Multiomics profiling of urothelial carcinoma in situ reveals CIS-specific gene signature and immune characteristics

Urothelial carcinoma in situ (CIS) is an aggressive phenotype of non-muscle-invasive bladder cancer. Molecular features unique to CIS compared to high-grade papillary tumors are underexplored. RNA sequencing of CIS, papillary tumors, and normal urothelium showed lower immune marker expression in CIS compared to papillary tumors. We identified a 46-gene expression signature in CIS samples including selectively upregulated known druggable targets MTOR, TYK2, AXIN1, CPT1B, GAK, and PIEZO1 and selectively downregulated BRD2 and NDUFB2. High expression of selected genes was significantly associated with CIS in an independent dataset. Mutation analysis of matched CIS and papillary tumors revealed shared mutations between samples across time points and mutational heterogeneity. CCDC138 was the most frequently mutated gene in CIS. The immunological landscape showed higher levels of PD-1-positive cells in CIS lesions compared to papillary tumors. We identified CIS lesions to have distinct characteristics compared to papillary tumors potentially contributing to the aggressive phenotype.

Endocrine-Sensitive Disease Rate in Postmenopausal Patients With Estrogen Receptor-Rich/ERBB2-Negative Breast Cancer Receiving Neoadjuvant Anastrozole, Fulvestrant, or Their Combination: A Phase 3 Randomized Clinical Trial

Importance

Adding fulvestrant to anastrozole (A+F) improved survival in postmenopausal women with advanced estrogen receptor (ER)-positive/ERBB2 (formerly HER2)-negative breast cancer. However, the combination has not been tested in early-stage disease.

Objective

To determine whether neoadjuvant fulvestrant or A+F increases the rate of pathologic complete response or ypT1-2N0/N1mic/Ki67 2.7% or less residual disease (referred to as endocrine-sensitive disease) over anastrozole alone.

Design, Setting, and Participants

A phase 3 randomized clinical trial assessing differences in clinical and correlative outcomes between each of the fulvestrant-containing arms and the anastrozole arm. Postmenopausal women with clinical stage II to III, ER-rich (Allred score 6-8 or >66%)/ERBB2-negative breast cancer were included. All analyses were based on data frozen on March 2, 2023.

Interventions

Patients received anastrozole, fulvestrant, or a combination for 6 months preoperatively. Tumor Ki67 was assessed at week 4 and optionally at week 12, and if greater than 10% at either time point, the patient switched to neoadjuvant chemotherapy or immediate surgery.

Main Outcomes and Measures

The primary outcome was the endocrine-sensitive disease rate (ESDR). A secondary outcome was the percentage change in Ki67 after 4 weeks of neoadjuvant endocrine therapy (NET) (week 4 Ki67 suppression).

Results

Between February 2014 and November 2018, 1362 female patients (mean [SD] age, 65.0 [8.2] years) were enrolled. Among the 1298 evaluable patients, ESDRs were 18.7% (95% CI, 15.1%-22.7%), 22.8% (95% CI, 18.9%-27.1%), and 20.5% (95% CI, 16.8%-24.6%) with anastrozole, fulvestrant, and A+F, respectively. Compared to anastrozole, neither fulvestrant-containing regimen significantly improved ESDR or week 4 Ki67 suppression. The rate of week 4 or week 12 Ki67 greater than 10% was 25.1%, 24.2%, and 15.7% with anastrozole, fulvestrant, and A+F, respectively. Pathologic complete response/residual cancer burden class I occurred in 8 of 167 patients and 17 of 167 patients, respectively (15.0%; 95% CI, 9.9%-21.3%), after switching to neoadjuvant chemotherapy due to week 4 or week 12 Ki67 greater than 10%. PAM50 subtyping derived from RNA sequencing of baseline biopsies available for 753 patients (58%) identified 394 luminal A, 304 luminal B, and 55 nonluminal tumors. A+F led to a greater week 4 Ki67 suppression than anastrozole alone in luminal B tumors (median [IQR], -90.4% [-95.2 to -81.9%] vs -76.7% [-89.0 to -55.6%]; P < .001), but not luminal A tumors. Thirty-six nonluminal tumors (65.5%) had a week 4 or week 12 Ki67 greater than 10%.

Conclusions and Relevance

In this randomized clinical trial, neither fulvestrant nor A+F significantly improved the 6-month ESDR over anastrozole in ER-rich/ERBB2-negative breast cancer. Aromatase inhibition remains the standard-of-care NET. Differential NET response by PAM50 subtype in exploratory analyses warrants further investigation.

Trial Registration

ClinicalTrials.gov Identifier: NCT01953588.

Kinase inhibitor pulldown assay (KiP) for clinical proteomics

Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169.

The Breast Cancer Proteome and Precision Oncology

The goal of precision oncology is to translate the molecular features of cancer into predictive and prognostic tests that can be used to individualize treatment leading to improved outcomes and decreased toxicity. Success for this strategy in breast cancer is exemplified by efficacy of trastuzumab in tumors overexpressing ERBB2 and endocrine therapy for tumors that are estrogen receptor positive. However, other effective treatments, including chemotherapy, immune checkpoint inhibitors, and CDK4/6 inhibitors are not associated with strong predictive biomarkers. Proteomics promises another tier of information that, when added to genomic and transcriptomic features (proteogenomics), may create new opportunities to improve both treatment precision and therapeutic hypotheses. Here, we review both mass spectrometry-based and antibody-dependent proteomics as complementary approaches. We highlight how these methods have contributed toward a more complete understanding of breast cancer and describe the potential to guide diagnosis and treatment more accurately.

Kinome Reprogramming Is a Targetable Vulnerability in ESR1 Fusion-Driven Breast Cancer

Transcriptionally active ESR1 fusions (ESR1-TAF) are a potent cause of breast cancer endocrine therapy (ET) resistance. ESR1-TAFs are not directly druggable because the C-terminal estrogen/anti-estrogen-binding domain is replaced with translocated in-frame partner gene sequences that confer constitutive transactivation. To discover alternative treatments, a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) was deployed to identify druggable kinases that are upregulated by diverse ESR1-TAFs. Subsequent explorations of drug sensitivity validated RET kinase as a common therapeutic vulnerability despite remarkable ESR1-TAF C-terminal sequence and structural diversity. Organoids and xenografts from a pan-ET-resistant patient-derived xenograft model that harbors the ESR1-e6>YAP1 TAF were concordantly inhibited by the selective RET inhibitor pralsetinib to a similar extent as the CDK4/6 inhibitor palbociclib. Together, these findings provide preclinical rationale for clinical evaluation of RET inhibition for the treatment of ESR1-TAF-driven ET-resistant breast cancer.

SIGNIFICANCE

Kinome analysis of ESR1 translocated and mutated breast tumors using drug bead-based mass spectrometry followed by drug-sensitivity studies nominates RET as a therapeutic target. See related commentary by Wu and Subbiah, p. 3159.

Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins

Triple-negative breast cancer (TNBC) constitutes 10%-15% of all breast tumors. The current standard of care is multiagent chemotherapy, which is effective in only a subset of patients. The original objective of this study was to deploy a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) to identify kinases elevated in non-pCR (pathologic complete response) cases for therapeutic targeting. Frozen optimal cutting temperature compound-embedded core needle biopsies were obtained from 43 patients with TNBC before docetaxel- and carboplatin-based neoadjuvant chemotherapy. KIPA was applied to the native tumor lysates that were extracted from samples with high tumor content. Seven percent of all identified proteins were kinases, and none were significantly associated with lack of pCR. However, among a large population of "off-target" purine-binding proteins (PBP) identified, seven were enriched in pCR-associated samples (P < 0.01). In orthogonal mRNA-based TNBC datasets, this seven-gene "PBP signature" was associated with chemotherapy sensitivity and favorable clinical outcomes. Functional annotation demonstrated IFN gamma response, nuclear import of DNA repair proteins, and cell death associations. Comparisons with standard tandem mass tagged-based discovery proteomics performed on the same samples demonstrated that KIPA-nominated pCR biomarkers were unique to the platform. KIPA is a novel biomarker discovery tool with unexpected utility for the identification of PBPs related to cytotoxic drug response. The PBP signature has the potential to contribute to clinical trials designed to either escalate or de-escalate therapy based on pCR probability.

Significance

The identification of pretreatment predictive biomarkers for pCR in response to neoadjuvant chemotherapy would advance precision treatment for TNBC. To complement standard proteogenomic discovery profiling, a KIPA was deployed and unexpectedly identified a seven-member non-kinase PBP pCR-associated signature. Individual members served diverse pathways including IFN gamma response, nuclear import of DNA repair proteins, and cell death.

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.

Abstract 5011: Targeting kinome reprogramming in ESR1 fusion-driven breast cancer

Background: Transcriptionally active ESR1 gene fusions (ESR1-TAF) are a potent cause of estrogen receptor alpha-positive (ERα+) breast cancer endocrine therapy (ET) resistance. These ESR1-TAF are gain-of-function mutations, exhibiting estrogen-independent cell growth, motility and ET resistance. They are not directly druggable because the ERα C-terminal ligand binding domain (LBD) encoding sequence is replaced with a translocated in-frame partner gene sequence. Herein we utilized proteomic approaches to develop novel targeted therapies against ESR1-TAF driven tumorigenesis.

Methods: ESR1 fusion cDNA constructs were expressed in ERα+ breast cancer cell lines (T47D and MCF7). Cell growth was assayed by an Alamar blue assay. A mass spectrometry (MS)-based Kinase Inhibitor Pulldown Assay (KIPA) was employed to identify druggable kinases that are commonly upregulated by diverse ESR1-TAFs. A panel of 22 ERα+ patient-derived xenograft (PDX) models were profiled using proteomics and phosphoproteomics to identify models with sensitivity to RET kinase inhibition.

Results: KIPA detected an increased abundance of a receptor tyrosine kinase, RET, in T47D cells expressing ESR1-TAFs in an estrogen-independent manner, compared to stable cell lines expressing transcriptionally inactive fusions as well as wild-type ERα protein. Interestingly, RET was also increased when constitutive activating ERα LBD point mutants, Y537S and D538G, were expressed in breast cancer cells. Inhibition of the RET kinase in vitro by repurposing pralsetinib, an FDA-approved RET inhibitor for advanced thyroid and non-small-cell lung cancers, demonstrated a significant reduction in the growth of cells expressing ESR1-TAFs and ERα LBD mutants. These data nominate RET kinase as a common therapeutic vulnerability for ESR1-TAF expressing breast cancers. Proteomic profiling of 22 biologically heterogenous ERα+ PDX tumors defined targetable pathways and predicted tumor subsets that were responsive to RET inhibition therapy. Organoids and xenografts from the pan-ET resistant WHIM18 PDX (that expresses the ESR1-YAP1 TAF) were inhibited by pralsetinib to a similar extent as the CDK4/6 inhibitor palbociclib. These data provide key preclinical rationale for the consideration of RET inhibition for the treatment of ESR1-TAF-driven ET-resistant breast cancer. Interestingly, the growth of WHIM37 PDX (that expresses ERα D538G) that had low level of RET and high level of GFRα-1, the co-receptor of RET, was also suppressed by pralsetinib. This data suggests that either RET or GFRα-1 is a predictive biomarker for RET inhibitor efficacy.

Conclusions: Kinome analysis of ESR1 translocated breast tumors using KIPA followed by drug sensitivity studies nominated RET as a new therapeutic target for ET-resistant ERα+ breast cancer.

Citation Format: Xuxu Gou, Beom-Jun Kim, Meenakshi Anurag, Jonathan T. Lei, Meggie N. Young, Matthew V. Holt, Diana Fandino, Craig T. Vollert, Purba Singh, Mohammad A. Alzubi, Anna Malovannaya, Lacey E. Dobrolecki, Michael T. Lewis, Shunqiang Li, Matthew J. Ellis, Charles E. Foulds. Targeting kinome reprogramming in ESR1 fusion-driven 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 5011.

Abstract P3-10-02: Cell cycle dysregulation in breast cancer: why the details matter

Cell cycle dysregulation is a prerequisite for cancer formation. However, whether the type of cell cycle dysregulation event a cell incurs during transformation to malignancy influences the type of cancer that evolves or clinical outcome is unknown. In a comprehensive analysis of cell cycle dysregulation in breast cancer patient tumors, we associate mutations in each of four cell cycle checkpoint kinase genes, ATM, CHEK2, ATR and CHEK1, with known tumor characteristics and clinical outcome, and test these associations experimentally using transgenic mice, patient-derived xenografts and breast cancer cell line model systems. Results of this work demonstrate that dysregulation of specific cell cycle checkpoint kinases differently impacts the type of breast cancer that evolves in patients and in experimental model systems, and influences treatment responsiveness and disease progression. For instance, CHEK2 mutations associate preferentially with the incidence of metastatic, premenopausal estrogen receptor (ER)+/HER2- breast cancer in patient data (p=0.001) that is resistant to standard frontline therapy (HR=6.15, p=0.01). These associations appear causal when tested in an immune-competent genetically-engineered mouse model of Chk2 loss, in patient-derived xenograft, and in cell line experiments. On the other hand, ATR mutation by itself is not frequent in ER+/HER2- breast cancer, but co-incident mutation of ATR and TP53 is 2-fold enriched (p=0.002) and associates with metastatic progression (HR=2.01, p=0.007). Concordantly, ATR dysregulation induces metastatic phenotypes in ER+/HER- TP53 mutant, but not in TP53 wildtype, cell lines. Together, these results systematize the impact of individual cell cycle checkpoint kinases on the evolution of cancer subtypes, and on disease progression. Statement of Significance These findings reframe the paradigm of breast cancer classification through the lens of early cell cycle dysregulation events by demonstrating that cell cycle decisions during malignant transformation can direct the type of breast cancer that evolves, how it will respond to treatment, and whether it will metastasize. This work provides rationale for streamlined testing of checkpoint kinase dysregulation to improve precision diagnostics for cancer patients.

Citation Format: Sinem Seker, Elena Oropeza, Sabrina Carrel, Aloran Mazumder, Nindo Punturi, Jonathan Lei, Meenakshi Anurag, Bora Lim, Matthew Bainbridge, Svasti Haricharan. Cell cycle dysregulation in breast cancer: why the details matter [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-10-02.

Abstract PD5-05: PD5-05 DAPK3 modulates migration and invasion of triple negative breast cancers

Triple negative breast cancer (TNBC) is associated with poorer prognosis compared to other subtypes of breast cancer due to aggressive metastatic behavior and lack of targeted therapies. Human kinases are a large family of proteins that play critical roles in multiple biological pathways, and aberrant expression or mutations of kinases drive cancer progression and metastasis. Therefore, we applied Mass Spectrometry (MS)-based Kinase-inhibitor pulldown (KiP) technology to profile unique kinase signatures associated with TNBC and prioritize novel regulators for this subtype. Human kinases were captured by a mixture of nine FDA-approved kinase inhibitors, each conjugated separately to sepharose beads to profile all the major branches of the kinome tree. We performed KiP assay in 16 patient-derived xenografts (PDXs) [PMC5379071] consisting of different molecular subtypes of breast cancers. Differential expression analysis identified Death Associated Protein Kinase 3 (DAPK3) as a significantly upregulated kinase in TNBC PDXs which somehow remains understudied. Furthermore, RNA-seq and proteomics data with the same set of PDXs revealed that the upregulation of DAPK3 expression in TNBC was exclusively at protein levels, not RNA levels. Consistently, DAPK3 protein levels were significantly elevated in TNBC cell lines in DepMap dataset. Genomic knockout of DAPK3 in SUM159 and MDA-MB-231 cells dramatically inhibited migration and invasion measured by the transwell assay. We also observed that DAPK3 knockout reduced the phosphorylation of Myosin Light Chain 2 (MLC2) at T18/S19 site, which was shown to regulate cancer cell invasion [PMC4195943]. DAPK3 belong to DAPK family protein, and has an N-terminus kinase domain with high homology to its family proteins, and a C-terminus leucine-zipper domain. While re-expression of wild-type (WT) DAPK3 cDNA can rescue the migration and invasion phenotype caused by DAPK3 knockout, kinase-dead mutant (D161N) and leucine-zipper-domain-deleted mutant (ΔLZ) cannot rescue the phenotype. Moreover, not only D161N, but also ΔLZ mutant cannot restore the phosphorylation level of MLC2 as DAPK3 WT does. Therefore, both kinase activity and leucin-zipper domain of DAPK3 are critical for the phosphorylation of its substrate MLC2 and thus migration and invasion phenotype. By unbiased Immunoprecipitation-Mass Spectrometry (IP-MS) method, we identified Leucine-Zipper Protein 1 (LUZP1) as one of the strongest interactors of DAPK3. Interestingly, LUZP1 also has a leucine-zipper domain on its N-terminus. Further study showed that DAPK3 binds to LUZP1 via its leucine-zipper domain as expected. Moreover, we observed a tight correlation between DAPK3 and LUZP1 protein expressions in the proteomics data of PDXs and DepMap cell lines (Pearson correlation coefficient is 0.90 and 0.81, respectively). However, the correlation at RNA levels is not significant. Besides, we found that DAPK3 protein stability, but not RNA, is dependent on LUZP1 presence in TNBC cells, strongly implying the roles of LUZP1 on the post-transcriptional regulation of DAPK3. To summarize, we demonstrated that DAPK3, as a novel TNBC-enriched protein, modulates migration and invasion possibly via MLC2 phosphorylation. Both kinase activity and leucine-zipper domain of DAPK3 is necessary for its functionality. We also found LUZP1 is a strong interactor and a potential regulator of DAPK3 in TNBC biology.

Citation Format: Junkai Wang, Beom-Jun Kim, Meenakshi Anurag, Xin Yu, Xiaoli Qi, Jin Wang, Bing Zhang, Chonghui Cheng, Matthew Ellis. PD5-05 DAPK3 modulates migration and invasion of triple negative breast cancers [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-05.

Abstract P2-23-01: Patient-derived xenografts allow deconvolution of single agent and combination chemotherapy responses in triple-negative breast cancer

Background: Triple-negative breast cancer (TNBC) patients frequently receive combination chemotherapy treatment, but a direct comparison of response to carboplatin, docetaxel, and their combination in 50 TNBC patient-derived xenografts (PDXs) showed that combination treatment was largely ineffective at generating enhanced responses over the best single agent. This suggests de-escalation of chemotherapy may be possible if molecular mechanisms and biomarkers underlying response to individual treatments can be identified. To this end, we performed multi-omics profiling for the 50 TNBC PDXs. Methods: Orthotopic TNBC PDXs were treated with four weekly cycles of docetaxel, carboplatin, or the combination. Changes in tumor volume after 4 weeks of treatment were assessed quantitatively and by modified RECIST criteria. Genomic, transcriptomic, and mass-spectrometry-based proteomic profiling were performed on baseline tumors prior to treatments to identify associations with chemotherapy response at the gene and pathway level. ProMS was used to integrate both RNA and protein data to select a 5 RNA feature combination for optimized prediction of carboplatin response in a logistic regression model. Publicly available neoadjuvant chemotherapy clinical datasets with transcriptomic data and response information used for validation/testing included TNBC samples from: GSE18864, I-SPY2 (GSE194040), and BrighTNess (GSE164458). Results: Proteogenomic profiles revealed distinct genes associated with response to each agent and their combination, respectively, suggesting distinct molecular mechanisms underlying response to each treatment. A substantial number of genes associated with single agent and combination treatment were validated in multiple independent patient cohorts receiving platinum and taxane containing neoadjuvant therapy, confirming clinical relevance of our PDX panel. For the same treatment, different types of molecular data identified distinct sets of associated genes, providing highly complementary information. At the pathway level, RNA and protein data converged to metabolic and E2F/G2M related pathways which were upregulated in PDXs resistant or responsive to all treatment types, respectively, while variable levels of MYC-related proliferation pathways were observed across all treatments suggesting pathways that are common across and unique to different treatments. Several individual genes found to be higher in PDXs with better response to either single-agent had discriminatory power in external clinical TNBC datasets treated with similar neoadjuvant chemotherapy regimens. In addition, a logistic regression-based carboplatin response prediction model trained to select a group of 5 RNA markers (TKT, MAGI2, ATF6B, MCM7, LRP6) using both RNA and protein data performed the best in predicting response to cisplatin in a clinical TNBC dataset vs predicting response to other datasets with taxane and platinum + taxane combination containing chemotherapy regimens, demonstrating specificity of the prediction model. These results suggest potential individual biomarkers or biomarker combinations to select TNBC tumors that may respond to either single agent carboplatin, docetaxel, or their combination. PDXs refractory to all treatment arms had higher levels of proteostasis-related pathways including proteasome degradation and the unfolded protein response (UPR) related to endoplasmic reticulum stress and altered levels of chromatin regulation. Subsequent pharmacological targeting of the UPR pathway and targeting HDACs enhanced chemotherapy response. Conclusion: Proteogenomic characterization identifies molecular mechanisms and putative biomarkers for stratifying TNBC tumors for single or combination chemotherapy treatments, suggests targeted therapies to augment chemotherapy response, and provides a valuable resource for researchers and clinicians.

Citation Format: Jonathan T. Lei, Chen Huang, Ramakrishnan R. Srinivasan, Suhas Vasaikar, Lacey E. Dobrolecki, Alaina N. Lewis, Na Zhao, Jin Cao, Susan G. Hilsenbeck, C. Kent Osborne, Mothaffar Rimawi, Matthew J. Ellis, Varduhi Petrosyan, Alexander B. Saltzman, Anna Malovannaya, John D. Landua, Bo Wen, Antrix Jain, Gerburg M. Wulf, Shunqiang Li, Daniel C. Kraushaar, Tao Wang, Xi Chen, Gloria V. Echeverria, Meenakshi Anurag, Bing Zhang, Michael T. Lewis. Patient-derived xenografts allow deconvolution of single agent and combination chemotherapy responses in triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-01.

Abstract P5-02-36: Proteogenomic profiling of fresh frozen core biopsies from CALGB 40601

Background: Targeted therapy for HER2+ breast cancer has significantly improved outcomes for this aggressive subtype. However, a subset of patients do not achieve pathological complete response (pCR). In CALGB 40601, a randomized Phase III Trial for neoadjuvant treatment of HER2+ primary breast cancer with Paclitaxel (T: taxane) combined with HER2 antibody therapy (H: Herceptin/Trastuzumab), the small molecule inhibitor Lapatinib (L), or the antibody-inhibitor combination, pCR frequency was 56% for the combination (THL arm), 46% for Trastuzumab (TH arm), and 32% for Lapatinib (TL arm, closed early because of lower efficacy) (PMID: 26527775). While a recent publication reports relapse-free survival (RFS), overall survival (OS), and RNA-based gene expression signatures that can predict pCR (PMID: 33095682), understanding the proteogenomic landscape of treatment response should facilitate identification of alternative and therapeutically tractable protein targets for treatment-resistant tumors. Methods: Microscaled proteogenomic profiling (PMID: 31988290) was performed on treatment-naïve, flash-frozen core needle biopsies from the CALGB 40601 trial obtained from the Alliance for Clinical Trials in Oncology tissue bank. Multi-omics profiling included whole-exome sequencing (WES), RNA-sequencing, and mass spectroscopy-based proteomics and phosphoproteomics from one or two cores from each patient. Results: Eighty baseline core biopsies from 54 patients, including 22 patients from the THL arm, 24 from the TH arm, and 8 from the TL arm, from the CALGB 40601 tissue archive were of sufficient quality to yield genomics, transcriptomics, and/or proteomics profiling data. The frequency of pCR for profiled samples was representative of the overall trial cohort. Linear models were employed to identify baseline determinants of pCR for each arm and to assess differences in genes associated with response between the TH and THL arms. Pathways associated with RNA processing, translation, and the proteasome were elevated in pCR tumors in TH and THL arms, while cell cycle, DNA replication and repair pathways were higher in pCR only in the THL arm. While enrichment of similar pathways was observed in pCR in the transcriptome, the proteome specifically showed enrichment of pathways associated with extracellular matrix and EMT in non-pCR in the THL but not the TH arm. In particular, “EMT”, “ECM-receptor interaction”, and “extracellular structure organization” constituted the most enriched pathways and GO terms that were higher in non-pCR than in pCR tumors from the combination arm (THL) in the proteomics data despite showing no enrichment in the transcriptomics data. Driving this pathway enrichment were several collagens and matrix metalloproteinases that were significantly elevated in non-pCR tumors at the protein but not the RNA level. Finally, kinase target enrichment of differential phosphorylation sites suggested that the activity of PAK1, a regulator of cytoskeletal remodeling, is elevated in non-pCR tumors from the THL arm (p=0.006), but not the TH arm (p=0.69). Conclusion: Proteogenomic analysis of archival HER2+ breast cancer core biopsies provides opportunities for identifying proteins and phosphorylation sites in treatment-naive tumors that are associated with pCR to neoadjuvant Paclitaxel/anti-HER2 therapy. Notably, proteomic but not transcriptomic data showed that ECM and EMT pathways were elevated in non-pCR tumors; thus, signatures encompassing these pathways may serve as biomarkers for aggressive HER2+ breast cancer that is more likely to evade treatment. Non-pCR tumors in the THL arm were also marked by elevated levels of PAK1 target phosphorylation sites, suggesting that this kinase may be a potential therapeutic target in HER2+ breast cancer that is refractory to combination anti-HER2 therapy.

Citation Format: Eric J. Jaehnig, Aranzazu Fernandez-Martinez, Tanmayi Vashist, Matthew V. Holt, LaTerrica Williams, Jonathan Lei, Beom-Jun Kim, Yongchao Dou, Viktoriya Korchina, Richard Gibbs, Donna Muzny, Harshavardhan Doddapaneni, Henry Rodriguez, Ana Robles, Tara Hiltke, DR Mani, Michael Gillette, Terry Hyslop, Yujia Wen, Linda McCart, George Miles, Steven Carr, Bing Zhang, Shankha Satpathy, Matthew Ellis, Meenakshi Anurag. Proteogenomic profiling of fresh frozen core biopsies from CALGB 40601 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-36.

Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer

Microscaled proteogenomics was deployed to probe the molecular basis for differential response to neoadjuvant carboplatin and docetaxel combination chemotherapy for triple-negative breast cancer (TNBC). Proteomic analyses of pretreatment patient biopsies uniquely revealed metabolic pathways, including oxidative phosphorylation, adipogenesis, and fatty acid metabolism, that were associated with resistance. Both proteomics and transcriptomics revealed that sensitivity was marked by elevation of DNA repair, E2F targets, G2-M checkpoint, interferon-gamma signaling, and immune-checkpoint components. Proteogenomic analyses of somatic copy-number aberrations identified a resistance-associated 19q13.31-33 deletion where LIG1, POLD1, and XRCC1 are located. In orthogonal datasets, LIG1 (DNA ligase I) gene deletion and/or low mRNA expression levels were associated with lack of pathologic complete response, higher chromosomal instability index (CIN), and poor prognosis in TNBC, as well as carboplatin-selective resistance in TNBC preclinical models. Hemizygous loss of LIG1 was also associated with higher CIN and poor prognosis in other cancer types, demonstrating broader clinical implications.

SIGNIFICANCE

Proteogenomic analysis of triple-negative breast tumors revealed a complex landscape of chemotherapy response associations, including a 19q13.31-33 somatic deletion encoding genes serving lagging-strand DNA synthesis (LIG1, POLD1, and XRCC1), that correlate with lack of pathologic response, carboplatin-selective resistance, and, in pan-cancer studies, poor prognosis and CIN. This article is highlighted in the In This Issue feature, p. 2483.

Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer

Circulating tumor DNA (ctDNA) in peripheral blood has been used to predict prognosis and therapeutic response for triple-negative breast cancer (TNBC) patients. However, previous approaches typically use large comprehensive panels of genes commonly mutated across all breast cancers. Given the reduction in sequencing costs and decreased turnaround times associated with panel generation, the objective of this study was to assess the use of custom micro-panels for tracking disease and predicting clinical outcomes for patients with TNBC. Paired tumor-normal samples from patients with TNBC were obtained at diagnosis (T0) and whole exome sequencing (WES) was performed to identify somatic variants associated with individual tumors. Custom micro-panels of 4-6 variants were created for each individual enrolled in the study. Peripheral blood was obtained at baseline, during Cycle 1 Day 3, at time of surgery, and in 3-6 month intervals after surgery to assess variant allele fraction (VAF) at different timepoints during disease course. The VAF was compared to clinical outcomes to evaluate the ability of custom micro-panels to predict pathological response, disease-free intervals, and patient relapse. A cohort of 50 individuals were evaluated for up to 48 months post-diagnosis of TNBC. In total, there were 33 patients who did not achieve pathological complete response (pCR) and seven patients developed clinical relapse. For all patients who developed clinical relapse and had peripheral blood obtained ≤ 6 months prior to relapse (n = 4), the custom ctDNA micro-panels identified molecular relapse at an average of 4.3 months prior to clinical relapse. The custom ctDNA panel results were moderately associated with pCR such that during disease monitoring, only 11% of patients with pCR had a molecular relapse, whereas 47% of patients without pCR had a molecular relapse (Chi-Square; p-value = 0.10). In this study, we show that a custom micro-panel of 4-6 markers can be effectively used to predict outcomes and monitor remission for patients with TNBC. These custom micro-panels show high sensitivity for detecting molecular relapse in advance of clinical relapse. The use of these panels could improve patient outcomes through early detection of relapse with preemptive intervention prior to symptom onset.

Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

BACKGROUND

Ductal carcinoma in situ (DCIS) is the most common type of in situ premalignant breast cancers. What drives DCIS to invasive breast cancer is unclear. Basal-like invasive breast cancers are aggressive. We have previously shown that NRAS is highly expressed selectively in basal-like subtypes of invasive breast cancers and can promote their growth and progression. In this study, we investigated whether NRAS expression at the DCIS stage can control transition from luminal DCIS to basal-like invasive breast cancers.

METHODS

Wilcoxon rank-sum test was performed to assess expression of NRAS in DCIS compared to invasive breast tumors in patients. NRAS mRNA levels were also determined by fluorescence in situ hybridization in patient tumor microarrays (TMAs) with concurrent normal, DCIS, and invasive breast cancer, and association of NRAS mRNA levels with DCIS and invasive breast cancer was assessed by paired Wilcoxon signed-rank test. Pearson's correlation was calculated between NRAS mRNA levels and basal biomarkers in the TMAs, as well as in patient datasets. RNA-seq data were generated in cell lines, and unsupervised hierarchical clustering was performed after combining with RNA-seq data from a previously published patient cohort.

RESULTS

Invasive breast cancers showed higher NRAS mRNA levels compared to DCIS samples. These NRAS^high lesions were also enriched with basal-like features, such as basal gene expression signatures, lower ER, and higher p53 protein and Ki67 levels. We have shown previously that NRAS drives aggressive features in DCIS-like and basal-like SUM102PT cells. Here, we found that NRAS-silencing induced a shift to a luminal gene expression pattern. Conversely, NRAS overexpression in the luminal DCIS SUM225 cells induced a basal-like gene expression pattern, as well as an epithelial-to-mesenchymal transition signature. Furthermore, these cells formed disorganized mammospheres containing cell masses with an apparent reduction in adhesion.

CONCLUSIONS

These data suggest that elevated NRAS levels in DCIS are not only a marker but can also control the emergence of basal-like features leading to more aggressive tumor activity, thus supporting the therapeutic hypothesis that targeting NRAS and/or downstream pathways may block disease progression for a subset of DCIS patients with high NRAS.

Poziotinib Inhibits HER2-Mutant-Driven Therapeutic Resistance and Multiorgan Metastasis in Breast Cancer

The pan-HER tyrosine kinase inhibitor (TKI) neratinib is therapeutically active against metastatic breast cancers harboring activating HER2 mutations, but responses are variable and often not durable. Here we demonstrate that recurrent HER2 mutations have differential effects on endocrine therapy responsiveness, metastasis, and pan-HER TKI therapeutic sensitivity. The prevalence and prognostic significance may also depend on whether the HER2 mutant has arisen in the context of lobular versus ductal histology. The most highly recurrent HER2 mutant, L755S, was particularly resistant to neratinib but sensitive to the pan-HER TKI poziotinib, alone or in combination with fulvestrant. Poziotinib reduced tumor growth, diminished multiorgan metastasis, and inhibited mTOR activation more effectively than neratinib. Similar therapeutic effects of poziotinib were observed in both an engineered HER2L755S MCF7 model and a patient-derived xenograft harboring a HER2G778_P780dup mutation. Overall, these findings support the need for clinical evaluation of poziotinib for the treatment of HER2-mutant metastatic breast cancer.

SIGNIFICANCE

Evaluation of the functional impact of HER2 mutations on therapy-induced resistance and metastasis identifies robust antitumor activity of poziotinib and supports the clinical evaluation of poziotinib in ER+ HER2 mutant breast cancer.

Evaluation of Sensitivity to Endocrine Therapy Index (SET2,3) for Response to Neoadjuvant Endocrine Therapy and Longer-Term Breast Cancer Patient Outcomes (Alliance Z1031)

PURPOSE

To evaluate prediction of response and event-free survival (EFS) following neoadjuvant endocrine therapy by SET2,3 index of nonproliferation gene expression related to estrogen and progesterone receptors adjusted for baseline prognosis.

EXPERIMENTAL DESIGN

A correlative study was conducted of SET2,3 measured from gene expression profiles of diagnostic tumor (Agilent microarrays) in 379 women with cStage II-III breast cancer from the American College of Surgeons Oncology Group Z1031 neoadjuvant aromatase inhibitor trial SET2,3 was dichotomized using the previously published cutoff. Fisher exact test was used to assess the association between SET2,3 and low proliferation at week 2-4 [Ki67 ≤ 10% or complete cell-cycle arrest (CCCA; Ki67 ≤ 2.7%)] and PEPI-0 rate in cohort B, and the association between SET2,3 and ypStage 0/I in all patients. Cox models were used to assess EFS with respect to SET2,3 excluding cohort B patients who switched to chemotherapy.

RESULTS

Patients with high SET2,3 had higher rate of pharmacodynamic response than patients with low SET2,3 (Ki67 ≤ 10% in 88.2% vs. 56.9%, P < 0.0001; CCCA in 50.0% vs. 26.2%, P = 0.0054), but rate of ypStage 0/I (24.0% vs. 20.4%, P = 0.4580) or PEPI = 0 (28.4% vs. 20.6%, P = 0.3419) was not different. Patients with high SET2,3 had longer EFS than patients with low SET2,3 (HR, 0.52, 95% confidence interval: 0.34-0.80; P = 0.0026).

CONCLUSIONS

This exploratory analysis of Z1031 data demonstrated a higher rate of pharmacodynamic suppression of proliferation and longer EFS in high SET2,3 disease relative to low SET2,3 disease. The ypStage 0/I rate and PEPI = 0 rate were similar with respect to SET2,3.

Abstract 3922: Proteomic profiling of muscle invasive bladder cancer

Background: Only one quarter of patients with muscle invasive urothelial bladder cancer (MIBC) gain approximately 5% improvement in 5-year overall survival from cisplatin-based neoadjuvant chemotherapy (NAC). For patients with residual invasive cancer post radical cystectomy there is no standard of care and high mortality. Previous TCGA projects focused on pre-NAC MIBC genomic and transcriptomic alterations and identified 5 molecular subtypes with differential risk and response. For this study we hypothesized that comprehensive proteomic and phosphoproteomic profiling of MIBC prior to NAC will further define mechanisms responsible for chemotherapy resistance, and identify specific and actionable targeted therapies for patients with NAC-resistant tumors.

Methods: OCT-embedded and flash frozen tissue samples from 143 eligible patients were processed and tested for proteomics quality control (QC). Samples containing &gt;45% tumor content, less than 10% muscle content and &gt;2,000 protein identifications in a single-shot quality control assay were selected for deep-scale proteomic and phosphoproteomic profiling. A final cohort of 60 samples (52 pre-treatment and 8 patient-matched post-treatment tumors) were multiplexed using tandem mass tags (TMT-11), fractionated by basic reverse phase chromatography and analyzed by liquid chromatography and mass spectrometry (LC-MS).

Results: Over 12,000 proteins were identified in total, and 8,353 proteins identified in all samples, including 425 kinases and 77 targets of FDA approved cancer therapies. Principal component analysis identified two distinct resistant clusters and one sensitive cluster. The samples were clustered based on the 5 TCGA subtypes which resulted in the sub stratification of the resistant clusters into two resistance-enriched basal-squamous clusters (BS1 and BS2 respectively), one infiltrated-luminal cluster (L1), one sensitive luminal cluster (L2) and one intermediary cluster (L3) (with 86% samples resistant). UV response, Epithelial to Mesenchymal transition and Myogenesis were significantly elevated in both L1 and L3 (resistant) relative to L2 (sensitive). Similar, these pathways are significantly altered in L1 relative to L3. EGFR, CDK6, ITPKC and CSNK1 were elevated in the B4 subtype, all of which are potentially druggable targets. Matched samples and phosphoproteomics data will be presented.

Conclusion: Surrounding non-tumor tissue can obfuscate true tumor signatures in MIBC, cohort selection through stringent pathologic QC allows proteomic profiling to identify tumor features that correlate with NAC resistance. This dataset provides proof of principle that actionable targets and subtype distinctions can be identified through discovery proteomics and further analysis in NAC treated cohorts are justified.

Citation Format: Matthew V. Holt, Meggie N. Young, Karoline Kremers, Alexander Saltzman, Antrix Jain, Mei Leng, Hugo Villanueva, Lacey E. Dobrolecki, Beom-Jun Kim, Meenakshi Anurag, Matthew J. Ellis, Anna Malovannaya, Seth P. Lerner. Proteomic profiling of muscle invasive bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3922.

Abstract 1010: LIG1 deletion predicts chemotherapy resistance, chromosomal instability, and poor prognosis in triple negative breast cancer

Introduction: Cytotoxic chemotherapy for sporadic Triple Negative Breast Cancer (TNBC) remains the standard of care and the recent approval for adjuvant PD1 therapy is not biomarker guided. Pathological complete response (pCR) is often not achieved and portends poor survival. Predictive markers for individual drugs have proven elusive.

Approach: Microscaled proteogenomics (MPG) was applied to snap-frozen TNBC clinical trial core needle biopsies obtained before treatment with carboplatin and docetaxel (WashU: NCT201404107 and BCM: NCT02544987). Clinical endpoints for discovery analysis were pathological complete response (pCR) and residual cancer burden (RCB). Standard non-parametric statistical tests were employed to identify proteogenomic features associated with these endpoints.

Results: Copy number aberrations (CNA) are a recurrent feature of TNBC and a potential driver of chemotherapy sensitivity. We therefore sought CNA with concordant changes at the mRNA and protein levels that also associate with pCR status. Genes located within a recurrent interstitial deletion at chromosomal location 19q13.3 were the most significantly down-regulated at mRNA and protein level in chemotherapy resistant cases. 19q13.3 encodes multiple DNA damage response (DDR) genes; however, only LIG1, a DNA ligase required for lagging strand synthesis and DNA repair, showed concordant changes at both the mRNA and protein level. In multiple independent TNBC data sets, LIG1 deletion was associated lack of pCR and poor metastasis-free survival. Additionally in the BrighTNess TNBC trial lower LIG1 mRNA levels were associated with increased chemotherapy resistance in the carboplatin containing arms (no pCR and residual cancer burden I-III; p=0.0008 and 0.003 respectively). In PDX-derived short-term cultures and PDXs treated with docetaxel or carboplatin, a specific association of carboplatin resistance with LIG1 deletion was observed. LIG1 depleted-tumors did not harbor elevated scores for homologous recombination defect signature, suggesting LIG1 loss is an orthogonal pathway for TNBC pathogenesis The high chromosomal instability index in LIG1 deletion tumors in our TNBC study was robustly reproduced in multiple datasets (including TCGA-BRCA ; Metastatic breast cancer project). LIG1 copy number deletion was also associated with poor progression free survival, and high chromosomal instability in multiple other cancers (including TCGA-​UCEC HR=2.23, TCGA-HNSC HR=1.46, TCGA-PRAD HR=2.07, TCGA- COAD HR=1.75 and TCGA-KIRP HR=4.00).

Conclusion: Deletion of LIG1 is associated with chromosomal instability in TNBC and occurs in tumors without genomic evidence for defects in homologous recombination. Other clinical features of LIG1 deleted TNBC and how LIG1 loss may cause chromosomal instability and tumorigenesis will be discussed.

Citation Format: Meenakshi Anurag, Eric Jaehnig, Jonathan Lei, Beom-Jun Kim, Anh Minh Tran Huynh, Yongchao Dou, Tanmayi Vashist, Erik Bergstrom, Xuxu Gou, Viktoriya Korchina, Donna Marie Muzny, Kristen Otte, Harshavardhan Doddapaneni, Lacey Dobrolecki, Gloria Vittone Echeverria, Bora Lim, Mothaffar Rimawi, Karsten Krug, Ian Hageman, Henry Rodriguez, Ana I. Robles, Tara Hiltke, Kent Osborne, Michael Gillette, George Miles, Steven Carr, Michael T Lewis, Bing Zhang, Foluso Ademuyiwa, Shankha Satpathy, Matthew J. Ellis. LIG1 deletion predicts chemotherapy resistance, chromosomal instability, and poor prognosis in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1010.

Abstract 2979: ElevatedNRASexpression as a potential driver of DCIS progression to basal-like invasive breast cancer

Background: Ductal carcinoma in situ (DCIS) is the most common type of in situ premalignant breast cancers. What drives a subset of luminal DCIS to transition to basal invasive breast cancers is unclear. Basal-like invasive breast cancers are aggressive and associated with the shortest overall survival and time to distant metastasis. We have previously shown that N-Ras is highly expressed selectively in the basal-like subtypes of invasive breast cancers and can promote their growth and progression. In this study, we investigated whether NRAS expression at the DCIS stage can control transition from luminal DCIS to basal-like invasive breast cancers.

Methods: Wilcoxon rank-sum test was conducted to assess the relative expression of NRAS in DCIS compared to invasive breast cancers in a patient cohort (GSE59248). NRAS levels were also determined by fluorescence in situ hybridization (FISH) in a collection of 21 patient tumor microarrays (TMAs) with concurrent normal, DCIS, and invasive breast cancer, and NRAS’s association with DCIS and invasive breast cancer was assessed by Wilcoxon signed rank test. How NRAS levels correlated with basal biomarkers in the TMAs, as well as in patient datasets GSE59248 and GSE3369 was determined by Pearson correlation. Gene expression changes in cell line were assessed by RNA-seq.

Results: Invasive breast cancers showed higher NRAS mRNA levels, as compared to DCIS samples. These NRAShigh lesions were also enriched with basal-like features, such as basal gene expression signature, lower ER, higher p53 protein levels, and higher Ki67 levels. We have shown previously that N-Ras is a driver for tumor growth in SUM102 cells, which is a DCIS-like cell line model displaying basal-like features. Here we found that NRAS-silencing in these cells induced a shift to a luminal gene expression pattern as determined by PAM50.

Conclusions: These data suggest that the rise of N-RAS levels in DCIS can not only mark but also control the emergence of basal-like features leading to more aggressive tumor activities. Targeting N-Ras and/or its downstream pathway may prevent the emergence of basal invasive breast cancers.

Citation Format: Ze-yi Zheng, Hanan Elsarraj, Yang Hong, Jonathan T. Lei, Meenakshi Anurag, Yichao Shen, Flora Lo, Long Feng, Zifan Zhao, Xiang H. Zhang, Fariba Behbod, Eric C. Chang. ElevatedNRASexpression as a potential driver of DCIS progression to basal-like invasive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2979.

Abstract CT026: The effect of intrinsic subtype on inhibition of tumor growth by anastrozole vs. fulvestrant vs. the combination: Results from the Alliance neoadjuvant endocrine therapy (NET) ALTERNATE trial

Introduction: The ALTERNATE trial randomized postmenopausal women with ER Allred 6-8 HER2- breast cancer to 6 months of NET with anastrozole (A), fulvestrant (F) or the combination (A+F). Biopsies were taken preNET and after 4-weeks(wks). Patients with Ki67 values &gt;10% at 4-wks were offered triage to neoadjuvant chemotherapy. Patients with on-treatment Ki67 ≤ 10% who completed NET underwent surgery and Ki67 was reassessed. The primary endpoint was endocrine-sensitive disease rate (ESDR). ESD is defined as pCR or PEPI-0 residual disease (pT1-2, pN0, Ki67 ≤ 2.7%). We previously reported that the ESDR difference between the F-containing arms and the A arm was not &gt;10% (ASCO 2020) and that baseline RNA-seq-based intrinsic subtypes predicted outcomes overall (SABCS 2021). Herein we describe relationships between PAM50 intrinsic subtype and Ki67 values by treatment arm because comparative drug effectiveness in adjuvant endocrine therapy studies in ER+ HER2- breast cancer can be predicted by the degree of Ki67 suppression (PMC3518447).

Methods: 743 of the 1297 eligible patients (A: 264; F: 231; A+F: 248) had RNA extracted from preNET frozen tumor biopsies with &gt;50% tumor content and subjected to RNA seq. Intrinsic subtypes were then assigned as LumA, LumB, and NonLum (Basal or HER2-E) using open-source PAM50-based informatics. Differences in the proportion with wk4 Ki67 &gt; 10%, % change in wk4 ki67, and surgical CCCA (Ki67 ≤ 2.7%) rate (sxCCCA) between treatments and by intrinsic subtype was assessed using stratified logistic regression, Wilcoxon rank sum test, and Fisher’s exact test, respectively. Analysis of sxCCCA excluded those who failed to complete NET for reasons other than disease progression or early Ki67 &gt;10%.

Results: Amongst the 358 LumA cases there were no significant differences in Ki67-based endpoints between treatments. Among the 292 LumB cases, the wk4 ki67 &gt; 10% rate was lower with A+F (19.4%) than A (43%) (P=0.0002) and was somewhat lower in F (31%) versus A (P=0.076). The % change in wk4 Ki67 in LumB cases, adjusted for baseline Ki67, showed markedly superior suppression for A+F versus A (-90% vs. -77%; P=&lt;0.0001) and versus F (-90% vs. -80%; P=0.0026). Furthermore sxCCCA rates were significantly higher with A+F than A (53% vs. 25% P = &lt;0.0001) and somewhat higher for F (37%) than A (p=0.068), indicating that superior antiproliferative effects for A+F persist after 6 months on therapy. Lack of Ki67 suppression in response to treatment was observed in the majority of 43 NonLum samples regardless of treatment.

Conclusion: The combination of A+F was significantly more effective than either drug alone for the control of LumB breast cancer cell proliferation. This suggests that A+F may be a more effective adjuvant endocrine therapy than A alone in LumB disease. The lower Ki67 suppression with A alone also suggests that poorer outcome in some LumB tumors may be due to insufficient ER targeting rather than ER-independent tumor growth

Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG), NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org. (MJE) CPRIT RR140033, P50-CA186784, P50-CA58223, U01-CA214125, U24-CA210954, Gift from Ralph and Lisa Eads, McNair Scholarship.

ClinicalTrials.gov Identifier: NCT01953588

Citation Format: Matthew J. Ellis, Meenakshi Anurag, Jeremy Hoog, Aranzazu Fernandez-Martinez, Cheng Fan, Richard Gibbs, Souzan Sanati, Kiran Vij, Mark Watson, Travis Dockter, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erica Crouch, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J. Hieken, Yang Wang, A. Marilyn Leitch, Gary W. Unzeitig, Eric Winer, Anna Weiss, Kelly Hunt, Ann H. Partridge, Charles M. Perou, Vera Suman, Cynthia X. Ma, Lisa A. Carey. The effect of intrinsic subtype on inhibition of tumor growth by anastrozole vs. fulvestrant vs. the combination: Results from the Alliance neoadjuvant endocrine therapy (NET) ALTERNATE trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT026.

Targeting kinome reprogramming in ESR1 fusion-driven metastatic breast cancer

1085

Background: Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor-alpha positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain is replaced by C-terminal sequences from many different gene partners. Transcriptionally active ESR1 fusions promoted hormone-independent cell growth, motility and resistance to endocrine therapy. The diversity of partner genes creates a considerable diagnostic challenge and no targeted treatments exist for ESR1 translocated tumors. Thus, we have established a transcriptional signature to diagnose the presence of an active ESR1 fusion (PMID: 34711608) and developed novel targeted therapies against ESR1 fusion-driven biology. Methods: Fifteen ESR1 fusion cDNA constructs were expressed in ER+ breast cancer cell lines by lentiviral transduction. Cell growth was assayed by Alamar blue assay. A mass spectrometry (MS)-based Kinase Inhibitor Pulldown Assay (KIPA) and tandem mass tag-based proteomics were performed to identify ESR1 fusion-driven druggable kinases for subsequent pharmacological inhibition. Results: KIPA profiling demonstrated an increase of multiple receptor tyrosine kinases including RET in T47D cells expressing active ESR1 fusions. Inhibition of RET by repurposing an FDA-approved drug significantly suppressed ESR1 fusion-driven cell growth in vitro, suggesting that despite marked diversity in the 3’ partners, common kinase activities were elevated and targetable. Proteogenomic profiling, including whole exome sequencing, RNA sequencing, and MS-based proteomics and phosphoproteomics were further performed on 22 ER+ patient-derived xenograft (PDX) tumors, which demonstrated different degrees of estradiol dependence. These integrated “omic” profiles defined targetable genes/pathways and predict tumor subsets that could be responsive to kinase inhibition therapy from this biologically heterogeneous panel of PDX tumors. WHIM18, a PDX naturally harboring the ESR1-YAP1 fusion showed elevated level of RET and CDK4/6 pathways. The tumor volumes were significantly reduced by the RET inhibitor. CDK4/6 inhibitor treatment showed similar tumor reductions to RET inhibition. Interestingly, WHIM9 PDX that expressed wild-type ESR1 conferred a comparable kinome profile to WHIM18. The tumor growth was significantly suppressed by RET or CDK4/6 inhibition. Therefore, pharmacological experiments validated proteogenomics-predicted drug response in two tested ER+ PDX models. Conclusions: Proteogenomics characterization of PDX tumors can drive clinical trial hypotheses. Here, we reveal therapeutic kinase vulnerabilities in ESR1 fusion-driven tumors as exemplified by RET inhibition, which will lay the framework for future clinical trials.

Abstract P2-13-24: Distinct HER2 allele specific therapeutic response and preclinical efficacy of poziotinib in metastatic ER+ HER2 mutant breast cancer

Background.Targeting HER2 gene amplification is one of the great achievements in oncology resulting in the use of a wide array of anti-HER2 agents in the clinic. Unfortunately, 20% of patients still relapse with secondary organ metastasis and are currently incurable. While only 1.6% of primary non-HER2-amplified ER+ breast cancers harbor HER2 mutations, 6-10% of all metastatic breast cancers harbor HER2 mutations, suggesting their causal role in contributing to metastasis. The clinical value of HER2 activating mutations is being tested with the pan-HER tyrosine kinase inhibitor neratinib in phase II clinical trials (NCT01670877, NCT01953926, and NCT02465060). To date, neratinib has elicited only modest responses in ER+ breast cancer, often rapidly followed by progression. This study characterizes HER2-mutant induced resistance to endocrine therapy or neratinib induced resistance and resulting metastasis, in order to determine a more effective rational therapeutic approach for treating ER+ HER2-mutant breast cancer. Methods.HER2 mutation frequency and its impact on patient outcome was determined using METABRIC primary breast cancer (BC) and MSK IMPACT metastatic BC ER+ sequencing studies. Effects of estrogen (E2), fulvestrant, or neratinib on cell growth and HER2 signaling were examined on ER+/ILC cells (MM134) stably expressing HER2/WT, HER2/S310F, and HER2/L755S. Cell growth was measured using CellTiter-Glo and HER2 signaling was analyzed by western blot analysis. Additionally, the effect of these ER+/ILC and IDC HER2 mutations on tumor growth and endocrine or neratinib treatment resistance was determined using fat pad injections and MIND xenografts in NOD-scid gamma mice. Results.We searched ER+ sequencing datasets and identified HER2 mutations that are highly enriched in ER+ ILC as compared to ER+ IDC. These activating HER2 mutations in ER+ ILC are associated with early relapse and poor overall survival. Moreover, we are finding that ILC patients harboring the recurrent HER2/L755S mutation have worse overall survival compared to non-mutant HER2 ILC. MM134 cells expressing HER2/S310F and HER2/L755S show increased cell growth, strongly activated autophosphorylation of HER2, and increased downstream signaling (pMAPK and pAKT) as compared to cells expressing HER2/WT upon treatment with fulvestrant (1μM). Three clinically relevant in vivo models including ILC HER2/L755S Mammary INtraDuctal (MIND) xenografts, IDC HER2/L755S fat pad xenografts, and IDC HCI-003 (an ER+ patient-derived xenograft (PDX) naturally harboring the exon 20 activating HER2G778_P780 dup) exhibit fulvestrant and neratinib resistance and lung and ovary metastases. In addition, we find that HER2 mutations induced mTOR signaling. In contrast, however, the pan-HER drug poziotinib does potently inhibit tumor growth and organ-specific metastasis and perturbs mTOR activation in these models. Conclusion.We demonstrate that clinically associated HER2 mutations drive endocrine therapy or neratinib resistance and poor patient outcome in ER+ patients. Our data propose the use of the irreversible pan-HER TKI poziotinib for treating endocrine therapy or neratinib refractory ER+ HER2-mutant metastatic breast cancer.

Citation Format: Shyam. M Kavuri, Rashi Kalra, Ching Hui Chen, Junkai Wang, Ahmad Bin Salam, Lacey Dobrolecki, Alaina Lewis, Christina Sallas, Clayton Yates, Carolina Gutierrez, Balasubramanyam Karanam, Meenakshi Anurag, Bora Lim, Matthew Ellis. Distinct HER2 allele specific therapeutic response and preclinical efficacy of poziotinib in metastatic ER+ HER2 mutant 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 P2-13-24.

Abstract PD9-03: Pam50 intrinsic subtype and risk of recurrence score (ROR) for the prediction of endocrine (ET) sensitivity and pathologic response to chemotherapy in postmenopausal women with clinical stage II/III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC) in the alternate trial (Alliance A011106)

Background: Neoadjuvant ET (NET) offers an opportunity to assess ET sensitivity for ER+ HER2- BC and potentially to tailor therapy. Ki67 &gt;10% on biopsy after 2-4 weeks (wks) of NET identifies patients (pts) with intrinsic ET resistance; while pathologic complete response (pCR) and modified preoperative endocrine prognostic index of 0 (mPEPI 0: pT1-2N0, Ki67 ≤2.7%) at surgery indicates sensitivity to ET. However, on-NET biopsy is not always acceptable or feasible and delays the ET sensitivity determination. PAM50 ROR score and intrinsic subtypes by tumor RNA profiling are prognostic in pts with early stage ER+ HER2- BC, and predict pCR rates to neoadjuvant chemotherapy (NCT) (PMC2667820). We therefore hypothesized that PAM50 analysis on pre-NET biopsies could predict the likelihood of a) a high on-NET Ki67, b) mPEPI-0 or pCR at surgery and, c) pCR for pts triaged to NCT. Methods: The ALTERNATE trial is a phase III study that randomized postmenopausal pts with clinical stage II/III ER+ (Allred score 6-8) HER2- BC to receive neoadjuvant anastrozole, fulvestrant, or both for 6 months before surgery. Research biopsy was required at pre-NET and wk 4, then optional at wk 12. Pts with Ki67 &gt;10% on biopsy at wk 4 or 12 discontinued NET and were offered NCT. PAM50 intrinsic subtype and ROR-P values were generated from mRNA sequencing (RNASeq) analysis on pre-NET biopsies using open-source informatics (PMC7723687) and evaluated for prediction of on-NET Ki67 &gt;10% at wk 4 or 12, pCR or mPEPI-0 post NET, and pCR post NCT. Results: 749 of 1,297 eligible trial pts were included in the analyses, after excluding 548 pts due to insufficient pre-NET tumor for RNASeq (n=511) or PAM50 normal subtype (n=37). Similar to the entire ALTERNATE population, the rate of Ki67 &gt;10% at wk 4 or 12 was 24.4% (95% CI: 21.4-27.7%) and the rate of mPEPI-0/pCR post NET was 19.8% (95% CI: 17.0-22.8%). There were 393 (52.5%) Lum A, 302 (40.3%) Lum B, and 54 (7.2%) non-Lum (9 Basal, 45 HER2-E) BCs. These included 196 (26.2%) ROR-P low, 354 (47.3%) ROR-P medium and 199 (26.6%) ROR-P high BCs. Both the rates of Ki67 &gt;10% at wk 4 or 12 and mPEPI-0/pCR differed significantly with respect to PAM50 subtype or ROR-P category, such that Lum A or ROR-P low BCs were least likely to have a Ki67 &gt;10% at wk 4 or 12 and most likely to achieve mPEPI-0/pCR (Table).

93 of 168 (55.4%) pts triaged to NCT had RNA-seq results, yielding 26 Lum A, 49 Lum B, 4 Basal and 14 HER2-E, with the pCR rates of 0%, 6.1%, 0%, and 21.4%, respectively. There were 10 ROR-P low, 39 medium, and 44 high tumors, with a pCR rate of 0%, 5.1% and 9.1%, respectively. Conclusion: These data indicate that both baseline ROR-P and intrinsic subtype are predictive of early on-NET Ki67 &gt; 10% and mPEPI 0/pCR at surgery after NET. For pts triaged to NCT based on an early on-NET Ki67 &gt;10%, the HER2-E group had the highest pCR rate (20%) and no pCRs were observed in Lum A. These data may be useful for directing neoadjuvant therapy in postmenopausal pts with ER+ HER2- BC. Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG), NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org. (MJE) CPRIT RR140033, P50CA186784, P50-CA58223, U01 CA214125, U24CA210954, Gift from Ralph and Lisa Eads, McNair Scholarship. Trials.gov Identifier: NCT01953588.

Table 1.Rates of Ki67 &gt;10% and mPEPI-0/pCR post NET by PAM50 subtype and ROR-P categoryKi67 &gt;10% at wk 4 or 12mPEPI 0/pCR post NETPAM50 SubtypenYes, n (%)PnNo, n (%)PLum A37251 (13.7%) 95% CI: 10.4-17.6%&lt;0.0001393104 (26.5%) 95%CI: 22.2-31.1%&lt;0.0001Lum B29394 (32.1%) 95% CI: 26.8-37.8%30243 (14.2%) 95%CI: 10.5-18.7%Non-luminal (Basal and HER2-E)5338 (71.7%) 95%CI: 57.6-83.2%541 (1.9%) 95%CI: 0.05-9.9%ROR-P CategorynYes, n (%)PnNo, n (%)PLow18018 (10.0%) 95%CI: 6.0-15.3%&lt;0.000119660 (30.6%) 95%CI: 24.2-37.6%&lt;0.0001Intermediate34474 (21.5%) 95%CI: 17.3-26.2%35471 (20.1%) 95%CI: 16.0-24.6%High19491 (46.9%) 95%CI: 39.7-54.2%19917 (8.5%) 95%CI: 5.1-13.3%

Citation Format: Cynthia X Ma, Meenakshi Anurag, Travis Dockter, Jeremy Hoog, Aranzazu Fernandez-Martinez, Cheng Fan, Richard Gibbs, Souzan Sanati, Kiran Vij, Mark Watson, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erika Crouch, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J Hieken, Yang Wang, A. Marilyn Leitch, Gary W Unzeitig, Anna Weiss, Eric P Winer, Kelly Hunt, Ann H Partridge, Lisa A Carey, Charles M Perou, Matthew J Ellis, Vera Suman. Pam50 intrinsic subtype and risk of recurrence score (ROR) for the prediction of endocrine (ET) sensitivity and pathologic response to chemotherapy in postmenopausal women with clinical stage II/III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC) in the alternate trial (Alliance A011106) [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 PD9-03.

Transcriptional reprogramming differentiates active from inactive ESR1 fusions in endocrine therapy-refractory metastatic breast cancer

Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor-alpha positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, EMT and resistance to fulvestrant. RNA sequencing identified a gene expression pattern specific to functionally active ESR1 gene fusions that was subsequently reduced to a diagnostic 24-gene signature. This signature was further examined in 20 ERα+ patient-derived xenografts (PDXs) and in 55 ERα+ MBC samples. The 24-gene signature successfully identified cases harboring ESR1 gene fusions and also accurately diagnosed the presence of activating ESR1 LBD point mutations. Therefore, the 24-gene signature represents an efficient approach to screening samples for the presence of diverse somatic ESR1 mutations and translocations that drive endocrine treatment failure in MBC.

Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways

Identifying new gene functions and pathways underlying diseases and biological processes are major challenges in genomics research. Particularly, most methods for interpreting the pathways characteristic of an experimental gene list defined by genomic data are limited by their dependence on assessing the overlapping genes or their interactome topology, which cannot account for the variety of functional relations. This is particularly problematic for pathway discovery from single-cell genomics with low gene coverage or interpreting complex pathway changes such as during change of cell states. Here, we exploited the comprehensive sets of molecular concepts that combine ontologies, pathways, interactions and domains to help inform the functional relations. We first developed a universal concept signature (uniConSig) analysis for genome-wide quantification of new gene functions underlying biological or pathological processes based on the signature molecular concepts computed from known functional gene lists. We then further developed a novel concept signature enrichment analysis (CSEA) for deep functional assessment of the pathways enriched in an experimental gene list. This method is grounded on the framework of shared concept signatures between gene sets at multiple functional levels, thus overcoming the limitations of the current methods. Through meta-analysis of transcriptomic data sets of cancer cell line models and single hematopoietic stem cells, we demonstrate the broad applications of CSEA on pathway discovery from gene expression and single-cell transcriptomic data sets for genetic perturbations and change of cell states, which complements the current modalities. The R modules for uniConSig analysis and CSEA are available through https://github.com/wangxlab/uniConSig.

Abstract 742: The integration of a structure-function rule and a transcriptional signature to assign ESR1 fusion activity in metastatic breast cancer

Background: In-frame chimeric ESR1 fusion proteins can cause endocrine therapy (ET) resistance in estrogen receptor-positive (ER+) metastatic breast cancer (MBC) (PMC6171747). Here, we further investigated multiple new examples of ESR1 fusions in order to differentiate between transcriptionally active “driver” ESR1 fusions from inactive, likely “passenger” events.

Methods: ESR1 fusions were identified by RNA-sequencing (RNA-seq) or whole genome sequencing in MBC (PMC5913625, PMC6872491 and unpublished). ESR1 fusion cDNA constructs were expressed in ER+ breast cancer cell lines. Cell proliferation and cell motility were assessed. RNA-seq followed by qPCR validation was conducted to examine individual transcriptional profiles.

Results: All ESR1 fusions studied contained the first six exons of ESR1 (e6) fused in-frame to diverse partner gene sequences that replaced the ESR1 drug/ligand binding domain. Fusions with a transcription factor (TF) or coactivator (CoA) gene partner, for example ESR1-YAP1, ESR1-ARNT2-e18 and ESR1-SOX9 activated fulvestrant-resistant cell growth and hormone-independent cell motility. Other ESR1-e6 fusions, including ESR1-DAB2, ESR1-GYG1, ESR1-PCMT1 and ESR1-ARID1B did not show these phenotypes. We thus conclude that in-frame ESR1-e6 fusions arising from inter-chromosomal translocations with 3' TF/CoA partners are likely to be active. However, the active ESR1-PCDH11X fusion involves a proto-cadherin and is therefore an exception to this rule. This outlier emphasizes the need to establish additional approaches to determine ESR1 fusion activity. RNA-seq of T47D cells expressing active and inactive ESR1 fusions defined a gene signature associated with active ESR1 fusions, with activation of estrogen response and epithelial-to-mesenchymal transition (EMT) genes. This transcriptional signature was present in a patient-derived xenograft bearing the ESR1-YAP1 fusion, and thus potentially identifies the presence of an active ESR1 fusion protein. We subsequently identified two new ESR1 fusions involving recurrent TF/CoA partners, ESR1-ARNT2-e2 and ESR1-LPP. Both demonstrated tumor cell growth and motility activation, as predicted by the functional rule. The gene activation patterns were similar to the three other active fusions suggesting that despite marked diversity in the 3' partners, the transcriptional activities were similar and potentially diagnostic.

Conclusion: The integration of the structure-function rule and the stereotypic transcriptional signature distinguishes pathogenic ESR1 fusions from non-active passenger events, thus prioritizing patients bearing ESR1 translocation-driven tumors for targeted therapeutic approaches.

Citation Format: Xuxu Gou, Meenakshi Anurag, Jonathan T. Lei, Sinem Seker, Adrian V. Lee, Dan R. Robinson, Matthew J. Ellis. The integration of a structure-function rule and a transcriptional signature to assign ESR1 fusion activity in metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 742.

Abstract 2490: Optimizing treatment strategy for NF1-depleted estrogen receptor positive breast cancer

Background: Germline mutations in the NF1 gene are responsible for neurofibromatosis type 1, which is the world's most common genetic disorder. NF1 is also a key tumor suppressor gene that is frequently somatically mutated in a wide range of cancers. Approximately 80% of breast cancer is driven by the estrogen receptor α (ER), encoded by the ESR1 gene, and ER-positive (ER+) breast cancer can be treated by endocrine therapy targeting the ER transcriptional pathway. NF1 encodes neurofibromin, which is best known as a GTPase Activating Protein (GAP) for repressing Ras signaling. However, in a recent study we presented evidence supporting the model that NF1 has a GAP-independent activity by also acting as a transcriptional co-repressor for ER. NF1 loss enhanced ER transcription causing resistance to tamoxifen and aromatase inhibition.

Approach and Results: In this study, we examined patient data from TCGA cohort and found that low NF1 mRNA levels associated with recurrence in luminal breast cancer, particularly in the luminal B subtype. Using purified components, we showed that full-length NF1 can directly bind ER. The ESR1-pE380Q mutation is a recurrent event in metastatic ER+ breast cancer. Our two-hybrid data showed that NF1 interacted less with the ER-E380Q than wild type ER, which agrees with structural analysis predicting co-repressors binding to be mediated by the ER-E380 residue. To assess how NF1-loss impacts ER-dependent gene expression in ER+ breast cancer cells, our ER ChIP-seq data showed that in the presence of estradiol, NF1-depletion promoted global ER recruitment to estrogen response elements (EREs) on chromatin. Expression of ERE-bound genes showed concordant expression changes by RNA-seq, confirming genome-wide transcriptional dysregulation of ER targeted genes by NF1 loss. ER+ NF1-depleted breast cancer cells responded initially to a selective ER degrader (SERD), such as fulvestrant and an oral SERD AZD9496, but acquired resistance with prolonged treatment. Resistance may be dependent on CDK4/6, a common growth pathway controlled by both Ras and ER. We showed that fulvestrant together with a CDK4/6 inhibitor Palbociclib can efficiently inhibit the growth of ER+ NF1-depleted breast cancer leading to tumor regression in a patient derived xenograft model.

Conclusion: The loss of the full length NF1 can stimulate both ER and Ras signaling, and it is possible to efficiently treat ER+ NF1-depleted breast cancer by a SERD, in combination with CDK4/6 inhibitor.

Citation Format: Zeyi Zheng, Jonathan T. Lei, Meenakshi Anurag, Long Feng, Purba Singh, Hilda Kennedy, Jin Cao, Xi Chen, Matthew J. Ellis, Eric C. Chang. Optimizing treatment strategy for NF1-depleted estrogen receptor positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2490.

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

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

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

Evaluation of sensitivity to endocrine therapy index (SET2,3) for response to neoadjuvant endocrine therapy (NET) and subsequent prognosis

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Background: Patients (pts) in Cohort A of the American College of Surgeons Oncology Group Z1031 (Alliance) trial of NET for cStage II-III breast cancer were randomized to anastrozole [ANA], letrozole [LET] or exemestane [EXE] for 16-18 weeks (wks). In Cohort B, pts chose between ANA and LET and switched to chemotherapy or surgery if a tumor biopsy after 2-4 wks of NET had Ki67 >10%. Treatments after surgery were not defined by the trial protocol. SET2,3 measures nonproliferation gene expression related to estrogen and progesterone receptors adjusting for a baseline prognostic index that combines clinical tumor and nodal stage and a 4-gene molecular subtype (RNA4) defined by ESR1, PGR, ERBB2 and AURKA. High SET2,3 in a pre-treatment biopsy using cStage information is defined as SET2,3 >1.77. Methods: 379 pts had gene expression data from a research tumor biopsy prior to NET (Agilent 44K microarrays). A bioinformatician blinded to pt treatment and clinical outcomes determined SET2,3. The trial statistician then examined the association between SET2,3 and pharmacodynamic response at 2-4 wks (N=141, Cohort B): Ki67 ≤10% and complete cell cycle arrest (CCCA Ki67 ≤2.7%); pathologic outcomes in pts who completed NET: ypStage 0/1 (N=329, Cohorts A&B), PEPI-0 rate (N=155, Cohort B); and event-free survival (EFS) post-registration (N=244, Cohorts A&B). We used Fisher’s exact tests to assess whether responses, and Cox modeling to evaluate whether EFS, differed with respect to SET2,3 status. Results: High SET2,3 in 48% of pts (183/379) was associated with older age (median: 66 vs 63 years; p=0.012); cStage II (95% vs 75%; p <0.001); and pre-NET Ki67 ≤10% (37% vs 20%; p< 0.001) in pts with low SET2,3. In Cohort B, pts with high SET2,3 had a higher rate of pharmacodynamic response in their tumor at wk 2-4 than pts with low SET2,3 (Table). In the subset of Cohort B pts with wk 2-4 Ki67 ≤10%, pre-treatment SET2,3 trended numerically higher in pts who achieved PEPI-0 score (p=0.049) but the proportion achieving PEPI-0 did not differ by SET2,3 high/low status (Table). EFS was significantly longer for pts with high SET2,3 than pts with low SET2,3 (HR[H/L]: 0.52; 95% CI: 0.34-0.80; p=0.003). Conclusions: An exploratory analysis of Z1031 data demonstrated that the rate of pharmacodynamic suppression of proliferation by NET at 2-4 wks was greater and EFS was longer for pts with breast cancer expressing high SET2,3 disease than pts with low SET2,3. Support: U10CA180821, U10CA180882, U24CA196171; https://acknowledgments.alliancefound.org ; Clinical trial information: NCT00265759. [Table: see text]

Immune Checkpoint Profiles in Luminal B Breast Cancer (Alliance)

BACKGROUND

Unlike estrogen receptor (ER)-negative breast cancer, ER-positive breast cancer outcome is less influenced by lymphocyte content, indicating the presence of immune tolerance mechanisms that may be specific to this disease subset.

METHODS

A supervised analysis of microarray data from the ACOSOG Z1031 (Alliance) neoadjuvant aromatase inhibitor (AI) trial identified upregulated genes in Luminal (Lum) B breast cancers that correlated with AI-resistant tumor proliferation (percentage of Ki67-positive cancer nuclei, Pearson r > 0.4) (33 cases Ki67 > 10% on AI) vs LumB breast cancers that were more AI sensitive (33 cases Ki67 < 10% on AI). Overrepresentation analysis was performed using WebGestalt. All statistical tests were two-sided.

RESULTS

Thirty candidate genes positively correlated (r ≥ 0.4) with AI-resistant proliferation in LumB and were upregulated greater than twofold. Gene ontologies identified that the targetable immune checkpoint (IC) components IDO1, LAG3, and PD1 were overrepresented resistance candidates (P ≤ .001). High IDO1 mRNA was associated with poor prognosis in LumB disease (Molecular Taxonomy of Breast Cancer International Consortium, hazard ratio = 1.43, 95% confidence interval = 1.04 to 1.98, P = .03). IDO1 also statistically significantly correlated with STAT1 at protein level in LumB disease (Pearson r = 0.74). As a composite immune tolerance signature, expression of IFN-γ/STAT1 pathway components was associated with higher baseline Ki67, lower estrogen, and progesterone receptor mRNA levels and worse disease-specific survival (P = .002). In a tissue microarray analysis, IDO1 was observed in stromal cells and tumor-associated macrophages, with a higher incidence in LumB cases. Furthermore, IDO1 expression was associated with a macrophage mRNA signature (M1 by CIBERSORT Pearson r = 0.62 ) and by tissue microarray analysis.

CONCLUSIONS

Targetable IC components are upregulated in the majority of endocrine therapy-resistant LumB cases. Our findings provide rationale for IC inhibition in poor-outcome ER-positive breast cancer.

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors. Multi-omic analysis identifies three molecular subtypes with high potential for treatment with CDK inhibitors, anti-EGFR antibody therapy, and immunotherapy, respectively. Altogether, proteogenomics provides a systematic framework to inform HNSCC biology and treatment.

Abstract PS18-07: Association between pathological response and tumor genomic profiling in triple negative breast cancer patients treated with neoadjuvant chemotherapy

Background: Triple negative breast cancer (TNBC) has a marked molecular diversity that promotes clinical heterogeneity. Less than 40% of TNBC patients will achieve a pathological complete response (pCR) to standard neoadjuvant chemotherapy. Patients who do not achieve pCR have a high risk of disease recurrence and subsequent death from breast cancer. Molecular characterization may identify TNBC patients unlikely to achieve pCR and subsequently develop recurrent disease. Methods: We are conducting a multicenter prospective study of clinical stages II and III TNBC patients treated with neoadjuvant docetaxel and carboplatin. We performed tumor whole exome sequencing on 56 patients pre-treatment samples to identify somatic mutation associated with pCR. Thirteen matching samples from cycle 1 day 3 (C1D3) were also analyzed to assess changes in somatic mutation profiles. Results: In this biomarker study, thirty-seven (66.1%) patients are Caucasians, 17 (30.4%) African American. Nineteen (33.9%) achieved pCR following six cycles of neoadjuvant docetaxel and carboplatin. 9063 variants were detected in 5386 unique genes. The overall mutation burden for patients who achieved pCR was not significantly different from non-pCR patients (median of 80 variants, IQR 51-135 in pCR, vs median 72, IQR 44-102 in non-pCR, Wilcoxon rank sum test p=0.78). As expected, TP53 is the most frequently mutated gene observed in 48 of all 56 patients (85.7%). There was a non-significant trend with lower TP53 mutations occurring in 78.9% of patients with pCR, versus 89.2% of non-pCR patients (OR 0.46, 95% CI 0.07 - 2.83; p value 0.42). BRCA2 somatic mutations were observed in 5.4% and 5.3% of pCR and non-pCR samples, respectively. No BRCA1 somatic mutations were identified. EGFR, RAD51AP2, SDK2, L1CAM, KPRP, CACNA1S, CFAP58, COL22A1, and COL4A5 were differentially mutated and almost exclusively found in pCR samples. PCDHA1 and TRMT9B were observed in 18.9% and 16.2%, respectively, of non-pCR samples only. There was a trend of higher variant counts in the thirteen matched samples at C1D3 (median of 82, IQR 49-157) versus corresponding pre-treatment samples (median of 72, IQR 42-92), Wilcoxon rank sum test p=0.29, suggesting clone emergence under treatment pressure. Using the Molecular Signatures Database v7.1, several gene families involved in immune related pathways showed differences between pCR and non-pCR samples. Additionally, borderline differences in hedgehog signaling pathway were identified between pCR and non-pCR samples. There were no differences in apoptosis, DNA repair, EMT, inflammatory response, NOTCH signaling pathways. Conclusion: Across TNBC tumors analyzed, TP53 mutation frequency does not differ in pCR versus non-pCR patients. Somatic mutations in EGFR, RAD51AP2, immune pathways genes, and hedgehog signaling pathway genes may predict pCR to docetaxel and carboplatin chemotherapy.

Citation Format: Foluso O Ademuyiwa, Jingqin Luo, Bryan Fisk, Gejae Jeffers, Tracy Summa, Isabella Grigsby, Mothaffar Rimawi, Meenakshi Anurag, Matthew Ellis, Obi Griffith, Malachi Griffith. Association between pathological response and tumor genomic profiling in triple negative breast cancer patients treated with neoadjuvant chemotherapy [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 PS18-07.

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

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

Citation Format: Jamunarani Veeraraghavan, Ragini Mistry, Sarmistha Nanda, Vidyalakshmi Sethunath, Martin Shea, Tamika Mitchell, Meenakshi Anurag, Michael A. Mancini, Fabio Stossi, C. Kent Osborne, Mothaffar F. Rimawi, Rachel Schiff. HER2 L755S mutation is acquired upon resistance to lapatinib and neratinib and confers cross-resistance to tucatinib and trastuzumab in HER2-positive breast cancer cell models [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD3-09.

Abstract PS17-03: Recurrent active ESR1 fusions render a diagnostic transcriptional signature in metastatic breast cancer

Background: We recently reported two ESR1 fusions (ESR1-YAP1 and ESR1-PCDH11X) that drive endocrine therapy (ET) resistance and metastasis in estrogen receptor positive (ER+) metastatic breast cancer (MBC) (PMC6171747). Here, we report the functional properties of additional ESR1 fusions in ET-resistant MBC with an emphasis on the identification of a transcriptional signature designed to diagnose the presence of an active ESR1 fusion for targeted therapies directed against ESR1 fusion-driven biology. Methods: ESR1 fusions were detected by RNA-seq in ER+ MBC samples. ESR1 fusions were reproduced as cDNA constructs and expressed in ER+ breast cancer cell lines. Hormone-independent cell growth was detected by an Alamar blue assay and activated cell motility by a scratch wound assay. The transcriptional properties of ESR1 fusions was studied by RNA-seq followed by qPCR-based validation. Signature performance was evaluated using a ROC analysis on ER+ patient derived xenografts (PDX) harboring a variety of ESR1 somatic events. Results: All ESR1 fusions studied encoded the first six exons of ESR1 fused in-frame to diverse partner genes, thus replacing the ESR1 drug/ligand binding domain (LBD). Fusions involving a known transcription factor (TF) or coactivator (CoA) gene, including ESR1-YAP1, ESR1-SOX9 and ESR1-ARNT2 drove fulvestrant-resistant cell growth and hormone-independent cell motility. Other ESR1-e6 fusions, including ESR1-DAB2, ESR1-GYG1, ESR1-PCMT1 and ESR1-ARID1B did not induce these properties. From these examples, a functional rule is emerging whereby inter-chromosomal ESR1 translocations fused in-frame to 3’ partner genes with a positive role in transcription are active. Intra-chromosomal fusions with genes with no transcriptional roles are likely inactive. The ESR1-PCDH11X fusion is an exception, suggesting the need for continued functional study of non-TF/CoA partner ESR1-e6 fusions. RNA-seq of T47D cells expressing the full panel of gene fusions demonstrated an overlapping pattern of transcriptional activation focused on estrogen response and epithelial-to-mesenchymal transition (EMT) genes driven by active fusions. This gene signature was well-preserved in a PDX naturally expressing the ESR1-YAP1 fusion. Interestingly, further study showed that a series of ET-resistant PDXs bearing a variety of ESR1 LBD point mutations induced a similar pattern to the active ESR1 fusion signature suggesting overlapping transcriptional regulatory events between ESR1 fusions and ESR1 LBD mutations. The ESR1-D538G mutation conferred the most comparable gene dysregulation to ESR1 fusions. The Y537S/N and E380Q mutations also reproduced the signature driving hormone-independent growth but with exceptions. Two PDX lines bearing either a fully heterozygous Y537S or L536P mutations were surprisingly completely estrogen-dependent. Neither of these examples exhibited the ESR1 fusion gene signature, suggesting an unknown secondary event needed to fully express the phenotype of some ESR1 mutants. The gene signature distinguished ESR1 mutations (constitutively active fusions and point mutations) from wild-type ESR1, with a 92.0% Area Under Curve. Conclusion: Here, we show that ESR1 fusions are recurrent somatic mutations that lead to drug resistance and metastasis by transcriptional reprogramming. We describe a fusion gene signature that may be useful to determine whether an ESR1 fusion or mutation is transcriptionally active and is capable of driving hormone-independent growth and endocrine therapy resistance.

Citation Format: Xuxu Gou, Meenakshi Anurag, Jonathan T Lei, Purba Singh, Sinem Seker, Adrian V Lee, Dan R Robinson, Matthew J Ellis. Recurrent active ESR1 fusions render a diagnostic transcriptional signature in metastatic breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-03.

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued to preserve post-translational modifications, including protein phosphorylation and acetylation. Proteogenomics challenged standard breast cancer diagnoses, provided detailed analysis of the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint therapy, and allowed more accurate assessment of Rb status for prediction of CDK4/6 inhibitor responsiveness. Phosphoproteomics profiles uncovered novel associations between tumor suppressor loss and targetable kinases. Acetylproteome analysis highlighted acetylation on key nuclear proteins involved in the DNA damage response and revealed cross-talk between cytoplasmic and mitochondrial acetylation and metabolism. Our results underscore the potential of proteogenomics for clinical investigation of breast cancer through more accurate annotation of targetable pathways and biological features of this remarkably heterogeneous malignancy.

Abstract 5118: Proteogenomics characterization of HPV-negative head and neck squamous cell carcinomas

Patients with head and neck squamous cell carcinomas (HNSCCs) are treated with surgery, radiation, chemotherapy, and limited targeted therapies. Compared to human papillomavirus (HPV)-positive HNSCCs, HPV-negative cases have worse treatment response and prognosis and represent an unmet clinical need. We performed comprehensive proteogenomic characterization of tumor specimens, matched normal adjacent tissues (NATs), and blood samples from 109 HPV-negative HNSCC patients. This cohort is dominated by tumors from oral cavity (45, 41%) and larynx (49, 45%). Somatic mutation and somatic copy number analyses validated previously reported genomic aberrations in HPV-negative HNSCC. Proteomics analysis linked p53 loss of heterozygosity to increased expression of EPCAM, a stemness marker. Additionally, FAT1 truncation mutations were associated with increased expression of proteins involved in keratinization, a key feature of SCC differentiation. Deletions of 3p and 9p led to the loss of genes encoding p16, chemokine receptors, and interferon/JAK/STAT signaling pathway proteins, whereas amplifications of 3q and 11q led to overexpression of proteins involved in cell proliferation and anti-apoptosis pathways. Comparative analysis of tumor and NAT proteomes and phosphoproteomes identified putative diagnostic biomarkers and druggable targets, and proteogenomic integration further identified putative neoantigens. Tumor site-specific characterization associated epigenetic silencing of neurofilaments with laryngeal but not oral cavity SCC. Protein targets of FDA approved or investigational drugs for HNSCC treatment showed high inter-tumor heterogeneity in their protein abundances. DNA copy number and RNA expression level were good surrogates of protein abundance for some targets, such as EGFR and PD-L1, but they failed to reflect protein levels or kinase activities for other targets, such as MMP9 and MTOR. Thus, there is a critical need for protein biomarker-driven treatment stratification. Deconvolution of bulk tumor gene expression data revealed an immune-hot subgroup and an immune-cold subgroup. Immune-hot tumors broadly overexpressed multiple immune checkpoints including PD-L1, IDO1, and CTLA4, underscoring the necessity of combination immune checkpoint inhibition to improve treatment efficacy. Immune-cold tumors were characterized by smoking, chromosomal instability, and activation of the CDK4/6-pRb axis, suggesting they could be targeted by CDK4/6 inhibitors. We also noted that EGFR-amplified tumors frequently harbor copy number aberrations of downstream signaling components of the EGFR pathway. This may explain the low response rate of EGFR-amplified tumors to EGFR inhibitors, and targeting multiple pathway components, including EGFR, PIK3CA and STAT3, may be required for these tumors. In summary, our integrative proteogenomic characterization revealed multiple novel insights into the pathogenesis and treatment of HPV-negative HNSCCs.

Citation Format: Chen Huang, Lijun Chen, Yize Li, Sara Savage, Michael Schnaubelt, Felipe V. Leprevost, Marcin Cieslik, Yongchao Dou, Bo Wen, Jonathan T. Lei, Kai Li, Eric Jaehnig, Zhiao Shi, Meenakshi Anurag, Jianbo Pan, Yingwei Hu, Rodrigo V. Eguez, David J. Clark, Matthew Wyczalkowski, Saravana M. Dhanasekaran, Chandan Kumar, Antonio Colaprico, Karsten Krug, Michael Gillette, D. R. Mani, Seungyeul Yoo, Jiayi Ji, Xiaoyu Song, Weiping Ma, Xi Steven Chen, Alex Pico, Nathan J. Edwards, Scott D. Jewell, Mathangi Thiagarajan, Emily S. Boja, Henry Rodriguez, Andrew Sikora, Pei Wang, Matthew Ellis, Gilbert S. Omenn, Li Ding, Alexey I. Nesvizhskii, Adel K. EI-Naggar, Daniel W. Chan, Hui Zhang, Bing Zhang, Clinical Proteomic Tumor Analysis Consortium. Proteogenomics characterization of HPV-negative head and neck squamous cell carcinomas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5118.

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

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

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

Abstract 5677: Recurrent transcriptionally active ESR1 fusions render therapeutic vulnerabilities to kinase inhibition in advanced breast cancer

Background: We recently reported two ESR1 fusions (ESR1-YAP1 and ESR1-PCDH11X) that drive endocrine therapy (ET) resistance and metastasis in estrogen receptor positive (ER+) metastatic breast cancer (MBC) (PMC6171747). Here we report additional ESR1 fusions with diverse C-terminal partner genes - ESR1-DAB2, ESR1-GYG1, ESR1-SOX9, ESR1-ARNT2, ESR1-PCMT1 and ESR1-ARID1B. Their functional characteristics and effects on kinase biology will be described.

Methods: ESR1 fusions were identified by RNA-seq in MBC using ChimeraScan to detect fusion junction reads. ESR1 fusion cDNA constructs were expressed in ER+ breast cancer cell lines. An alamarBlue assay assessed cell proliferation. RNA-seq followed by mRNA-qPCR assessed the transcriptional properties. A scratch wound assay assessed cell motility. A Kinase Inhibitor Pulldown (KIP) mass spectrometry-based assay was conducted to examine ESR1 fusion-driven druggable kinases.

Results: All fusions retained the first 6 exons (e6) of ESR1, fused in-frame to C-terminal sequences of diverse partner genes. In addition to ESR1-YAP1 and ESR1-PCDH11X fusions, ESR1-SOX9 and ESR1-ARNT2 drove fulvestrant-resistant growth. RNA-seq revealed fusion-specific transcriptional signatures indicating enrichment of estrogen responsive and epithelial-to-mesenchymal transition (EMT) pathways that were confirmed by mRNA-qPCR. Transcriptionally active ESR1 fusions also promoted hormone-independent cell motility. KIP profiling demonstrated an increase in protein abundance of multiple receptor tyrosine kinases including RET and insulin like growth factor 1 receptor (IGF1R) in T47D cells expressing active ESR1 fusion proteins, both of which have been previously implicated in driving ET and MBC. Both proteins were also elevated in a patient-derived xenograft naturally harboring the ESR1-YAP1 fusion. Combinatorial inhibition of RET and IGF1R significantly suppressed ESR1 fusion-driven cell growth in vitro. Neither transcriptional activation nor kinase upregulation was observed in other ESR1-e6 fusions. Lastly, we report recurrent examples of specific known active ESR1 fusions: ESR1-PCDH11X (3 examples) (TEMPUS unpublished data) and ESR1-ARNT2 (2 examples) (PMC6872491).

Conclusion: A subset of ESR1-e6 fusions are active, drive ET resistance and metastasis/EMT in experimental models. When ESR1 is fused in-frame with another transcriptional regulator, activity is predictable. However, recurrent partners that have non-transcriptional roles (PCDH11X) suggests cDNA expression-based functional screens should be continued. A common pattern of kinase activation indicates that ESR1 fusion specific therapeutic strategies could be devised.

Citation Format: Xuxu Gou, Jonathan Lei, Beom-Jun Kim, Meenakshi Anurag, Sinem Seker, Saif Rehman, Adrian V. Lee, Kevin White, Michael Caldwell, Jonathan Ball, Dan R. Robinson, Matthew J. Ellis. Recurrent transcriptionally active ESR1 fusions render therapeutic vulnerabilities to kinase inhibition in advanced breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5677.

Abstract 5467: Outlier analysis to identify determinants of therapeutic resistance in breast cancer

Tumors are typically characterized by variable responses to targeted therapy driven by the heterogeneity of drivers among tumors. Inter-tumor heterogeneity also results in different resistance determinants to the same therapeutic agent. Outlier analysis has been applied extensively to identify drivers of cancer when comparing a heterogenous population of tumor samples to a relatively homogenous population of normal samples. However, the application of outlier analysis has rarely been applied to identify intrinsic determinants of resistance to targeted cancer therapies. We recently applied outlier analysis to baseline proteomics data collected from HER2/ERBB2 positive breast cancer patients treated with anti-HER2 therapy, comparing protein levels in each patient that did not show pathological complete response (pCR) to the population of patients that did. Three of the five non-pCR patients were outliers for low expression of the ERBB2 protein relative to the pCR patients, suggesting that lack of protein expression of the direct therapeutic target drives resistance in some cases whereas other mechanisms contribute to resistance in other cases. Here, we systematically evaluate the ability of multiple outlier analysis methods, including the method we implemented for the HER2 study (outlieR), to identify molecular genes associated with poor prognosis in estrogen receptor (ESR1) positive patients receiving hormone therapy (targeting ESR1) using a large-scale publicly available dataset which contains baseline gene expression and survival data for ~2000 breast cancer patients (METABRIC). Specifically, we compared expression data from tumors of 72 patients that showed poor prognosis (died of disease within 5 years) to data from 226 tumors from patients with good prognosis (did not die of disease, with at least five years of follow-up time). For this evaluation, we focused on the direct target of hormone therapy, ESR1, and growth factor receptors associated with endocrine therapy resistance. Scores from outlier analysis methods consistently ranked ESR1, EGFR, and genes associated with the ERBB2 locus (amplification of the locus drives ERBB2 gene expression in HER2 positive breast cancer) more highly than the the T-test metric did, with the outlieR method outperforming another established method, Outlier Sums (OS), in most cases. Furthermore, four targets of FDA-approved drugs, including two genes in the MAPK pathway, were amongst the top 200 genes identified by the outlieR method, whereas TOP2A was the only approved target in the top 200 genes identified by the T-test, a target of cytotoxic chemotherapy treatments. Finally, the outlieR method generates outlier scores for each gene in each non-responder relative to the set of non-responders, allowing for the evaluation of genes associated with resistance on a patient-by-patient basis. These observations suggest that outlier analysis can be used to prioritize molecular features as potential mechanisms of resistance and alternative drug targets by accounting for heterogeneity between resistant tumors.

Citation Format: Eric James Jaehnig, Meenakshi Anurag, Jonathan T. Lei, Bing Zhang. Outlier analysis to identify determinants of therapeutic resistance in breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5467.

Correction to: Mismatch repair protein loss in breast cancer: clinicopathological associations in a large British Columbia cohort

In the original publication of the article, the funding statement was published incompletely. The corrected funding statement should read as below.

Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer

We report that neurofibromin, a tumor suppressor and Ras-GAP (GTPase-activating protein), is also an estrogen receptor-α (ER) transcriptional co-repressor through leucine/isoleucine-rich motifs that are functionally independent of GAP activity. GAP activity, in turn, does not affect ER binding. Consequently, neurofibromin depletion causes estradiol hypersensitivity and tamoxifen agonism, explaining the poor prognosis associated with neurofibromin loss in endocrine therapy-treated ER⁺ breast cancer. Neurofibromin-deficient ER⁺ breast cancer cells initially retain sensitivity to selective ER degraders (SERDs). However, Ras activation does play a role in acquired SERD resistance, which can be reversed upon MEK inhibitor addition, and SERD/MEK inhibitor combinations induce tumor regression. Thus, neurofibromin is a dual repressor for both Ras and ER signaling, and co-targeting may treat neurofibromin-deficient ER⁺ breast tumors.

Abstract GS2-05: Microscaled proteogenomic methods for precision oncology

Cancer proteogenomics combines genomics, transcriptomics and mass spectrometry-based proteomics to gain insights into cancer biology and treatment responsiveness. While proteogenomics analyses have already shown great potential to deepen our understanding of cancer tissue complexity and signaling, how a patient’s tumor changes upon treatment has largely been the province of genomics. This is due to technical difficulties associated with doing proteogenomic analysis on clinic-derived core-needle biopsies. To address this critical need, we have developed a “microscaled” proteogenomics approach for tumor-rich OCT-embedded core needle biopsies. Tissue-sparing specimen processing (“Biopsy Trifecta EXTraction”, BioTExt) and microscaled proteomics (MiProt) methodologies allowed generation of deep-scale proteogenomics datasets, with copy number and transcript information for &gt;20,000 genes and mass spectrometry-based identification and quantification of nearly all expressed proteins in a tumor (&gt;10,000 proteins) and more than &gt;20,000 phosphosites starting with just 25 micrograms of protein per sample. In order to understand the capabilities and limitations our our approach relative to more conventional deepscale proteomics requiring &gt;10X more starting material, we compared preclinical patient derived xenograft (PDX) models at conventional scale with data obtained by core-needle biopsy of the same tissues. Comparable depth and biological insights were obtained from the cores relative to surgically resected tumors. As a proof-of-concept for implementation in clinical trials, we applied microscaled proteogenomic methods to a small-scale clinical study where biopsies were accrued from patients with ERBB2+ locally advanced breast cancer before and 48 to 72 hours after the first dose of neoadjuvant Trastuzumab-based chemotherapy. Multi-omics comparisons were conducted between samples associated with residual disease versus samples associated with complete pathological response. Integrative, microscaled proteogenomic analyses efficiently diagnosed the molecular bases of diverse candidate treatment resistance mechanisms including: 1) absence of ERBB2 amplification (false-ERBB2+); 2) insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification (pseudo-ERBB2+); 3) resistance features in true-ERBB2+ cases including androgen receptor signaling, mucin expression and an inactive immune microenvironment; 4) lack of acute phospho-ERBB2 down-regulation in non-pCR cases. In summary, we have developed a robust proteogenomics pipeline well suited for large-scale cancer clinical studies to identify potential resistance mechanism in patients. We conclude that microscaled cancer proteogenomics could improve diagnostic precision in the clinical setting.

Citation Format: Shankha Satpathy, Eric Jaehnig, Krug Karsten, Beom-Jun Kim, Alexander Saltzman, Doug Chan, Kimberly Holloway, Meenakshi Anurag, Chen Huang, Purba Singh, Ari Gao, Noel Namai, Yongchao Dou, Bo Wen, Suhas Vasaikar, David Mutch, Mark Watson, Cynthia Ma, Foluso Ademuyiwa, Mothaffar Rimawi, Jeremy Hoog, Samuel Jacobs, Anna Malovannaya, Terry Hyslop, D.R Mani, Charles Perou, George Miles, Bing Zhang, Michael Gillette, Steven Carr, Matthew Ellis. Microscaled proteogenomic methods for precision oncology [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 GS2-05.

Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer

RNA sequencing (RNA-seq) detects estrogen receptor alpha gene (ESR1) fusion transcripts in estrogen receptor-positive (ER⁺) breast cancer, but their role in disease pathogenesis remains unclear. We examined multiple ESR1 fusions and found that two, both identified in advanced endocrine treatment-resistant disease, encoded stable and functional fusion proteins. In both examples, ESR1-e6>YAP1 and ESR1-e6>PCDH11X, ESR1 exons 1-6 were fused in frame to C-terminal sequences from the partner gene. Functional properties include estrogen-independent growth, constitutive expression of ER target genes, and anti-estrogen resistance. Both fusions activate a metastasis-associated transcriptional program, induce cellular motility, and promote the development of lung metastasis. ESR1-e6>YAP1- and ESR1-e6>PCDH11X-induced growth remained sensitive to a CDK4/6 inhibitor, and a patient-derived xenograft (PDX) naturally expressing the ESR1-e6>YAP1 fusion was also responsive. Transcriptionally active ESR1 fusions therefore trigger both endocrine therapy resistance and metastatic progression, explaining the association with fatal disease progression, although CDK4/6 inhibitor treatment is predicted to be effective.