Therapy Resistance and Metachronous Metastasis in HER2+ Breast Cancer

Therapy resistance and metastatic progression are primary causes of cancer-related mortality. Disseminated tumor cells possess adaptive traits that enable them to reprogram their metabolism, maintain stemness, and resist cell death, facilitating their persistence to drive recurrence. The survival of disseminated tumor cells also depends on their ability to modulate replication stress in response to therapy while colonizing inhospitable microenvironments. In this study, we discovered that the nuclear translocation of AXL, a TAM receptor tyrosine kinase, and its interaction with WRNIP1, a DNA replication stress response factor, promotes the survival of HER2+ breast cancer cells that are resistant to HER2-targeted therapy and metastasize to the brain. In preclinical models, knocking down or pharmacologically inhibiting AXL or WRNIP1 attenuated protection of stalled replication forks. Furthermore, deficiency or inhibition of AXL and WRNIP1 also prolonged metastatic latency and delayed relapse. Together, these findings suggest that targeting the replication stress response, which is a shared adaptive mechanism in therapy-resistant and metastasis-initiating cells, could reduce metachronous metastasis and enhance the response to standard-of-care therapies.

SIGNIFICANCE

Nuclear AXL and WRNIP1 interact and mediate replication stress response, promote therapy resistance, and support metastatic progression, indicating that targeting the AXL/WRNIP1 axis is a potentially viable therapeutic strategy for breast cancer.

Mapping Cellular Interactions from Spatially Resolved Transcriptomics Data

Cell-cell communication (CCC) is essential to how life forms and functions. However, accurate, high-throughput mapping of how expression of all genes in one cell affects expression of all genes in another cell is made possible only recently, through the introduction of spatially resolved transcriptomics technologies (SRTs), especially those that achieve single cell resolution. However, significant challenges remain to analyze such highly complex data properly. Here, we introduce a Bayesian multi-instance learning framework, spacia, to detect CCCs from data generated by SRTs, by uniquely exploiting their spatial modality. We highlight spacia's power to overcome fundamental limitations of popular analytical tools for inference of CCCs, including losing single-cell resolution, limited to ligand-receptor relationships and prior interaction databases, high false positive rates, and most importantly the lack of consideration of the multiple-sender-to-one-receiver paradigm. We evaluated the fitness of spacia for all three commercialized single cell resolution ST technologies: MERSCOPE/Vizgen, CosMx/Nanostring, and Xenium/10X. Spacia unveiled how endothelial cells, fibroblasts and B cells in the tumor microenvironment contribute to Epithelial-Mesenchymal Transition and lineage plasticity in prostate cancer cells. We deployed spacia in a set of pan-cancer datasets and showed that B cells also participate in PDL1/PD1 signaling in tumors. We demonstrated that a CD8+ T cell/PDL1 effectiveness signature derived from spacia analyses is associated with patient survival and response to immune checkpoint inhibitor treatments in 3,354 patients. We revealed differential spatial interaction patterns between γδ T cells and liver hepatocytes in healthy and cancerous contexts. Overall, spacia represents a notable step in advancing quantitative theories of cellular communications.

Neratinib + fulvestrant + trastuzumab for HR-positive, HER2-negative, HER2-mutant metastatic breast cancer: outcomes and biomarker analysis from the SUMMIT trial

BACKGROUND

HER2 mutations are targetable alterations in patients with hormone receptor-positive (HR+) metastatic breast cancer (MBC). In the SUMMIT basket study, patients with HER2-mutant MBC received neratinib monotherapy, neratinib + fulvestrant, or neratinib + fulvestrant + trastuzumab (N + F + T). We report results from 71 patients with HR+, HER2-mutant MBC, including 21 (seven in each arm) from a randomized substudy of fulvestrant versus fulvestrant + trastuzumab (F + T) versus N + F + T.

PATIENTS AND METHODS

Patients with HR+ HER2-negative MBC with activating HER2 mutation(s) and prior cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) therapy received N + F + T (oral neratinib 240 mg/day with loperamide prophylaxis, intramuscular fulvestrant 500 mg on days 1, 15, and 29 of cycle 1 then q4w, intravenous trastuzumab 8 mg/kg then 6 mg/kg q3w) or F + T or fulvestrant alone. Those whose disease progressed on F + T or fulvestrant could cross-over to N + F + T. Efficacy endpoints included investigator-assessed objective response rate (ORR), clinical benefit rate (RECIST v1.1), duration of response, and progression-free survival (PFS). Plasma and/or formalin-fixed paraffin-embedded tissue samples were collected at baseline; plasma was collected during and at end of treatment. Extracted DNA was analyzed by next-generation sequencing.

RESULTS

ORR for 57 N + F + T-treated patients was 39% [95% confidence interval (CI) 26% to 52%); median PFS was 8.3 months (95% CI 6.0-15.1 months). No responses occurred in fulvestrant- or F + T-treated patients; responses in patients crossing over to N + F + T supported the requirement for neratinib in the triplet. Responses were observed in patients with ductal and lobular histology, 1 or ≥1 HER2 mutations, and co-occurring HER3 mutations. Longitudinal circulating tumor DNA sequencing revealed acquisition of additional HER2 alterations, and mutations in genes including PIK3CA, enabling further precision targeting and possible re-response.

CONCLUSIONS

The benefit of N + F + T for HR+ HER2-mutant MBC after progression on CDK4/6is is clinically meaningful and, based on this study, N + F + T has been included in the National Comprehensive Cancer Network treatment guidelines. SUMMIT has improved our understanding of the translational implications of targeting HER2 mutations with neratinib-based therapy.

Acquired Secondary HER2 Mutations Enhance HER2/MAPK Signaling and Promote Resistance to HER2 Kinase Inhibition in Breast Cancer

HER2 mutations drive the growth of a subset of breast cancers and are targeted with HER2 tyrosine kinase inhibitors (TKI) such as neratinib. However, acquired resistance is common and limits the durability of clinical responses. Most HER2-mutant breast cancers progressing on neratinib-based therapy acquire secondary mutations in HER2. It is unknown whether these secondary HER2 mutations, other than the HER2T798I gatekeeper mutation, are causal to neratinib resistance. Herein, we show that secondary acquired HER2T862A and HER2L755S mutations promote resistance to HER2 TKIs via enhanced HER2 activation and impaired neratinib binding. While cells expressing each acquired HER2 mutation alone were sensitive to neratinib, expression of acquired double mutations enhanced HER2 signaling and reduced neratinib sensitivity. Computational structural modeling suggested that secondary HER2 mutations stabilize the HER2 active state and reduce neratinib binding affinity. Cells expressing double HER2 mutations exhibited resistance to most HER2 TKIs but retained sensitivity to mobocertinib and poziotinib. Double-mutant cells showed enhanced MEK/ERK signaling, which was blocked by combined inhibition of HER2 and MEK. Together, these findings reveal the driver function of secondary HER2 mutations in resistance to HER2 inhibition and provide a potential treatment strategy to overcome acquired resistance to HER2 TKIs in HER2-mutant breast cancer.

SIGNIFICANCE

HER2-mutant breast cancers acquire secondary HER2 mutations that drive resistance to HER2 tyrosine kinase inhibitors, which can be overcome by combined inhibition of HER2 and MEK.

Protein arginine methyltransferase 5 (PRMT5) is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer

CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with estrogen receptor-positive (ER+) breast cancer. However, patients treated with CDK4/6i eventually develop drug resistance and progress. RB1 loss-of-function alterations confer acquired resistance to CDK4/6i, but the optimal therapy for these patients is unclear. Using a genome-wide CRISPR screen, we identified protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in ER+/RB1-knockout (RBKO) breast cancer cells. PRMT5 inhibition blocked cell cycle G1-to-S transition independent of RB, thus arresting growth of RBKO cells. Proteomics analysis uncovered fused in sarcoma (FUS) as a downstream effector of PRMT5. Pharmacological inhibition of PRMT5 resulted in dissociation of FUS from RNA polymerase II (Pol II), Ser2 Pol II hyperphosphorylation, and intron retention in genes that promote DNA synthesis. Treatment with the PRMT5i inhibitor pemrametostat and fulvestrant synergistically inhibited growth of ER+/RB-deficient patient-derived xenografts, suggesting dual ER and PRMT5 blockade as a novel therapeutic strategy to treat ER+/RB-deficient breast cancer.

Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor-positive Breast Cancers for Targeted Treatment

NF1 is a key tumor suppressor that represses both RAS and estrogen receptor-α (ER) signaling in breast cancer. Blocking both pathways by fulvestrant (F), a selective ER degrader, together with binimetinib (B), a MEK inhibitor, promotes tumor regression in NF1-depleted ER⁺ models. We aimed to establish approaches to determine how NF1 protein levels impact B+F treatment response to improve our ability to identify B+F sensitive tumors. We examined a panel of ER⁺ patient-derived xenograft (PDX) models by DNA and mRNA sequencing and found that more than half of these models carried an NF1 shallow deletion and generally have low mRNA levels. Consistent with RAS and ER activation, RET and MEK levels in NF1-depleted tumors were elevated when profiled by mass spectrometry (MS) after kinase inhibitor bead pulldown. MS showed that NF1 can also directly and selectively bind to palbociclib-conjugated beads, aiding quantification. An IHC assay was also established to measure NF1, but the MS-based approach was more quantitative. Combined IHC and MS analysis defined a threshold of NF1 protein loss in ER⁺ breast PDX, below which tumors regressed upon treatment with B+F. These results suggest that we now have a MS-verified NF1 IHC assay that can be used for patient selection as a complement to somatic genomic analysis.

Significance

A major challenge for targeting the consequence of tumor suppressor disruption is the accurate assessment of protein functional inactivation. NF1 can repress both RAS and ER signaling, and a ComboMATCH trial is underway to treat the patients with binimetinib and fulvestrant. Herein we report a MS-verified NF1 IHC assay that can determine a threshold for NF1 loss to predict treatment response. These approaches may be used to identify and expand the eligible patient population.

Targeting CXCR4 abrogates resistance to trastuzumab by blocking cell cycle progression and synergizes with docetaxel in breast cancer treatment

BACKGROUND

Although trastuzumab and other HER2-targeted therapies have significantly improved survival in patients with HER2 overexpressed or amplified (HER2+) breast cancer, a significant proportion of patients do not respond or eventually develop clinical resistance. Strategies to reverse trastuzumab resistance remain a high clinical priority. We were the first to report the role of CXCR4 in trastuzumab resistance. The present study aims to explore the therapeutic potential of targeting CXCR4 and better understand the associated mechanisms.

METHODS

Immunofluorescent staining, confocal microscopy analysis, and immunoblotting were used to analyze CXCR4 expression. BrdU incorporation assays and flow cytometry were used to analyze dynamic CXCR4 expression. Three-dimensional co-culture (tumor cells/breast cancer-associated fibroblasts/human peripheral blood mononuclear cells) or antibody-dependent cellular cytotoxicity assay was used to mimic human tumor microenvironment, which is necessary for testing therapeutic effects of CXCR4 inhibitor or trastuzumab. The FDA-approved CXCR4 antagonist AMD3100, trastuzumab, and docetaxel chemotherapy were used to evaluate therapeutic efficacy in vitro and in vivo. Reverse phase protein array and immunoblotting were used to discern the associated molecular mechanisms.

RESULTS

Using a panel of cell lines and patient breast cancer samples, we confirmed CXCR4 drives trastuzumab resistance in HER2+ breast cancer and further demonstrated the increased CXCR4 expression in trastuzumab-resistant cells is associated with cell cycle progression with a peak in the G2/M phases. Blocking CXCR4 with AMD3100 inhibits cell proliferation by downregulating mediators of G2-M transition, leading to G2/M arrest and abnormal mitosis. Using a panel of trastuzumab-resistant cell lines and an in vivo established trastuzumab-resistant xenograft mouse model, we demonstrated that targeting CXCR4 with AMD3100 suppresses tumor growth in vitro and in vivo, and synergizes with docetaxel.

CONCLUSIONS

Our findings support CXCR4 as a novel therapeutic target and a predictive biomarker for trastuzumab resistance in HER2+ breast cancer.

Limiting mitochondrial plasticity by targeting DRP1 induces metabolic reprogramming and reduces breast cancer brain metastases

Disseminated tumor cells with metabolic flexibility to utilize available nutrients in distal organs persist, but the precise mechanisms that facilitate metabolic adaptations remain unclear. Here we show fragmented mitochondrial puncta in latent brain metastatic (Lat) cells enable fatty acid oxidation (FAO) to sustain cellular bioenergetics and maintain redox homeostasis. Depleting the enriched dynamin-related protein 1 (DRP1) and limiting mitochondrial plasticity in Lat cells results in increased lipid droplet accumulation, impaired FAO and attenuated metastasis. Likewise, pharmacological inhibition of DRP1 using a small-molecule brain-permeable inhibitor attenuated metastatic burden in preclinical models. In agreement with these findings, increased phospho-DRP1 expression was observed in metachronous brain metastasis compared with patient-matched primary tumors. Overall, our findings reveal the pivotal role of mitochondrial plasticity in supporting the survival of Lat cells and highlight the therapeutic potential of targeting cellular plasticity programs in combination with tumor-specific alterations to prevent metastatic recurrences.

Abstract 3934: PRMT5 is an actionable target in CDK4/6 inhibitor-resistant ER+/Rb-deficient breast cancer

RB1 loss-of-function genomic alterations confer resistance to CDK4/6 inhibitors (CDK4/6i) and are enriched post treatment of CDK4/6i in estrogen receptor-positive (ER+) metastatic breast cancer. ER+/Rb-deficient breast cancer is a rising patient population in need of novel therapeutic strategies. Herein, we used a genome-wide CRISPR screen and identified protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in this refractory breast cancer subtype. sgRNA-induced depletion of PRMT5 arrested growth of MCF-7 and T47D RB1 knockout (RBKO) cells. PRMT5 catalyzes symmetric dimethylation of arginine (SDMA). In RBKO cells carrying doxycycline-inducible shRNA targeting the 3’UTR of PRMT5, rescue with wild-type but not an enzymatically dead mutant of PRMT5 restored cell growth, supporting that PRMT5 methyltrasferase activity is essential for growth of these cells. Gene set enrichment analysis (GSEA) of RNA-seq data revealed significant downregulation of cell cycle-related Hallmark gene signatures in RBKO cells treated with PRMT5 siRNA versus control siRNA. Both gene silencing and pharmacological blockade of PRMT5 with the small molecule inhibitor pemrametostat impeded G1-to-S cell cycle progression in MCF-7 and T47D RBKO cells and in lung, prostate, and triple-negative breast cancer cells with natural RB1 mutations or deletions, suggesting that PRMT5 inhibition can block the G1-to-S transition even in the absence of Rb. To identify the protein interactome of PRMT5 and the mechanism by which it promotes cell cycle progression in Rb-deficient cells, we performed proteomics analysis of Co-IP mass spectrometry and an SDMA post-translational modification scan and pinpointed FUS (fused in sarcoma) as a putative downstream effector of PRMT5. FUS is known to regulate RNA polymerase II (Pol II)-mediated transcription. Inhibition of PRMT5 with pemrametostat significantly reduced SDMA levels on FUS and dissociated FUS from Pol II as evidenced by FUS Co-IP and immunoblot analysis. ChIP-seq analysis revealed that treatment of RBKO cells with pemrametostat derepressed phosphorylation of Ser2 in the C-terminus of Pol II at transcription start sites (TSS) of genes involved in cell cycle progression. In accordance with the abnormal accumulation of pSer2 Pol II at TSS, pemrametostat treatment also resulted in an increased Pol II pausing index and an enrichment of intron retention splicing variants. Finally, therapeutic inhibition of PRMT5 with pemrametostat synergized with fulvestrant (a selective ER degrader) against growth of ER+/Rb-deficient breast cancer cell line- and patient-derived xenografts in mice, suggesting this combination as a novel therapeutic strategy for ER+/Rb-deficient metastatic breast cancers.

Citation Format: Chang-Ching Lin, Tsung-Cheng Chang, Yunguan Wang, Yanfeng Zhang, Andrew Lemoff, Yisheng V. Fang, He Zhang, Dan Ye, Isabel Soria-Bretones, Alberto Servetto, Kyung-min Lee, Xuemei Luo, Joseph J. Otto, Hiroaki Akamatsu, David W. Cescon, Lin Xu, Yang Xie, Joshua T. Mendell, Ariella B. Hanker, Carlos L. Arteaga. PRMT5 is an actionable target in CDK4/6 inhibitor-resistant ER+/Rb-deficient breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3934.

Targeting CXCR4 abrogates resistance to trastuzumab by blocking cell cycle progression and synergizes with docetaxel in breast cancer treatment

Background: Although trastuzumab and other HER2-targeted therapies have significantly improved survival in patients with HER2 overexpressed or amplified (HER2+) breast cancer, a significant proportion of patients do not respond or eventually develop clinical resistance. Strategies to reverse trastuzumab resistance remain a high clinical priority. We were the first to report the role of CXCR4 in trastuzumab resistance. The present study aims to explore the therapeutic potential of targeting CXCR4 and better understand the associated mechanisms. Methods: Immunofluorescent staining, confocal microscopy analysis, and immunoblotting were used to analyze CXCR4 expression. BrdU incorporation assays and flow cytometry were used to analyze dynamic CXCR4expression. Three-dimensional co-culture (tumor cells/ breast cancer-associated fibroblasts / human peripheral blood mononuclear cells) or antibody-dependent cellular cytotoxicity assay was used to mimic human tumor microenvironment, which is necessary for testing therapeutic effect of CXCR4 inhibitor or trastuzumab. The FDA-approved CXCR4 antagonist AMD3100, trastuzumab, and docetaxel chemotherapy were used to evaluate therapeutic efficacy in vitro and in vivo. Reverse phase protein array and immunoblotting were used to discern the associated molecular mechanisms. Results: Using multiple cell lines and patient breast cancer samples we confirmed CXCR4 drives trastuzumab resistance in HER2+ breast cancer and further demonstrated that the increased CXCR4 expression in trastuzumab-resistant cells is associated with cell cycle progression with a peak in the G2/M phases. Blocking CXCR4 with AMD3100 inhibits cell proliferation by downregulating mediators of G2-M transition, leading to G2/M arrest and abnormal mitosis. Using multiple trastuzumab-resistant cell lines and an in vivo established trastuzumab-resistant xenograft mouse model, we demonstrated that targeting CXCR4 with AMD3100 suppresses tumor growth in vitro and in vivo, and synergizes with docetaxel. Conclusions: Our findings support CXCR4 as a novel therapeutic target and a predictive biomarker for trastuzumab resistance in HER2+ breast cancer.

Epigenetic Repression of STING by MYC Promotes Immune Evasion and Resistance to Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer

The MYC oncogene is frequently amplified in triple-negative breast cancer (TNBC). Here, we show that MYC suppression induces immune-related hallmark gene set expression and tumor-infiltrating T cells in MYC-hyperactivated TNBCs. Mechanistically, MYC repressed stimulator of interferon genes (STING) expression via direct binding to the STING1 enhancer region, resulting in downregulation of the T-cell chemokines CCL5, CXCL10, and CXCL11. In primary and metastatic TNBC cohorts, tumors with high MYC expression or activity exhibited low STING expression. Using a CRISPR-mediated enhancer perturbation approach, we demonstrated that MYC-driven immune evasion is mediated by STING repression. STING repression induced resistance to PD-L1 blockade in mouse models of TNBC. Finally, a small-molecule inhibitor of MYC combined with PD-L1 blockade elicited a durable response in immune-cold TNBC with high MYC expression, suggesting a strategy to restore PD-L1 inhibitor sensitivity in MYC-overexpressing TNBC.

Abstract P5-17-09: A genome-wide CRISPR screen identifies PRMT5 as a novel therapeutic target in ER+/RB1-deficient breast cancer

Background: CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with advanced estrogen receptor-positive (ER+) breast cancer. However, this benefit is transient as virtually all these tumors eventually develop drug resistance and recur. Clinical studies have reported an association of RB1 loss-of-function genomic alterations with acquired resistance to CDK4/6i. Given the enrichment of RB1 alterations post CDK4/6i treatment, ER+/RB1-deficient breast cancer will become a rising patient population in need of discovery of novel treatment strategies. In this study, we sought to identify actionable vulnerabilities for this refractory breast cancer subtype using a genome-wide CRISPR screen. Methods: RB1 was knocked out in ER+ MCF-7 and T47D breast cancer cells using CRISPR-Cas9; complete gene knockout was confirmed by PCR-based genotyping, Sanger sequencing, and immunoblot analysis. Isogenic RB1 knockout (RBKO) and wild-type (WT) T47D cells were used for the genome-wide CRISPR screen. MAGeCKFlute was used to identify differentially essential genes in T47D RBKO vs WT cells; Gene Ontology (GO) analysis was used to prioritize hits. MCF-7 and T47D RBKO cells were used for validating and studying the function of the identified genes. Results: Knockout of RB1 in MCF-7 and T47D cells increased IC50 of abemaciclib, palbociclib, and ribociclib 10-200 fold compared to WT cells. RNA-seq analysis showed upregulation of E2F target gene expression in RBKO vs WT cells. The CRISPR screen revealed that CCND1 and CDK4 lost their essentiality in T47D RBKO cells, suggesting that loss of RB1 uncouples the CDK4/Cyclin D1 complex from E2F-regulated transcription. GO analysis of the top 50 differentially essential hits of RBKO vs WT cells showed an enrichment of protein arginine methyltransferase activity, primarily PRMT5, which post-translationally mono-methylates and symmetrically di-methylates protein arginine. In agreement with this finding, PRMT5 knockout by three individual sgRNAs resulted in more potent growth inhibition of MCF-7 and T47D RBKO cells than WT cells. Further, transfection of PRMT5 siRNA or treatment with the PRMT5 small molecule inhibitor GSK3326595 - currently in clinical trials - resulted in G1 arrest of MCF-7 and T47D RBKO cells as assayed by propidium iodide staining but did not induce caspase 3/7 or PARP cleavage (apoptosis). RNA-seq of PRMT5 siRNA vs control siRNA in MCF-7 and T47D RBKO cells exhibited significant downregulation of E2F Hallmark gene signature, further suggesting PRMT5 inhibition as a strategy to suppress E2F-regulated gene expression when cells lose Rb. The CRISPR screen also revealed that transcription factors that drive ER signaling, such as FOXA1, GATA3, MYC, SPDEF, and ESR1 (the gene encoding ERα), were commonly essential in both T47D WT and RBKO cells. Estrogen deprivation or treatment with fulvestrant inhibited estrogen responsive element (ERE) luciferase reporter activity, expression of putative E2F target genes, and proliferation of both WT and RBKO cells, suggesting that ER+ cells still rely on ERα irrespective of RB1 status. Treatment of MCF-7 and T47D RBKO cells with fulvestrant and GSK3326595 resulted in more potent growth inhibition than each drug alone, suggesting a novel approach to treat ER+/RB1-deficient breast cancer. We are currently testing the antitumor activity of fulvestrant plus GSK3326595 against RBKO xenografts as well as the requirement of arginine methyltransferase activity associated with PRMT5 for growth of ER+/RB1-deficient breast cancer cells. Conclusion: PRMT5 is essential for proliferation of ER+/RB1-deficient breast cancer cells. Targeting PRMT5 in combination with anti-estrogens is a novel and testable strategy to suppress E2F-regulated cell cycle progression of this CDK4/6 inhibitor-resistant breast cancer subtype.

Citation Format: Chang-Ching Lin, Tsung-Cheng Chang, Alberto Servetto, Kyung-min Lee, He Zhang, Yunguan Wang, Dan Ye, Sumanta Chatterjee, Dhivya R Sudhan, Hiroaki Akamatsu, Yang Xie, Joshua T Mendell, Ariella B Hanker, Carlos L Arteaga. A genome-wide CRISPR screen identifies PRMT5 as a novel therapeutic target in ER+/RB1-deficient breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-17-09.

Abstract PD2-01: A platform of CDK4/6 inhibitor-resistant patient-derived breast cancer organoids illuminates mechanisms of resistance and therapeutic vulnerabilities

CDK4/6 inhibitors (CDK4/6i) in combination with antiestrogens have revolutionized the treatment of ER+ metastatic breast cancer (MBC), significantly prolonging survival. However, this combination is not curative, and tumors eventually acquire resistance. Following progression on this combination, patients are left with limited treatment options. A diverse array of mechanisms of resistance to CDK4/6i + antiestrogens have been described. However, laboratory models that capture this heterogeneity of resistance mechanisms are lacking. Patient-derived organoids (PDOs) provide a rapid, robust and reliable platform that recapitulates intra-tumor heterogeneity, partially mimics the cancer microenvironment, and accurately predicts drug response. We aspired to generate a platform of CDK4/6i-resistant breast cancer PDOs to serve as models for understanding acquired resistance to CDK4/6i + antiestrogens and identifying therapies to overcome resistance. We successfully established 16 PDOs out of 32 biopsies (50% efficiency) of metastates from patients with ER+ MBC progressing on CDK4/6i (palbociclib or abemaciclib) + antiestrogens (letrozole or fulvestrant; median response to combination = 9 months). Our collection includes PDOs derived from lobular (n=3) and inflammatory (n=2) breast cancers and reflects racial/ethnic diversity (50% white/not Hispanic; 18.8% Hispanic; 12.5% Black; 12.5% other/unknown). Next-gen sequencing reports were available for 10 patients from which organoids were established, revealing alterations associated with CDK4/6i and/or antiestrogen resistance, including ESR1 (n=2), HER2/ERBB2 (n=2), PTEN (n=2), CCNE1 (n=1), NF1 (n=1), and ARID1A (n=1). Furthermore, one biopsy and its derived organoid lost ER expression, and 5 harbored PIK3CA activating mutations. Thus far, we have performed targeted DNA-sequencing on 7 PDOs and found 13/15 (86.7%) concordance with driver mutations from tumor NGS reports. PDOs established from CDK4/6i-resistant biopsies maintained resistance to palbociclib or abemaciclib ± fulvestrant (500 nM each) in 3D cell viability assays (6 days of treatment). In contrast, control PDOs established from primary ER+ breast cancer surgical samples (n=2) were sensitive to each CDK4/6i ± fulvestrant (median viability for combination=25.6-31.5% for control vs 65.2-80.5% for resistant). GSEA analysis of RNA-seq data from control (n=2) and CDK4/6i-resistant (n=6) PDOs cultured in estrogen-depleted media ± 200 nM palbociclib revealed that palbociclib treatment resulted in downregulation of E2F target and G2M checkpoint signatures in control but not resistant PDOs. Next, we performed a high-throughput screen of 1,000 compounds in 3 resistant PDOs. One PDO showed exquisite sensitivity to G2/M cell cycle checkpoint components, including CDK1, PLK1, Aurora kinase, ATR, Chk1, and Wee1 inhibitors. Finally, treatment of 10 resistant PDOs with the CDK2/4/6 inhibitor PF-06873600 revealed that the CCNE1 (cyclin E1)-amplified PDO was highly sensitive (IC50=130 nM vs >1000 nM), supporting that CCNE1-amplified tumors are vulnerable to CDK2 inhibition. Conclusions: PDOs can be successfully established from ER+ MBC biopsies, maintain the resistant phenotype in culture, retain driver alterations found in tumors from which they were derived, and fail to suppress E2F targets following treatment with CDK4/6i. Therefore, these PDOs represent valuable models to understand and explore diverse mechanisms of CDK4/6i resistance and therapeutic vulnerabilities.

Citation Format: Ariella B. Hanker, Sumanta Chatterjee, Yunguan Wang, Dan Ye, Dhivya R. Sudhan, Brian M. Larsen, Lauren C. Smith, Yilin Zhang, Vishal Kandagatla, Kuntal Majmudar, Ezequiel Renzulli, Saurabh Mendiratta, Kimberly Blackwell, Alana L. Welm, Sunati Sahoo, Nisha Unni, Cheryl M. Lewis, Tao Wang, Ameen A. Salahudeen, Carlos L. Arteaga. A platform of CDK4/6 inhibitor-resistant patient-derived breast cancer organoids illuminates mechanisms of resistance and therapeutic vulnerabilities [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD2-01.

Abstract GS3-09: Loss of ASXL1 tumor suppressor promotes resistance to CDK4/6 inhibitors in ER+ breast cancer

Background: CDK4/6 inhibitors (CDK4/6i) in combination with antiestrogens have prolonged survival of patients with ER+ metastatic breast cancer. However, this combination is not curative mainly due to acquired drug resistance. Knowledge about mechanisms of such resistance remains quite incomplete. We report herein a forward-genetics screen to discover a broad spectrum of novel somatic mutations causal to CDK4/6i resistance. Methods: We used CRISPR/Cas9 to delete the DNA mismatch repair (MMR) gene MSH2 in MCF7 and T47D ER+ breast cancer cells. Deficiency of DNA MMR proteins such as MSH2 results in a high nucleotide substitution rate which, in turn, predisposes cells to acquire drug resistance-associated mutations. MSH2-/- MCF7 and T47D cells were infected with a lentiviral barcode library containing ~1000 unique DNA barcodes. MSH2-/- barcoded cells were expanded for ~25 doublings to allow the accumulation of random mutations. Clones resistant to CDK4/6i were selected in the presence of IC90 of palbociclib (200 nM) or abemaciclib (500 nM) for 4-6 weeks. CDK4/6i resistant clones with unique barcode IDs were subjected to whole exome sequencing (WES). Results: Following drug selection, ~73 uniquely barcoded resistant colonies emerged from MCF7 and T47D MSH2-/- clonal lines. As expected, MCF7 and T47D MSH2-/- clones harbored a high mutation burden compared to parental cells. Candidate variants were distilled based on (a) functionality prediction and (b) mutation frequency in Project GENIE. We observed RB1 (5/73 clones; 6.8%) mutations in CDK4/6i resistant clones, providing proof-of-principle that this approach can identify clinically-relevant drug resistant alterations. Overall, we identified non-synonymous alterations in 2,206 genes in T47D palbociclib-resistant, 2,195 genes in T47D abemaciclib-resistant, and 1,312 genes in MCF7 palbociclib-resistant lines. A secondary screen of the 10 genes recurrently mutated in all three CDK4/6i resistant groups identified loss of ASXL1 as top hit. ASXL1 encodes a polycomb repressive complex protein that regulates chromatin accessibility. Loss of ASXL1 has been implicated in myeloid transformation through epigenetic reprogramming. WES of 76 CDK4/6i resistant tumor biopsies (DFCI/MBCproject cohort) identified ASXL1 alterations in two and four patients with acquired and primary resistance, respectively (6/76=7.9%). One of the tumors that progressed after an initial response to palbociclib had acquired the same ASXL1 R549C mutation that was identified in our screen. Among 1,769 tumors from patients treated with CDK4/6i (TEMPUS database), 37 exhibited ASXL1 alterations (4 frameshift, 6 truncating, 3 in-frame del, 24 missense mutations). DNAseq of patient-derived organoids established from post-CDK4/6i metastases identified ASXL1 mutations in 2/7 organoids (29%). ASXL1-/- MCF7 and T47D cells were cross-resistant to fulvestrant. GSEA analysis of RNA-seq data showed upregulation of E2F targets in palbociclib-treated cells stably transduced with ASXL1 shRNA but not control shRNA (Enrichment score=0.75, q=1.00E-09). This was associated with maintenance of RB phosphorylation in the presence of CDK4/6i, markedly higher levels of CDK2, CDK6, cyclins E and A, and downregulation of p21 and p27. Finally, siRNAs targeting CDK2 or cyclin A reduced the viability of ASXL1-deficient T47D cells by 50% and 90%, respectively. Conclusions: An accelerated mutagenesis approach using MMR-deficient ER+ breast cancer cells identified loss of ASXL1 as a novel mechanism of resistance to CDK4/6i. ASXL1 alterations were found in ~8% of tumors from patients with de novo or acquired resistance to CDK4/6i. Knockdown of CDK2 and cyclin A restored sensitivity to CDK4/6i and reduced viability of ASXL1 deficient cells, suggesting CDK2 inhibitors are a treatment approach against these drug-resistant tumors.

Citation Format: Dhivya R. Sudhan, Sumanta Chatterjee, Jiwoong Kim, Yunguan Wang, Vishal Kandagatla, Dan Ye, Chang-Ching Lin, Jorge Gomez Tejeda Zanudo, Esha Jain, Arnaldo Marin, Alberto Servetto, Kyung-min Lee, Juan Manuel Povedano, David McFadden, Alex Barrett, Nikhil Wagle, Ariella B. Hanker, Carlos L. Arteaga. Loss of ASXL1 tumor suppressor promotes resistance to CDK4/6 inhibitors in ER+ breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS3-09.

Metabolic diversity within breast cancer brain-tropic cells determines metastatic fitness

HER2+ breast cancer patients are presented with either synchronous (S-BM), latent (Lat), or metachronous (M-BM) brain metastases. However, the basis for disparate metastatic fitness among disseminated tumor cells of similar oncotype within a distal organ remains unknown. Here, employing brain metastatic models, we show that metabolic diversity and plasticity within brain-tropic cells determine metastatic fitness. Lactate secreted by aggressive metastatic cells or lactate supplementation to mice bearing Lat cells limits innate immunosurveillance and triggers overt metastasis. Attenuating lactate metabolism in S-BM impedes metastasis, while M-BM adapt and survive as residual disease. In contrast to S-BM, Lat and M-BM survive in equilibrium with innate immunosurveillance, oxidize glutamine, and maintain cellular redox homeostasis through the anionic amino acid transporter xCT. Moreover, xCT expression is significantly higher in matched M-BM brain metastatic samples compared to primary tumors from HER2+ breast cancer patients. Inhibiting xCT function attenuates residual disease and recurrence in these preclinical models.

Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity

Activating mutations in HER2 (ERBB2) drive the growth of a subset of breast and other cancers and tend to co-occur with HER3 (ERBB3) missense mutations. The HER2 tyrosine kinase inhibitor neratinib has shown clinical activity against HER2-mutant tumors. To characterize the role of HER3 mutations in HER2-mutant tumors, we integrate computational structural modeling with biochemical and cell biological analyses. Computational modeling predicts that the frequent HER3E928G kinase domain mutation enhances the affinity of HER2/HER3 and reduces binding of HER2 to its inhibitor neratinib. Co-expression of mutant HER2/HER3 enhances HER2/HER3 co-immunoprecipitation and ligand-independent activation of HER2/HER3 and PI3K/AKT, resulting in enhanced growth, invasiveness, and resistance to HER2-targeted therapies, which can be reversed by combined treatment with PI3Kα inhibitors. Our results provide a mechanistic rationale for the evolutionary selection of co-occurring HER2/HER3 mutations and the recent clinical observations that HER3 mutations are associated with a poor response to neratinib in HER2-mutant cancers.

Nuclear FGFR1 Regulates Gene Transcription and Promotes Antiestrogen Resistance in ER+ Breast Cancer

PURPOSE

FGFR1 overexpression has been associated with endocrine resistance in ER⁺ breast cancer. We found FGFR1 localized in the nucleus of breast cancer cells in primary tumors resistant to estrogen suppression. We investigated a role of nuclear FGFR1 on gene transcription and antiestrogen resistance.

EXPERIMENTAL DESIGN

Tumors from patients treated with letrozole were subjected to Ki67 and FGFR1 IHC. MCF7 cells were transduced with FGFR1(SP-)(NLS) to promote nuclear FGFR1 overexpression. FGFR1 genomic activity in ER⁺/FGFR1-amplified breast cancer cells ± FOXA1 siRNA or ± the FGFR tyrosine kinase inhibitor (TKI) erdafitinib was examined by chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq). The nuclear and chromatin-bound FGFR1 interactome was investigated by mass spectrometry (MS).

RESULTS

High nuclear FGFR1 expression in ER⁺ primary tumors positively correlated with post-letrozole Ki67 values. Nuclear FGFR1 overexpression influenced gene transcription and promoted resistance to estrogen suppression and to fulvestrant in vivo. A gene expression signature induced by nuclear FGFR1 correlated with shorter survival in the METABRIC cohort of patients treated with antiestrogens. ChIP-Seq revealed FGFR1 occupancy at transcription start sites, overlapping with active transcription histone marks. MS analysis of the nuclear FGFR1 interactome identified phosphorylated RNA-Polymerase II and FOXA1, with FOXA1 RNAi impairing FGFR1 recruitment to chromatin. Treatment with erdafitinib did not impair nuclear FGFR1 translocation and genomic activity.

CONCLUSIONS

These data suggest nuclear FGFR1 contributes to endocrine resistance by modulating gene transcription in ER⁺ breast cancer. Nuclear FGFR1 activity was unaffected by FGFR TKIs, thus supporting the development of treatment strategies to inhibit nuclear FGFR1 in ER+/FGFR1 overexpressing breast cancer.

Abstract GS1-06: FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified breast cancer

Background: FGFR1 amplification occurs in ~ 15% of ER+ breast cancers. In these tumors, nuclear FGFR1 has been shown to interact with DNA, but its role in transcriptional regulation is unclear. Thus, we investigated the genomic role of FGFR1 in ER+/FGFR1-amplified breast cancer. Results: FGFR1 ChIP-Seq detected 4,412 DNA binding sites in CAMA1 ER+/FGFR1-amplified breast cancer cells cultured in estrogen-free conditions. Of these binding sites, 67% were enriched at promoter regions. ChIP-qPCR confirmed FGFR1 binding to several promoter regions in a second ER+/FGFR1-amplified cell line, MDA-MB-134, and a patient derived xenograft, HCI-011. To determine the nuclear FGFR1 interactome, we performed FLAG immunoprecipitation of mixed nuclear and chromatin fractions of CAMA1 cells transduced with a 3XFLAG-FGFR1 plasmid, followed by mass spectrometry (MS) of FLAG antibody pulldowns. MS revealed RNA Polymerase II subunits among the top nuclear FGFR1 interacting proteins. FGFR1 mainly bound Pol II phosphorylated on Ser5 (Pol II S5P), a marker of transcription initiation, in CAMA1, MDA-MB-134 and HCI-011 cell extracts. Pol II S5P ChIP-Seq revealed that 2,867/4,412 (65%) FGFR1 peaks were shared with Pol II S5P. ChIP-Seq also showed that 95% of FGFR1 peaks overlapped with both H3K4me3 and H3K27ac, markers of active transcription. Consistent with these results, RNA-Seq of CAMA1 cells showed that expression of FGFR1-bound genes was markedly higher than non FGFR1-bound genes (p<0.0001), suggesting that FGFR1 binds to actively transcribed genes. In addition to Pol II, MS detected FOXA1 among FGFR1 interacting proteins. ChIP-Seq analysis revealed FOXA1 enriched at FGFR1-bound loci. siRNA-mediated FOXA1 knockdown reduced FGFR1 distribution to several genomic loci in CAMA1 cells, as measured by FGFR1 ChIP-Seq, suggesting that FOXA1 mediates FGFR1 recruitment to chromatin. We next transduced MCF-7 cells with an FGFR1(SP-)(NLS) plasmid, where the NLS sequence forces nuclear import of the resulting protein. To determine the role of FGFR1 on transcriptional regulation, we used Binding and Expression Target Analysis (BETA), integrating FGFR1 ChIP-Seq and RNA-Seq results from MCF7FGFR1(SP-)(NLS) vs MCF7EV cells. This analysis predicted a direct role for genomic-bound FGFR1 in activating gene expression (p=8.01e-6). MCF7FGFR1(SP-)(NLS) cells were markedly less sensitive to fulvestrant compared to control cells. Gene Set Enrichment Analysis (GSEA) of the 1,009 genes upregulated in MCF7FGFR1(SP-)(NLS) cells and bound by FGFR1 at a genomic level revealed a strong enrichment of estrogen response early (q=2.2e-44) and late (q=6.4e-33) genes, suggesting that nuclear FGFR1 induces an ERα-associated transcriptional profile that may contribute to endocrine resistance. Finally, an expression signature associated with nuclear FGFR1 correlated with endocrine resistance in three cohorts of patients with ER+ breast cancer treated with aromatase inhibitors. We next studied the effect of growth factor stimulation on FGFR1 transcriptional function. Stimulation with FGF2 enhanced nuclear FGFR1 import in CAMA1 cells, as well as FGFR1-Pol II S5P association. Notably, these effects were not abrogated by treatment with the FGFR1 inhibitor erdafitinib. ChIP-Seq revealed that erdafitinib did not impair the FGFR1 genomic distribution. These results do not support a causal link between the FGFR1 activated TK and the receptor’s activity in the nucleus. Conclusions: We have demonstrated a role for nuclear FGFR1 in transcriptional regulation in breast cancer. FGFR1-induced gene expression contributes to endocrine resistance and is not affected by FGFR TKIs. These findings provide a rationale for developing treatment strategies to inhibit nuclear FGFR1 in ER+/FGFR1-amplified breast cancer.

Citation Format: Alberto Servetto, Rahul Kollipara, Luigi Formisano, Chang-Ching Lin, Kyung-min Lee, Dhivya R Sudhan, Ariella B Hanker, Sumanta Chatterjee, Angel Guerrero-Zotano, Paula Gonzalez-Ericsson, Saurabh Mendiratta, Hiroaki Akamatsu, Nicholas James, Ralf Kittler, Carlos L Arteaga. FGFR1 associates with gene promoters and regulates gene transcription: Implications for endocrine resistance in ER+/FGFR1-amplified 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 GS1-06.

A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics

We present an oblique plane microscope (OPM) that uses a bespoke glass-tipped tertiary objective to improve the resolution, field of view, and usability over previous variants. Owing to its high numerical aperture optics, this microscope achieves lateral and axial resolutions that are comparable to the square illumination mode of lattice light-sheet microscopy, but in a user friendly and versatile format. Given this performance, we demonstrate high-resolution imaging of clathrin-mediated endocytosis, vimentin, the endoplasmic reticulum, membrane dynamics, and Natural Killer-mediated cytotoxicity. Furthermore, we image biological phenomena that would be otherwise challenging or impossible to perform in a traditional light-sheet microscope geometry, including cell migration through confined spaces within a microfluidic device, subcellular photoactivation of Rac1, diffusion of cytoplasmic rheological tracers at a volumetric rate of 14 Hz, and large field of view imaging of neurons, developing embryos, and centimeter-scale tissue sections.

Overcoming Endocrine Resistance in Breast Cancer

Estrogen receptor-positive (ER+) breast cancer is the most common breast cancer subtype. Treatment of ER+ breast cancer comprises interventions that suppress estrogen production and/or target the ER directly (overall labeled as endocrine therapy). While endocrine therapy has considerably reduced recurrence and mortality from breast cancer, de novo and acquired resistance to this treatment remains a major challenge. An increasing number of mechanisms of endocrine resistance have been reported, including somatic alterations, epigenetic changes, and changes in the tumor microenvironment. Here, we review recent advances in delineating mechanisms of resistance to endocrine therapies and potential strategies to overcome such resistance.

Abstract PD7-04: Fibroblast growth factor receptor 1 associates with promoters genome-wide and regulates gene transcription in ER+/FGFR1-amplified breast cancer: Implications for endocrine resistance

Background: FGFR1 amplification occurs in about 15% of estrogen receptor-positive (ER+) breast cancers and is associated with resistance to endocrine therapy. In these tumors, nuclear FGFR1 has been shown to interact with ERα and alter gene expression through binding to chromatin. However, the mechanisms underpinning nuclear FGFR1-mediated gene transcription remain unclear. Thus, we sought to elucidate mechanisms to explain the genomic role of FGFR1 in ER+/FGFR1-amplified breast cancer.Results: FGFR1 ChIP-Seq detected 4408 DNA binding sites in CAMA1 ER+/FGFR1-amplified breast cancer cells cultured in estrogen-free conditions; 67% of these sites were enriched at promoter regions, suggesting a role of FGFR1 in gene transcription regulation. ChIP-qPCR assay confirmed FGFR1 binding to promoter regions of genes such as CCND1, MYC, VEGFA, JUNB and SMAD5 in both CAMA1 and MDA-MB-134 ER+/FGFR1-amplified cells and also in an ER+/FGFR1-amplified patient derived xenograft (HCI-011). RNA-Seq of CAMA1 cells revealed that expression of FGFR1-bound genes was substantially higher than non FGFR1-bound genes (p<0.0001), suggesting FGFR1 binds to genes that are actively transcribed. Consistent with these results, precipitation with a FGFR1 antibody followed by immunoblot analysis showed association of FGFR1 with RNA Polymerase II (Pol II) in CAMA1, MDA-MB-134 and HCI-011 cell extracts. FGFR1 mainly bound with Pol II phosphorylated in Ser5 (Pol II S5P), a post-translational modification required for transcriptional activity. ChIP-Seq in CAMA1 cells with a Pol II S5P antibody revealed that 2867 of 4408 (65%) FGFR1 binding sites overlapped with Pol II S5P peaks, with a distribution centered on a similar location near the transcription start site. This interaction was validated by ChIP-reChIP assay, via sequential immunoprecipitation of FGFR1 and Pol II. Analysis of the METABRIC cohort showed that 1096/4408 (25%) FGFR1 DNA binding sites overlapped with genes differentially expressed in FGFR1-amplified vs FGFR1 non-amplified ER+ breast cancers. From this 1096-overexpressed gene list and using Gene Set Variation Analysis (GSVA), we developed a signature score for the top 102 genes (LogFC>0.25), representing those whose expression is likely regulated by FGFR1. This high signature score was associated with worse disease free survival (DFS; 263.7 months vs not reached; HR=1.72, CI 1.39-2.12; p<0.0001) and overall survival (OS; 145.1 vs 174.1 months; HR=1.24, CI 1.07-1.43; p=0.0003) in the ER+/HER2− cohort in METABRIC. This high signature score also correlated with high tumor grade (p<0.0001) and a worse Nottingham prognostic index (p<0.0001). Finally, we investigated cofactors influencing FGFR1 genomic function. Since nuclear FGFR1 has been shown to interact with ERα, we examined those cofactors involved in ER transcription. We initially focused on the FOXA1 pioneer factor, which mediates transcription factor binding to chromatin in ER+ breast cancer cells. Precipitation with a FGFR1 antibody followed by FOXA1 immunoblot analysis demonstrated an association of FGFR1 with FOXA1 in CAMA1 and MDA-MB-134 cells. ChIP in CAMA1 cells revealed FOXA1 enrichment at promoter regions bound by FGFR1. Further, siRNA-mediated FOXA1 knockdown in CAMA1 cells markedly reduced FGFR1 binding to several promoter regions, preliminarily including CCND1, JUNB, SMAD5, MYC and TOB1, as measured by ChIP-qPCR. Conclusions: These findings suggest a prominent role of FGFR1 in gene transcription regulation in breast cancer. Whether this transcriptional action is causal to antiestrogen resistance in ER+/FGFR1-amplified breast cancer is under active investigation and will be reported at the Symposium.

Citation Format: Alberto Servetto, Rahul Kollipara, Luigi Formisano, Kyung-min Lee, Dhivya R Sudhan, Ariella B Hanker, Sumanta Chatterjee, Albert Lin, Saurabh Mendiratta, Nicholas James, Ralf Kittler, Carlos L Arteaga. Fibroblast growth factor receptor 1 associates with promoters genome-wide and regulates gene transcription in ER+/FGFR1-amplified breast cancer: Implications for endocrine resistance [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 PD7-04.

Abstract GS6-04: Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, breast cancer progression, and HER2 inhibitor sensitivity

Activating mutations in HER2 (ERBB2) drive the growth of a subset of breast cancers. The HER2 tyrosine kinase inhibitor (TKI) neratinib has shown clinical activity against cancers harboring HER2 activating mutations. Co-occurring HER2 and HER3 (ERBB3) mutations have been reported to co-occur in patients with breast cancer, suggesting the possibility of cooperativity of both oncogenes.

Interrogation of the Project GENIE database revealed that gain-of-function missense mutations in HER2 and HER3 exhibit statistically significant co-occurence [q value=0.006 (breast cancer); q=1.01x10−26 (all cancer types)]. On the other hand, HER3 mutations were nearly absent in cancers harboring HER2 in-frame insertions and cancers with HER2 amplification. In breast cancer, co-occurring HER3 mutations were mutually exclusive with PIK3CA mutations, suggestive of potential functional redundancy.

Sixty-eight unique breast cancers from cBioPortal, GENIE, and Foundation Medicine were found to harbor co-occurring mutations in HER2 and HER3, the most common of which were L755S, V777L, L869R/Q, and S310F, each with HER3E928G. Computational structural modeling suggested that the E928G substitution in HER3 enhances the interface energy between HER2 and HER3 kinase domains. This was confirmed by co-immunoprecipitation assays in HEK293 cells transfected with wild-type (WT) or mutant HER2 and HER3. This binding was further enhanced between HER3E928G and HER2 missense mutants. Further, structural modeling of L755S, V777L, and L869R/Q in HER2 revealed that each of these mutations increase HER2 kinase activation. Accordingly, each of these HER2 mutants, as well has HER2S310F in the extracellular domain, increased ligand-independent P-HER2 and P-HER3 in HEK293 cells. P-HER3 levels were the highest HEK293 in cells co-expressing HER2 and HER3 mutations. Similar results were observed in MCF10A breast epithelial cells stably expressing mutant HER2 and mutant HER3. Enhanced activation of the PI3K pathway (P-AKT and P-S6) was observed in cells expressing both mutations compared to cells expressing mutant HER2 with HER3WT or vice-versa.

MCF10A HER2WT/HER3E982G cells did not form colonies in ligand-free 3D Matrigel assays, whereas cells expressing HER2L755S/HER3WT formed organized acini. In contrast, HER2L755S/HER3E928G acini were highly invasive. Addition of the HER3 ligand neuregulin (NRG) to HER2L755S/HER3WT cells phenocopied the effect of HER3E928G. Interestingly, MCF10A cells expressing the HER2Y772_A775 (YVMA) insertion together with HER3WT also formed invasive acini in the absence of NRG, suggesting that this HER2 insertion mutation is more transforming than HER2 missense mutations. Similar results were obtained with invasion assays using Matrigel-coated chambers.

Finally, we examined the effects of HER2/HER3 co-mutations on sensitivity to HER2 inhibitors. Structural analysis was performed of the HER3/HER2 kinase domain complex docked with neratinib. HER3E928G, when bound to HER2, is located close to the neratinib-binding pocket of HER2 and was predicted to reduce HER2/neratinib binding affinity. Similarly, co-expression of HER3E928G reduced the ability of neratinib to inhibit P-HER3, P-AKT, P-S6, and growth of MCF10A cells expressing HER2/HER3 co-mutations. The PI3Kα inhibitor alpelisib restored neratinib sensitivity.

Conclusions: Co-expression of mutant HER2 and mutant HER3 promotes ligand-independent HER2/HER association, HER3 phosphorylation, and cancer cell invasion via enhanced activation of the PI3K pathway; this enhanced signaling output is incompletely blocked by neratinib. Therefore, breast cancers expressing co-occurring HER2 and HER3 mutations may require the addition of a PI3Kα inhibitor to a HER2 TKI.

Citation Format: Ariella B. Hanker, Harikrishna Sekar Jayanthan, Dan Ye, Chang-Ching Lin, Hiroaki Akamatsu, Jonathan H. Sheehan, James P. Koch, Dhivya R. Sudhan, Monica Red Brewer, Alberto Servetto, Jie He, Vincent A. Miller, Alshad S. Lalani, Jens Meiler, Carlos L. Arteaga. Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, breast cancer progression, and HER2 inhibitor sensitivity [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 GS6-04.

Hyperactivation of TORC1 Drives Resistance to the Pan-HER Tyrosine Kinase Inhibitor Neratinib in HER2-Mutant Cancers

We developed neratinib-resistant HER2-mutant cancer cells by gradual dose escalation. RNA sequencing identified TORC1 signaling as an actionable mechanism of drug resistance. Primary and acquired neratinib resistance in HER2-mutant breast cancer patient-derived xenografts (PDXs) was also associated with TORC1 hyperactivity. Genetic suppression of RAPTOR or RHEB ablated P-S6 and restored sensitivity to the tyrosine kinase inhibitor. The combination of the TORC1 inhibitor everolimus and neratinib potently arrested the growth of neratinib-resistant xenografts and organoids established from neratinib-resistant PDXs. RNA and whole-exome sequencing revealed RAS-mediated TORC1 activation in a subset of neratinib-resistant models. DNA sequencing of HER2-mutant tumors clinically refractory to neratinib, as well as circulating tumor DNA profiling of patients who progressed on neratinib, showed enrichment of genomic alterations that converge to activate the mTOR pathway.

Abstract 4402: FGFR1 signaling modulates estrogen-independent ER transcriptional activity in ER+/FGFR1-amplified breast cancer cells

Background: FGFR1 amplification occurs in about 15% of estrogen receptor-positive (ER+) breast cancers and is associated with resistance to endocrine therapy. In these tumors, nuclear FGFR1 has been shown to interact with ERα. In addition, FGFR1 has been demonstrated to alter gene expression through binding to chromatin. However, the mechanisms underpinning nuclear FGFR1-mediated gene transcription remain unclear. Thus, we sought to elucidate the genomic and non-genomic role of FGFR1 in ER+/FGFR1-amplified breast cancer.

Methods: FGFR1 ChIP-Seq and ERα ChIP-Seq were performed on CAMA1 ER+/FGFR1-amplified breast cancer cells. ChIP-qPCR was employed to quantify DNA binding events. For ChIP-Seq, immunoblot, RT-qPCR, Estrogen Response Element (ERE) luciferase reporter and growth assays, CAMA1 cells were plated in estrogen-free media for 24 hours and then stimulated with 100 ng/ml FGF3 or 1 nM β-Estradiol.

Results: FGFR1 ChIP-Seq detected 2211 DNA binding sites in CAMA1 cells cultured in estrogen-free conditions. Gene Set Enrichment Analysis (GSEA) revealed that the TNFα signaling via NF-KB, MYC targets, G2M checkpoints, ERE early and ERE late response genes (all FDR <0.00001) were among the most enriched gene sets. The majority of binding sites occurred in promoter regions, supporting a role of FGFR1 in regulation of gene transcription. FGFR1 ChIP-qPCR confirmed FGFR1 binding to promoter regions of oncogenes including CCND1, MYC, VEGFA, JUNB and SMAD5. FGF3 stimulation of CAMA1 cells further enriched FGFR1 binding to the CCND1 promoter and upregulation of CCND1 mRNA and protein levels. These effects were ablated upon addition of the pan-FGFR tyrosine kinase inhibitor rogaratinib. Motif analysis revealed CTCF (CCCTC binding factor) as the most enriched motif (p=1e-91). siRNA-mediated knockdown of CTCF inhibited FGF3-induced ERα transcriptional activity and proliferation of CAMA1 cells. These results suggest a role for CTCF in mediating the transcriptional programs regulated by FGFR1. We reported an association of nuclear FGFR1 and ERα in ER+/FGFR1-amplified breast cancer cells. Thus, we next investigated the role of FGF3-induced FGFR signaling on estrogen-independent ERα transcription using ERα ChIP-Seq. FGF3 stimulation of CAMA1 cells resulted in 407 DNA binding sites of which 155 were unique compared to cells in the absence of ligand. GSEA of these 155 peaks revealed enrichment for ERE early (p=3.08e-17) and ERE late (p=2.6e-5) response genes. FGF3-mediated induction of ERα transcriptional program was confirmed by ERE reporter assay and was abrogated by treatment with rogaratinib.

Conclusions: These findings suggest a FGFR1 kinase-dependent role on ER-mediated transcription in ER+/FGFR1-amplified breast cancer cells. We are currently performing mass spectrometry analysis to identify binding partners of nuclear FGFR1 that mediate its transcriptional function.

Citation Format: Alberto Servetto, Luigi Formisano, Rahul Kollipara, Dhivya R. Sudhan, Kyung-min Lee, Sumanta Chatterjee, Ariella B. Hanker, Saurabh Mendiratta, Ralf Kittler, Carlos L. Arteaga. FGFR1 signaling modulates estrogen-independent ER transcriptional activity in ER+/FGFR1-amplified breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4402.

Challenges for the Clinical Development of PI3K Inhibitors: Strategies to Improve Their Impact in Solid Tumors

The PI3K pathway is mutated and aberrantly activated in many cancers and plays a central role in tumor cell proliferation and survival, making it a rational therapeutic target. Until recently, however, results from clinical trials with PI3K inhibitors in solid tumors have been largely disappointing. Here, we describe several factors that have limited the success of these agents, including the weak driver oncogenic activity of mutant PI3K, suboptimal patient selection in trials, drug-related toxicities, feedback upregulation of compensatory mechanisms when PI3K is blocked, increased insulin production upon PI3Kα inhibition, lack of mutant-specific inhibitors, and a relative scarcity of studies using combinations with PI3K antagonists. We also suggest strategies to improve the impact of these agents in solid tumors. Despite these challenges, we are optimistic that isoform-specific PI3K inhibitors, particularly in combination with other agents, may be valuable in treating appropriately selected patients with PI3K-dependent tumors. SIGNIFICANCE: Despite the modest clinical activity of PI3K inhibitors in solid tumors, there is an increasing understanding of the factors that may have limited their success. Strategies to ameliorate drug-related toxicities, use of rational combinations with PI3K antagonists, development of mutant-selective PI3K inhibitors, and better patient selection should improve the success of these targeted agents against solid tumors.

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.

Abstract PD3-05: Co-occurring gain-of-function mutations in HER2 and HER3 cooperate to enhance HER2/HER3 binding, HER-dependent signaling, and breast cancer growth

ERBB2, the gene encoding HER2, is mutated in 2-4% of breast cancers. The HER2 tyrosine kinase inhibitor neratinib has shown clinical activity against breast cancers harboring HER2 activating mutations, suggesting these tumors depend on HER2 signaling. Co-occurring HER2 and HER3 (ERBB3) mutations have been reported in patients who respond to neratinib (Hanker et al., Cancer Discov. 2017) suggesting the possibility of cooperativity of both oncogenes. Co-expression of the mutant intracellular domains of HER2 and HER3 in HEK293 cells enhanced phosphorylation of HER3 and ERK compared to expression of either mutant alone, which was blocked by 100 nM neratinib. Interrogation of TCGA, METABRIC, Project GENIE, and Foundation Medicine datasets revealed that gain-of-function mutations in ERBB2 and ERBB3 co-occur with a statistically significant frequency. For example, in GENIE, ERBB2 mutations co-occur with mutations in ERBB3 (8.3% of ERBB2-mutant vs 2.3% of ERBB2 WT; q=1.37x10-10).

We hypothesized that co-occurring mutations in HER2 and HER3 cooperate to enhance HER2 signaling and dependence and breast cancer progression.

Thirty-four unique breast cancers were found to harbor co-occurring mutations in HER2 and HER3, the most common of which were ERBB2L755S/ERBB3E928G (n=10), ERBB2V777L/ERBB3E928G(n=6), and ERBB2L869R/Q/ERBB3E928G (n=4). Using co-immunoprecipitation assays with HER2 and HER3 antibodies in transfected HEK293 cells, we found that co-expression of HER3E928G with wild type (WT) HER2, or co-expression of HER2L755S or HER2L869R with HER3WT, slightly increased HER2-HER3 dimerization. However, binding was strongest between double mutants. This was accompanied by the highest levels of Y1289 p-HER3 in cells expressing both HER3E928G and each HER2L755S, HER2V777L, or HER2L869R compared to cells expressing each HER2 or HER3 mutant with a respective WT heterodimer partner. Structural modeling of the HER2L869R/HER3E928G double-mutant predicted that the HER3 mutation, located at the dimer interface, may enhance heterodimerization of the kinase domains through decreased bulk and electrostatic repulsion. We also noted that the HER2L755S mutation is predicted to be in close proximity to HER3E928G (<4 Å) and may impact binding affinity. Investigation of the structural basis for the enhanced binding of other double mutants is in progress.

MCF7 “knock-in” cells incorporating HER2L755S, HER2V777L, or HER2L869R (or HER2WT) were stably transduced with HER3E928G or HER3WT. Co-expression of double mutants strongly enhanced estrogen-independent growth in 3D Matrigel over cells expressing either mutant alone. We are currently testing inhibitors of HER2/HER3 signaling, including neratinib ± trastuzumab, trastuzumab + pertuzumab, and the ERBB1-3 antibody mixture Sym013, to determine therapeutic strategies to block the cooperative growth induced by co-occurring HER2 and HER2 mutations.

Conclusions: Co-expression of mutant HER2 and mutant HER3 promotes HER2/HER binding, HER3 phosphorylation, and breast tumor cell proliferation. We aim to identify therapeutic vulnerabilities for patients with co-occurring HER2 and HER3 mutations.

Citation Format: Hanker AB, Koch JP, Ye D, Sliwoski G, Sheehan J, Kinch LN, Red Brewer M, He J, Miller VA, Lalani AS, Cutler, Jr. RE, Croessmann S, Zabransky DJ, Meiler J, Arteaga CL. Co-occurring gain-of-function mutations in HER2 and HER3 cooperate to enhance HER2/HER3 binding, HER-dependent signaling, and breast cancer growth [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD3-05.

Abstract 1828: Hyperactivation of mTORC1 drives acquired resistance to the pan HER tyrosine kinase inhibitor neratinib in HER2 mutant cancers

Background: Tumor genomic profiling has identified patients with cancers harboring activating ERBB2 (HER2) mutations that are sensitive to HER2 targeted therapies. In the SUMMIT phase II ‘basket' trial, a subset of patients with ERBB2 mutant cancers have exhibited significant clinical benefit from treatment with the pan-HER irreversible tyrosine kinase inhibitor (TKI) neratinib. However, durable responses to neratinib are few, suggesting mechanisms of de novo and acquired drug resistance. Thus, we sought to identify druggable mechanisms of resistance to neratinib.

Methods: We utilized 5637 bladder cancer (with HER2S310F) and OVCAR8 ovarian cancer (with HER2G776V) cells. Drug resistant cells were developed by exposing cells to increasing concentrations of neratinib over 6 months (5637, 600 nM; OVCAR8, 2 µM). Neratinib resistant H1781 lung cancer cells (with HER2G776>VC) and MCF7 breast cancer cells (with L755S or V777L) knock-in mutations are currently being developed. For immunoblot and drug sensitivity assays, neratinib resistant cells were maintained drug-free for 96 hours and then retreated with neratinib and other inhibitors. Candidate pathways/genes driving neratinib resistance were identified by performing RNA sequencing and whole exome sequencing in drug-resistant and -sensitive cells.

Results: Neratinib-resistant 5637 and OVCAR8 cells were cross-resistant to the HER2 TKIs afatinib and lapatinib. Immunoblot analysis of both cells treated with neratinib showed effective suppression of HER2, EGFR and HER3 phosphorylation. However, they exhibited a striking increase in S6 kinase (S6K) activity and S6 phosphorylation compared to drug-sensitive parental cells, which was maintained in the presence of supra-pharmacological levels of neratinib (1 µM). S6 phosphorylation and viability of drug resistant cells was completely ablated by the combination of neratinib and the mTORC1 inhibitor everolimus, but not with the PI3Kα inhibitor alpelisib, the pan-PI3K inhibitor buparlisib, or the AKT inhibitor MK-2206, suggesting PI3K- and AKT-independent activation of mTORC1. Gene set enrichment analysis (GSEA) of RNA seq data from the drug-resistant cells revealed significant enrichment of K-Ras pathway components in addition to mTORC1 pathway. Consistent with these results, whole exome sequencing revealed activating alterations of the Ras pathway including a truncating mutation in RASA2 and a P200L mutation in PIK3CA Ras binding domain; thereby suggesting potential Ras mediated mTOR activation driving neratinib resistance. Studies are underway to confirm the contribution of Ras pathway in mTOR mediated neratinib resistance.

Conclusions: These data suggest that hyperactivation of mTORC1 promotes acquired resistance to neratinib across histologically distinct ERBB2-mutant cancers.

Citation Format: Dhivya R. Sudhan, Ariella B. Hanker, Angel Guerrero-Zotano, Luigi Formisano, Yan Guo, Qi Liu, Francesca Avogadri-Connors, Richard E. Cutler, Alshad S. Lalani, Richard Bryce, Alan Auerbach, Carlos L. Arteaga. Hyperactivation of mTORC1 drives acquired resistance to the pan HER tyrosine kinase inhibitor neratinib in HER2 mutant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1828.

Genomic alterations of ERBB receptors in cancer: clinical implications

The ERBB family of receptor tyrosine kinases has been implicated in carcinogenesis for over three decades with rigorous attention to EGFR and HER2. ERBB receptors, consisting of EGFR, HER2, HER3, and HER4 are part of a complicated signaling network that activates downstream signaling pathways including PI3K/AKT, Ras/Raf/MAPK, JAK/STAT and PKC. It is well established that EGFR is amplified and/or mutated in gliomas and non-small-cell lung carcinoma while HER2 is amplified and/or over-expressed in breast, gastric, ovarian, non-small cell lung carcinoma, and several other tumor types. With the advent of next generation sequencing and large scale efforts to explore the entire spectrum of genomic alterations involved in human cancer progression, it is now appreciated that somatic ERBB receptor mutations occur at relatively low frequencies across multiple tumor types. Some of these mutations may represent oncogenic driver events; clinical studies are underway to determine whether tumors harboring these alterations respond to small molecule EGFR/HER2 inhibitors. Recent evidence suggests that some somatic ERBB receptor mutations render resistance to FDA-approved EGFR and HER2 inhibitors. In this review, we focus on the landscape of genomic alterations of EGFR, HER2, HER3 and HER4 in cancer and the clinical implications for patients harboring these alterations.

Abstract 1008: Gain-of-function kinase library screen identifies FGFR1 amplification as a mechanism of resistance to antiestrogens and CDK4/6 inhibitors in ER+ breast cancer

The CDK4/6 inhibitor palbociclib was recently 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. 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 (Novartis). In MCF7 cells treated with fulvestrant alone or with ribociclib, we identified 21 and 17 kinases, respectively, which induced a >30% increase in cell viability compared to control cells; 11 of these kinases overlapped in both treatment 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 11 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 five genes showed only FGFR1 to be amplified/overexpressed in 17% 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, each 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 regressions in all mice without associated toxicity. Treatment of FGFR-amp cells with FGF-2 strongly induced CCND1 (cyclin D1) expression. Downregulation of CCND1 with CCND1 RNAi oligonucleotides or kinase inhibition with erdafitinib restored sensitivity of FGFR1-amp cells to fulvestrant/palbociclib. Conversely, overexpression of CCND1 in MCF7 cells induced resistance to estrogen deprivation and fulvestrant ± palbociclib. At this time, we are examining whether FGFR1 amplification measured by FISH correlates with maintenance of proliferation (Ki67) in 110 patients with ER+/HER2- breast cancer treated with palbociclib for 14 days immediately before surgery (Arnedos et al. ASCO 2016). In summary, using a gain-of-function ORF kinome screen, we identified FGFR1 amplification as a mechanism of resistance to anti-ER therapies ± CDK4/6 inhibitors. Based on these data we propose FGFR inhibitors should be tested in combination with ER antagonists and CDK4/6 inhibitors in patients with ER+/FGFR amplified breast cancer.

Citation Format: Luigi Formisano, Yao Lu, Valerie M. Jansen, Joshua A. Bauer, Ariella B. Hanker, Melinda E. Sanders, Paula González-Ericsson, Sunkyu Kim, Monica Arnedos, Fabrice André, Carlos L. Arteaga. 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 American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1008. doi:10.1158/1538-7445.AM2017-1008

Extracellular Matrix/Integrin Signaling Promotes Resistance to Combined Inhibition of HER2 and PI3K in HER2+ Breast Cancer

PIK3CA mutations are associated with resistance to HER2-targeted therapies. We previously showed that HER2⁺/PIK3CA^H1047R transgenic mammary tumors are resistant to the HER2 antibodies trastuzumab and pertuzumab but respond to PI3K inhibitor buparlisib (TPB). In this study, we identified mechanisms of resistance to combined inhibition of HER2 and PI3K. TPB-resistant tumors were generated by treating HER2⁺/PIK3CA^H1047R tumor-bearing mice long term with the drug combination. RNA sequencing of TPB-resistant tumors revealed that extracellular matrix and cell adhesion genes, including collagen II (Col2a1), were markedly upregulated, accompanied by activation of integrin β1/Src. Cells derived from drug-resistant tumors were sensitive to TBP when grown in vitro, but exhibited resistance when plated on collagen or when reintroduced into mice. Drug resistance was partially reversed by the collagen synthesis inhibitor ethyl-3,4-dihydroxybenzoate. Inhibition of integrin β1/Src blocked collagen-induced resistance to TPB and inhibited growth of drug-resistant tumors. High collagen II expression was associated with significantly lower clinical response to neoadjuvant anti-HER2 therapy in HER2⁺ breast cancer patients. Overall, these data suggest that upregulation of collagen/integrin/Src signaling contributes to resistance to combinatorial HER2 and PI3K inhibition. Cancer Res; 77(12); 3280-92. ©2017 AACR.

HER2-Overexpressing Breast Cancers Amplify FGFR Signaling upon Acquisition of Resistance to Dual Therapeutic Blockade of HER2

Purpose: Dual blockade of HER2 with trastuzumab and lapatinib or pertuzumab has been shown to be superior to single-agent trastuzumab. However, a significant fraction of HER2-overexpressing (HER2⁺) breast cancers escape from these drug combinations. In this study, we sought to discover the mechanisms of acquired resistance to the combination of lapatinib + trastuzumab.Experimental Design: HER2⁺ BT474 xenografts were treated with lapatinib + trastuzumab long-term until resistance developed. Potential mechanisms of acquired resistance were evaluated in lapatinib + trastuzumab-resistant (LTR) tumors by targeted capture next-generation sequencing. In vitro experiments were performed to corroborate these findings, and a novel drug combination was tested against LTR xenografts. Gene expression and copy-number analyses were performed to corroborate our findings in clinical samples.Results: LTR tumors exhibited an increase in FGF3/4/19 copy number, together with an increase in FGFR phosphorylation, marked stromal changes in the tumor microenvironment, and reduced tumor uptake of lapatinib. Stimulation of BT474 cells with FGF4 promoted resistance to lapatinib + trastuzumab in vitro Treatment with FGFR tyrosine kinase inhibitors reversed these changes and overcame resistance to lapatinib + trastuzumab. High expression of FGFR1 correlated with a statistically shorter progression-free survival in patients with HER2⁺ early breast cancer treated with adjuvant trastuzumab. Finally, FGFR1 and/or FGF3 gene amplification correlated with a lower pathologic complete response in patients with HER2⁺ early breast cancer treated with neoadjuvant anti-HER2 therapy.Conclusions: Amplification of FGFR signaling promotes resistance to HER2 inhibition, which can be diminished by the combination of HER2 and FGFR inhibitors. Clin Cancer Res; 23(15); 4323-34. ©2017 AACR.

An Acquired HER2T798I Gatekeeper Mutation Induces Resistance to Neratinib in a Patient with HER2 Mutant-Driven Breast Cancer

We report a HER2^T798I gatekeeper mutation in a patient with HER2^L869R-mutant breast cancer with acquired resistance to neratinib. Laboratory studies suggested that HER2^L869R is a neratinib-sensitive, gain-of-function mutation that upon dimerization with mutant HER3^E928G, also present in the breast cancer, amplifies HER2 signaling. The patient was treated with neratinib and exhibited a sustained partial response. Upon clinical progression, HER2^T798I was detected in plasma tumor cell-free DNA. Structural modeling of this acquired mutation suggested that the increased bulk of isoleucine in HER2^T798I reduces neratinib binding. Neratinib blocked HER2-mediated signaling and growth in cells expressing HER2^L869R but not HER2^L869R/T798I In contrast, afatinib and the osimertinib metabolite AZ5104 strongly suppressed HER2^L869R/T798I-induced signaling and cell growth. Acquisition of HER2^T798I upon development of resistance to neratinib in a breast cancer with an initial activating HER2 mutation suggests HER2^L869R is a driver mutation. HER2^T798I-mediated neratinib resistance may be overcome by other irreversible HER2 inhibitors like afatinib.Significance: We found an acquired HER2 gatekeeper mutation in a patient with HER2-mutant breast cancer upon clinical progression on neratinib. We speculate that HER2^T798I may arise as a secondary mutation following response to effective HER2 tyrosine kinase inhibitors (TKI) in other cancers with HER2-activating mutations. This resistance may be overcome by other irreversible HER2 TKIs, such as afatinib. Cancer Discov; 7(6); 575-85. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 539.

Abstract P3-03-03: An acquired HER2 T798I gatekeeper mutation induces resistance to neratinib in a patient with HER2 mutant-driven breast cancer

ERBB2, the gene encoding HER2, is mutated in 2-4% of breast cancers. The HER2 irreversible tyrosine kinase inhibitor (TKI) neratinib has shown clinical activity against breast cancer cells harboring HER2 activating mutations. Here, we report for the first time an acquired gatekeeper HER2T798I mutation in a patient with HER2-mutant breast cancer after an initial exceptional response to neratinib.

A patient with ER+/PR+/HER2-negative invasive lobular breast cancer progressing on standard therapy was found to harbor a L869R kinase domain mutation in HER2. HER2L869R is homologous to the known activating mutation EGFRL861R/Q. MCF10A breast epithelial cells expressing HER2L869R displayed enhanced HER2-mediated signaling and were resistant to lapatinib and trastuzumab but sensitive to neratinib. The patient was enrolled in the phase II SUMMIT trial (NCT01953926) and treated with neratinib, achieving a partial response lasting 16 months before developing progression. Next gen sequencing of DNA from both a new skin metastasis and plasma cell-free DNA (cfDNA) identified HER2L869R (8.7% cfDNA), whereas a novel HER2T798I mutation was detected only in plasma at 1.3%. Deep sequencing of pre-therapy tumor tissue and plasma did not detect HER2T798I, suggesting that this mutation arose upon resistance. HER2T798I has not been reported in TCGA, COSMIC, or among plasma samples from 17,345 cancer patients subjected to digital DNA sequencing using the Guardant360 assay.

HER2T798I is homologous to the EGFRT790M, KITT670I and BCR-ABLT315I gatekeeper mutations known to mediate resistance to erlotinib/gefitinib and imatinib. To examine if HER2T798I mediates resistance to neratinib, we employed biochemical and biological assays and molecular modeling of wild-type (WT) HER2 and HER2T798I. Structural modeling showed the increased bulk of the isoleucine at position 798 would result in a steric clash with neratinib, thus reducing drug binding. We stably expressed HER2WT, HER2T798I, HER2L869R and HER2L869R/T798I in MCF10A cells and NR6 mouse fibroblasts. Neratinib (10-100 nM) blocked HER2-mediated signaling in cells expressing HER2WT or HER2L869R but did not in cells expressing HER2T798I. The EGFR irreversible TKI osimertinib (100 nM), which isselective for mutant EGFR (including EGFRT790M) and approved for treatment of NSCLC expressing EGFRT790M, failed to inhibit HER2WT, HER2L869R or HER2T798I. In contrast, either the EGFR/HER2 irreversible TKI afatinib or AZ5104, a metabolite of osimertinib, strongly blocked signaling induced by HER2WT, HER2L869R or HER2T798I. Cells expressing HER2T798M displayed a significantly higher IC50 to neratinib than cells expressing HER2WT, whereas afatinib or AZ5014 were very active against all cells (IC50<10 nM).

Conclusions: The acquisition of a T798I gatekeeper mutation in HER2 upon development of clinical resistance to neratinib in a breast cancer with an initial activating mutation in HER2 strongly suggests that HER2L869R is a driver mutation. We speculate that HER2T798I may arise as a secondary mutation following response to effective HER2 TKIs in other cancers with HER2 activating mutations. Certain irreversible EGFR inhibitors may be effective in patients with HER2-driven breast cancer resistant to neratinib.

Citation Format: Hanker AB, Red Brewer M, Sheehan JH, Koch JP, Lanman R, Hyman DM, Cutler, Jr. RE, Lalani AS, Cross D, Lovly CM, Meiler J, Arteaga CL. An acquired HER2 T798I gatekeeper mutation induces resistance to neratinib in a patient with HER2 mutant-driven breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-03-03.

Transcriptome- and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA H1047R in HER2/ER-positive breast cancer

PURPOSE

Phosphatidylinositol 3-kinase (PI3K)/AKT pathway aberrations are common in human breast cancer. Furthermore, PIK3CA mutations are commonly associated with resistance to anti-epidermal growth factor receptor 2 (HER2) or anti-estrogen receptor (ER) agents in HER2 or ER positive (HER2⁺/ER⁺) breast cancer. Hence, deciphering the underlying mechanisms of PIK3CA mutations in HER2⁺/ER⁺ breast cancer would provide novel insights into elucidating resistance to anti-HER2/ER therapies.

METHODS

In this study, we systematically investigated the biological consequences of PIK3CA ^H1047R in HER2⁺/ER⁺ breast cancer by uniquely incorporating mRNA transcriptomic data from The Cancer Genome Atlas and proteomic data from reverse-phase protein arrays.

RESULTS

Our integrative bioinformatics analyses revealed that several important pathways such as STAT3 and VEGF/hypoxia were selectively altered by PIK3CA ^H1047R in HER2⁺/ER⁺ breast cancer. Protein differential expression analysis indicated that an elevated eIF4G might promote tumor angiogenesis and growth via regulation of the hypoxia-activated switch in HER2⁺ PIK3CA ^H1047R breast cancer. We observed hypo-phosphorylation of EGFR in HER2⁺ PIK3CA ^H1047R breast cancer versus HER2⁺PIK3CA^wild-type (PIK3CA ^WT). In addition, ER and PIK3CA ^H1047R might cooperate to activate STAT3, MAPK, AKT, and Hippo pathways in ER⁺ PIK3CA ^H1047R breast cancer. A higher YAP_pS127 level was observed in ER⁺ PIK3CA ^H1047R patients than that in an ER⁺ PIK3CA ^WT subgroup. By examining breast cancer cell lines having both microarray gene expression and drug treatment data from the Genomics of Drug Sensitivity in Cancer and the Stand Up to Cancer datasets, we found that the elevated YAP1 mRNA expression was associated with the resistance of BCL-2 family inhibitors, but with the sensitivity to MEK/MAPK inhibitors in breast cancer cells.

CONCLUSIONS

In summary, these findings shed light on the functional consequences of PIK3CA ^H1047R-driven breast tumorigenesis and resistance to the existing therapeutic agents in HER2⁺/ER⁺ breast cancer.

Abstract 302: ECM/Integrin signaling promotes resistance to the combination of HER2 and PI3K inhibitors in HER2+, PIK3CA-mutant breast cancer

HER2 amplification and activating mutations in PIK3CA, the gene encoding the p110α subunit of PI3K, often co-occur in breast cancer. We generated a transgenic mouse model of HER2-overexpressing (HER2+), PIK3CAH1047R-mutant breast cancer. In these mice, PIK3CAH1047R accelerates HER2-mediated tumor formation and promotes resistance to HER2 inhibitors (Hanker et al. PNAS 2013). HER2+/PIK3CA tumor growth was inhibited by treatment with the HER2 antibodies trastuzumab and pertuzumab in combination with the pan-PI3K inhibitor BKM120 (TPB). We sought to discover mechanisms of acquired resistance to the triple therapy by long-term treatment of established HER2+/PIK3CA tumors. Tumor transplants derived from a transgenic HER2+/PIK3CA tumor were initially growth inhibited by TPB. After several weeks, a subset of transplants (3/11) resumed growth in the presence of continuous TPB therapy. TPB-resistant tumors were cross-resistant to the combination of T + P + BYL719 (a p110α-specific inhibitor).

Whole exome sequencing did not identify acquired somatic alterations in TPB-resistant tumors, including in HER2. However, RNA-seq revealed significant transcriptional upregulation of extracellular matrix (ECM) genes and genes involved in cell adhesion, including collagens, tenascins, and thrombospondins. Likewise, trichrome staining revealed a significant increase in collagen fibers and IHC analysis confirmed increased Tenascin expression in the TPB-resistant tumor stroma. In addition, western blot analysis revealed increased expression of an activated form of integrin β1, a substrate for ECM ligands such as collagen, as well as P-SrcY416 (activated by integrins/focal adhesion). We also found that transcription of many of these genes is induced by short-term TPB treatment in human breast cancer cell lines by qRT-PCR.

Interestingly, primary tumor cells derived from TPB-resistant tumors no longer displayed resistance when grown in vitro. These cells regained TPB resistance when re-introduced into mice. Plating primary tumor cells on growth factor-reduced Matrigel or on Collagen I-coated plates restored resistance, suggesting that the ECM directly promotes TPB resistance. We are currently investigating whether inhibition of Integrin/Src signaling reverses TPB resistance. We are also exploring whether components of the ECM are altered in residual disease specimens from HER2+ breast cancer patients treated with neoadjuvant anti-HER2 therapies. Our data suggest that upregulation of ECM/integrin/Src signaling contributes to resistance to combinations of HER2 and PI3K inhibitors, and strongly support the growing body of literature indicating that components of the tumor microenvironment promote resistance to targeted therapies.

Citation Format: Ariella B. Hanker, Monica Valeria Estrada, Junfei Zhao, Feixiong Cheng, Preston D. Moore, Darren Tyson, Violeta Sanchez, Brent N. Rexer, Melinda Sanders, Zhongming Zhao, Thomas P. Stricker, Carlos L. Arteaga. ECM/Integrin signaling promotes resistance to the combination of HER2 and PI3K inhibitors in HER2+, PIK3CA-mutant breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 302.

Abstract PR05: The effect of chemotherapy on HER2+ breast cancer heterogeneity measured by STAR-FISH: Detection of PIK3CA mutation and HER2 amplification at single-cell level in situ

Current therapies in HER2-positive breast cancer are effective in only a subset of cases and part of the resistance is attributed to single nucleotide mutation H1047R in PIK3CA. Conventional PIK3CA mutation detection methods require isolation of DNA from the tumor bulk, which requires relatively large amount of tissue and may not detect mutations in rare cancer cells.

We developed a novel method, Specific-To-Allele PCR-FISH (STAR-FISH), which allows for in situ detection of point mutation and gene amplification at single cell level. The assay consists of in situ PCR steps with mutation specific primers, followed by hybridization of a fluorescently labeled DNA probe homologous to PCR primer overhangs and probes for genomic regions of interest. The STAR-FISH signals present in intact formalin-fixed paraffin embedded (FFPE) samples are imaged and quantified in each individual nucleus within a tissue, with false discovery rate at 0.001, which facilitates identification of sub-populations of cells with different genetic makeup. The method was validated against FACS, immunofluorescence, droplet digital PCR, and MassArray; high correlation of the results was observed (R2=0.901 -0.9037, p<0.001).

We applied STAR-FISH for PIK3CA hot-spot mutation and HER2 amplification to FFPE samples of HER2 positive breast tumors from 22 patients. For each case a chemotherapy naïve core needle biopsy and a post-neoadjuvant chemotherapy sample upon tumor resection were collected. STAR-FISH analysis was performed on 3-5 regions of each sample, to account for intratumor heterogeneity. Long-term patient survival data after adjuvant treatment, mostly with trastuzumab, were available for all the patients.

High-sensitivity of STAR-FISH allowed us to detect rare single cells carrying PIK3CA mutation in most of the pre-treatment samples. After adjuvant chemotherapy the frequency of these cells was significantly increased. Since the STAR-FISH signals are quantified in each individual nucleus, subpopulations of cells with PIK3CA mutation or HER2 amplification or both features can be distinguished. Based on frequencies of cells within each of these subpopulations we calculated Shannon diversity index for each pre- and post-chemotherapy sample. The index was significantly increased after treatment. However, only topologic and not overall changes in diversity predicted poor long-term survival of the patients.

In addition to analyzing the frequency of cells with PIK3CA mutation, HER2 amplification or both changes, STAR-FISH also assesses the spatial distribution of genetically distinct subtypes. We have found that cells with PIK3CA mutation, irrespective of their HER2 status, are much more dispersed within tumors after neaodjuvant chemotherapy, whereas cells with HER2 amplification and wild-type PIK3CA cluster together. These results suggest that PIK3CA mutant cells are more migratory and invasive, in agreement with prior studies of cell lines and animal models.

STAR-FISH provides a unique view into genetic intratumor heterogeneity since thousands of cells within different regions of a single tumor biopsy can be analyzed within their tissue environment. Application of this novel in situ method allowed us to detect rare cells with PIK3CA mutation, pre-existing in the majority of treatment-naïve tumors and increasing in frequency after neoadjuvant chemotherapy. Moreover, STAR-FISH data revealed the correlation of chemotherapy-induced changes in intratumor heterogeneity with long-term survival of HER2+ breast cancer patients and support the significance of tumor diversity in situ analyses.

Citation Format: Michalina Janiszewska, Lin Liu, Vanessa Almendro, Yanan Kuang, Cloud Paweletz, Britta Weigelt, Rita A. Sakr, Tari A. King, Sarat Chandarlapaty, Jorge S. Reis-Filho, Ariella B. Hanker, Carlos L. Arteaga, Park So Yeon, Franziska Michor, Kornelia Polyak. The effect of chemotherapy on HER2+ breast cancer heterogeneity measured by STAR-FISH: Detection of PIK3CA mutation and HER2 amplification at single-cell level in situ. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr PR05.

Trastuzumab improves tumor perfusion and vascular delivery of cytotoxic therapy in a murine model of HER2+ breast cancer: preliminary results

To employ in vivo imaging and histological techniques to identify and quantify vascular changes early in the course of treatment with trastuzumab in a murine model of HER2+ breast cancer. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was used to quantitatively characterize vessel perfusion/permeability (via the parameter K (trans) ) and the extravascular extracellular volume fraction (v e ) in the BT474 mouse model of HER2+ breast cancer (N = 20) at baseline, day one, and day four following trastuzumab treatment (10 mg/kg). Additional cohorts of mice were used to quantify proliferation (Ki67), microvessel density (CD31), pericyte coverage (α-SMA) by immunohistochemistry (N = 44), and to quantify human VEGF-A expression (N = 29) throughout the course of therapy. Longitudinal assessment of combination doxorubicin ± trastuzumab (N = 42) tested the hypothesis that prior treatment with trastuzumab will increase the efficacy of subsequent doxorubicin therapy. Compared to control tumors, trastuzumab-treated tumors exhibited a significant increase in K (trans) (P = 0.035) on day four, indicating increased perfusion and/or vessel permeability and a simultaneous significant increase in v e (P = 0.01), indicating increased cell death. Immunohistochemical and ELISA analyses revealed that by day four the trastuzumab-treated tumors had a significant increase in vessel maturation index (i.e., the ratio of α-SMA to CD31 staining) compared to controls (P < 0.001) and a significant decrease in VEGF-A (P = 0.03). Additionally, trastuzumab dosing prior to doxorubicin improved the overall effectiveness of the therapies (P < 0.001). This study identifies and validates improved perfusion characteristics following trastuzumab therapy, resulting in an improvement in trastuzumab-doxorubicin combination therapy in a murine model of HER2+ breast cancer. This data suggests properties of vessel maturation. In particular, the use of DCE-MRI, a clinically available imaging method, following treatment with trastuzumab may provide an opportunity to optimize the scheduling and improve delivery of subsequent cytotoxic therapy.

In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer

Detection of minor, genetically distinct subpopulations within tumors is a key challenge in cancer genomics. Here we report STAR-FISH (specific-to-allele PCR-FISH), a novel method for the combined detection of single-nucleotide and copy number alterations in single cells in intact archived tissues. Using this method, we assessed the clinical impact of changes in the frequency and topology of PIK3CA mutation and HER2 (ERBB2) amplification within HER2-positive breast cancer during neoadjuvant therapy. We found that these two genetic events are not always present in the same cells. Chemotherapy selects for PIK3CA-mutant cells, a minor subpopulation in nearly all treatment-naive samples, and modulates genetic diversity within tumors. Treatment-associated changes in the spatial distribution of cellular genetic diversity correlated with poor long-term outcome following adjuvant therapy with trastuzumab. Our findings support the use of in situ single cell-based methods in cancer genomics and imply that chemotherapy before HER2-targeted therapy may promote treatment resistance.

Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer

Mutations in PIK3CA, the gene encoding the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K) have been shown to transform human mammary epithelial cells (MECs). These mutations are present in all breast cancer subtypes, including basal-like breast cancer (BLBC). Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 72 protein expression changes in human basal-like MECs with knock-in E545K or H1047R PIK3CA mutations versus isogenic MECs with wild-type PIK3CA. Several of these were secreted proteins, cell surface receptors or ECM interacting molecules and were required for growth of PIK3CA mutant cells as well as adjacent cells with wild-type PIK3CA. The proteins identified by MS were enriched among human BLBC cell lines and pointed to a PI3K-dependent amphiregulin/EGFR/ERK signaling axis that is activated in BLBC. Proteins induced by PIK3CA mutations correlated with EGFR signaling and reduced relapse-free survival in BLBC. Treatment with EGFR inhibitors reduced growth of PIK3CA mutant BLBC cell lines and murine mammary tumors driven by a PIK3CA mutant transgene, all together suggesting that PIK3CA mutations promote tumor growth in part by inducing protein changes that activate EGFR.

Abstract PD5-8: HER2/PIK3CAH1047R transgenic mammary tumors develop acquired resistance to triple therapy with trastuzumab, pertuzumab and PI3K inhibitors via multiple mechanisms

HER2 amplification and activating mutations in PIK3CA, the gene encoding the p110α subunit of PI3K, often co-occur in breast cancer. We generated a transgenic mouse model of HER2-overexpressing (HER2+), PIK3CAH1047R-mutant breast cancer. In these mice, PIK3CAH1047R accelerates HER2-mediated mammary epithelial transformation and metastatic progression, confers stem cell-like properties to HER2-overexpressing cancers and generates resistance to the combination of trastuzumab and pertuzumab (Hanker et al. PNAS 2013). HER2+/PIK3CA tumor growth was inhibited by treatment with the HER2 antibodies trastuzumab and pertuzumab in combination with the pan-PI3K inhibitor BKM120 (TPB). We sought to discover mechanisms of acquired resistance to the triple therapy by long-term treatment of established HER2+/PIK3CA tumors. We used tumor transplants derived from two HER2+/PIK3CA transgenic mice, #564 and #635. Tumor transplants from model 564 were initially growth inhibited by TPB, but did not regress. A subset of 564 transplants (3/11) resumed growth in the presence of continuous TPB therapy. All transplants (n=9) from model 635 regressed to a volume of &lt;100 mm3 within 6 weeks of treatment. All tumors recurred and 2 tumors continued growth when re-treated with TPB. Resistance was maintained following passaging in mice and tumors were cross-resistant to trastuzumab/pertuzumab/BYL719, a p110α-specific inhibitor. TPB-resistant tumor 635-2 expressed p95 HER2, which was not detected in untreated tumors. In contrast, HER2 expression was significantly reduced in TPB-resistant tumor 635-3. P-AKT remained suppressed in some resistant tumors, but was restored in others. Short-term TPB treatment strongly suppressed P-S6 in sensitive tumors, whereas P-S6 was no longer inhibited in all TPB-resistant tumors from both models. We are currently performing whole-exome sequencing and RNA-sequencing on TPB-resistant vs. untreated tumors in order to identify additional mechanisms of resistance. In parallel, we established human HER2+, PIK3CA-mutant cell lines (MDA-MB 453, UACC893, and HCC1954) resistant to TPB by long-term treatment (&gt;5 months) in the presence of the three drugs. Similar to the TPB-resistant tumors, P-S6 was no longer inhibited following TPB treatment in the resistant cell lines. Treatment with the TORC1/2 inhibitor MLN0128 abolished levels of P-S6 in HER2+/PIK3CAH1047R tumors. Combined treatment with MLN0128 and TPB inhibited growth of the drug-resistant tumors. Interestingly, Both TPB-resistant HER2+/PIK3CAH1047R tumor lines displayed resistance to the antibody-drug conjugate trastuzumab-DM1 (T-DM1) in vitro and in vivo, despite maintenance of HER2 overexpression. In addition, HCC1954 cells selected for resistance to TPB in culture were 66-fold less sensitive to T-DM1 than parental cells, despite maintaining equal levels of HER2 by western blot. These data suggest that multiple mechanisms may contribute to resistance to dual HER2 and PI3K blockade, including re-activation of mTOR signaling. We speculate that a similar heterogeneity of resistance mechanisms may occur in HER2+/PIK3CA-mutant metastases in patients.

Citation Format: Ariella B Hanker, Benjamin Bulen, Monica Red Brewer, Christian D Young, Kirsten M Farrar, Rebecca S Cook, Thomas P Stricker, Carlos L Arteaga. HER2/PIK3CAH1047R transgenic mammary tumors develop acquired resistance to triple therapy with trastuzumab, pertuzumab and PI3K inhibitors via multiple mechanisms [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD5-8.

Abstract 1822: HER2/PIK3CAH1047R transgenic tumors develop acquired resistance to triple therapy with trastuzumab, pertuzumab, and PI3K inhibitors via multiple mechanisms

The HER2 (ERBB2) oncogene is amplified in 20-25% of breast cancers and is associated with poor patient outcome. Activating mutations in PIK3CA, the gene encoding the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), occur in ∼30% of breast cancers. HER2 amplification and PIK3CA mutations often co-occur in breast cancer. Aberrant activation of the PI3K pathway correlates with a diminished response to HER2-directed therapies. We previously generated a conditional transgenic mouse model of HER2-overexpressing (HER2+), PIK3CAH1047R-mutant breast cancer. We showed that PIK3CAH1047R accelerates HER2-mediated breast epithelial transformation and metastatic progression, alters the intrinsic phenotype of HER2-overexpressing cancers and generates resistance to FDA-approved combinations of anti-HER2 therapies (Hanker et al. PNAS 2013). HER2+/PIK3CA tumor growth was inhibited by treatment with the HER2 antibodies trastuzumab and pertuzumab in combination with the pan-PI3K inhibitor BKM120 (TPB). We sought to discover mechanisms of acquired resistance to the triple therapy by long-term treatment of established HER2+/PIK3CA tumors. We utilized tumor transplants derived from two HER2+/PIK3CA transgenic mice, #564 and #635. Tumor transplants from model 564 were initially growth inhibited by TPB, but did not regress. A subset of 564 transplants (3/11) resumed growth in the presence of continuous TPB therapy. Resistance was maintained following passaging in mice and tumors were cross-resistant to trastuzumab/pertuzumab/BYL719, a p110α-specific inhibitor. P-AKT remained suppressed in resistant tumors, whereas P-ERK was elevated.

All transplants (n=9) from model 635 regressed to a volume of &lt;100 mm3 within 6 weeks of treatment. All tumors recurred within 2 months; 2 tumors continued growth when re-treated with TPB. Unlike the 564 resistant tumors, P-AKT was restored in the 635 resistant tumors, while short-term TPB treatment strongly inhibited P-AKT in the 635 tumors. TPB-resistant tumor 635-2 expressed p95 HER2, which was not detected in untreated tumors. In contrast, HER2 expression was significantly reduced in TPB-resistant tumor 635-3. We are currently performing whole-exome sequencing on TPB-resistant vs. untreated tumors in order to determine the mechanisms of resistance. Both 564 and 635 TPB-resistant tumor transplants displayed resistance to the antibody-drug conjugate trastuzumab-DM1, despite maintenance of HER2 overexpression. These early data suggest that multiple mechanisms may contribute to resistance to dual HER2 blockade in combination with PI3K inhibitors. In parallel, we are currently establishing human HER2+, PIK3CA-mutant cell lines resistant to TPB. We speculate that a similar heterogeneity of mechanisms of acquired resistance may occur in different HER2+/PIK3CA-mutant metastases in patients.

Citation Format: Ariella B. Hanker, Christian D. Young, Thomas P. Stricker, Rebecca S. Cook, Carlos L. Arteaga. HER2/PIK3CAH1047R transgenic tumors develop acquired resistance to triple therapy with trastuzumab, pertuzumab, and PI3K inhibitors via multiple mechanisms. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1822. doi:10.1158/1538-7445.AM2014-1822

Abstract B015: Knock-in of PIK3CA mutations in MCF10A mammary epithelial cells modifies their proteomic profile to resemble basal-like breast cancer and stimulate EGFR-dependent cell proliferation

PIK3CA, the gene encoding the p110α catalytic subunit of phosphatidylinositol-3 kinase (PI3K), is frequently mutated in breast cancer. Activating mutations in PIK3CA are known to transform mammary epithelial cells (MECs). Genomic knock-in of the two most frequent hot-spot PIK3CA mutations (E545K or H1047R) into MCF10A MECs resulted in growth factor-independent proliferation. Shotgun LC-MS/MS mass spectrometry analysis of wild type, E545K and H1047R MCF10A cell lysates revealed 73 proteins uniquely altered in the both mutant cell lines compared to wild type cells. KEGG pathway analysis demonstrated that PIK3CA mutant cells have elevated levels of proteins involved in focal adhesion, ECM-receptor interactions and actin cytoskeleton regulation. Nearly half the proteins upregulated in the mutant cells are secreted or involved in extracellular matrix (ECM) processing or signaling. The EGFR ligand amphiregulin was five-fold higher in the conditioned media harvested from PIK3CA mutant cells as compared to wild type cells. The conditioned media of PIK3CA mutant cells, but not that of wild-type cells, was sufficient to stimulate proliferation and EGFR phosphorylation in wild type MCF10A cells. Proliferation and EGFR activation were inhibited with an amphiregulin-neutralizing antibody or with EGFR neutralizing antibodies and kinase inhibitors. PIK3CA mutant cells downregulated PTPRF, a receptor tyrosine phosphatase. EGFR signaling and proliferation were stimulated in wild type cells when PTPRF was downregulated with siRNA, suggesting that PIK3CA mutant MCF10A cells activate EGFR-dependent proliferation by suppression of a negative regulatory phosphatase and increased secretion of amphiregulin.

The expression of transglutaminase 2, peroxidasin, fibronectin, integrin α5, laminin β3, laminin γ2, thrombospondin and EphA2, eight proteins upregulated in PIK3CA mutant MCF10A cells, was evaluated in a panel of breast cancer cell lines. All eight proteins were more highly expressed in basal-like compared to luminal-like breast cancer cell lines. The expression of PTPRF, which is decreased in PIK3CA mutant MCF10A cells, was lower in basal-like cell lines. Interrogation of microarray data demonstrated that the RNA signal of proteins upregulated in mutant PIK3CA MCF10A cells correlated with decreased relapse-free survival in basal-like, but not in luminal-like breast cancer. siRNA-mediated silencing of peroxidasin, laminin γ2, EphA2, integrin β1 or amphiregulin reduced the proliferation of PIK3CA mutant MCF10A cells, suggesting that these proteins are necessary for maintenance of the transformed phenotype. siRNA-mediated silencing of peroxidasin and EphA2 proteins also reduces the proliferation of basal-like breast cancer cells. Our proteomic analysis of PIK3CA mutant MCF10A cells revealed mechanisms of autocrine and paracrine induced proliferation and alterations mostly limited to basal-like breast cancer cells. These may serve as therapeutic targets in this subtype of breast cancer.

Citation Format: Christian D. Young, Lisa J. Zimmerman, Corbin A. Whitwell, Ariella B. Hanker, Thomas Stricker, Dana M. Brantley-Sieders, Ben Ho Park, Daniel C. Liebler, Rebecca S. Cook, Carlos L. Arteaga. Knock-in of PIK3CA mutations in MCF10A mammary epithelial cells modifies their proteomic profile to resemble basal-like breast cancer and stimulate EGFR-dependent cell proliferation. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B015.