Abstract GS3-03: Genomic analysis of 733 HER2+ breast cancers identifies recurrent pathways alterations associated with anti-HER2 resistance and new therapeutic vulnerabilities
Authors: Ferraro Emanuela , Smith Alison , Safonov Anton , De Lara Paulino Tallon , Bernado' Cristina , Lahuerta Enrique J. Arenas , Arribas Joaquín , Solit David , Reis-Filho Jorge S. , Rosen Neal , Norton Larry , Modi Shanu , Robson Mark E. , Dang Chau T. , Curigliano Giuseppe , Chandarlapaty Sarat , Razavi Pedram 
Published: March 2022

Abstract
Background:The introduction of anti-HER2 therapies, trastuzumab and pertuzumab (HP) to the treatment of metastatic HER2-positive breast cancer has had a transformational impact on the outcomes for this disease. Nevertheless, disease progression is ultimately observed in most patients within 3 years carrying the potential for morbidity and potentially more toxic therapies. To identify selective strategies to prevent disease progression, we sought to elucidate mechanisms of resistance to anti-HER2 therapies by analyzing a large cohort of genomically and clinically annotated HER2+ breast cancers. Methods: Patients with advanced HER2+ breast cancer who underwent prospective clinical tumor sequencing utilizing MSK-IMPACT assay between April 2014 and February 2021 were included in the analysis. Clinical HER2 positivity was defined as per ASCO/CAP guidelines. Cox proportional hazard models were used to determine the association between genomic alterations and progression-free survival (PFS) on 1st line HP and taxane-based therapy (THP). Only patients with a sequenced pre-treatment tumor sample were included in the survival analysis. Recurrent mutations identified were modeled in HER2+ breast cancer cell lines using short hairpin RNAs and CRISPR/Cas9, and the sensitivity of these isogenic pairs to HER2-targeted therapies was evaluated via metabolic and colony formation assays of cell proliferation. Results: We identified 733 ERBB2-amplified primary (n=385) and metastatic (n=348) that underwent sequencing. Concurrent PIK3CA mutations were identified in 30% of the tumors. Pathogenic activating alterations involving the MAPK pathway were observed in 12.8% of tumors with the most frequent alterations being NF1 loss, ERBB2 and RAS activating mutations. MAPK alterations were significantly enriched in the metastatic tumors (16.6%) compared to the treatment-naïve primaries (9.8%, p=0.020). The outcome analysis included 145 patients with advanced clinically HER2+ breast cancer whose tumors were sequenced prior to starting 1st line THP. Twenty percent (29/145) of tumors did not show genomic ERBB2 amplification as detected by NGS and had a significantly worse outcome (median PFS of 9.4 months [95% CI 5.5-19] and 23 months [95% CI 17-30], respectively; p=0.015). PIK3CA mutations were also associated with a shorter PFS (mutant: 13 months [95%CI: 7.7-18] vs wild type: 23 months [95%CI 17-16], p=0.0013). We further found reduced PFS in MAPK altered tumors (median PFS 9.9 months; 95% CI: 5.5-17) compared to the rest of the population (median PFS 21 months; 95% CI: 17-30; p=0.01). On multivariable analysis adjusted for estrogen receptor status, and presence of PIK3CA/AKT1/PTEN mutations and genomic ERBB2 amplification, MAPK pathway alterations were independently associated with worse outcome (HR: 2.25; 95% CI: 1.29, 3.93; multivariate p = 0.0043). To establish a causal role for MAPK alterations in reducing efficacy of anti-HER2 therapy, we depleted NF1 expression or expressed mutant KRAS or BRAF in a panel of HER2+ breast cancer cell lines. Consistently, MAPK-altered cell lines exhibited resistance to FDA approved HER2 inhibitors in vitro and in vivo. Conclusions: This clinicogenomic analysis of mechanisms of resistance to anti-HER2 therapy demonstrated that PIK3CA activating mutations and lack of genomic ERBB2 amplification as detected by tumor sequencing are associated with shortened PFS on HP-based therapy. Our analysis uniquely identified MAPK pathway alterations as additional potential drivers of resistance to anti-HER2 therapy. Inhibition of the PI3K or MAPK pathway in such tumors may represent a new therapeutic strategy to extend H/P benefit.
Citation Format: Emanuela Ferraro, Alison Smith, Anton Safonov, Paulino Tallon De Lara, Cristina Bernado', Enrique J. Arenas Lahuerta, Joaquín Arribas, David Solit, Jorge S. Reis-Filho, Neal Rosen, Larry Norton, Shanu Modi, Mark E. Robson, Chau T. Dang, Giuseppe Curigliano, Sarat Chandarlapaty, Pedram Razavi. Genomic analysis of 733 HER2+ breast cancers identifies recurrent pathways alterations associated with anti-HER2 resistance and new therapeutic vulnerabilities [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS3-03.