Abstract P4-04-02: Identifying ERBB-2 activating mutations (mts) in HER2 negative tumors for clinical trials – Impact of institute-wide genomic testing and trial matching on trial enrollment in clinical practice

Introduction

Tailored treatment trials with biomarker-driven hypotheses are becoming an important strategy in drug development. Umbrella, basket and enrichment trials with eligibility predicated upon results of tumor sequencing are increasingly common. Several institutional and commercial genomic assays have been developed. However, the value of broad-based testing in recruiting patients (pts) to molecular-based clinical trials designed for small subgroups has not been fully evaluated and has been challenging to assess in a real-world setting. We evaluated the likelihood of trial enrollment based upon an institute-wide genomic test.

Methods

Since 2013, all pts with metastatic breast cancer (MBC) seen at least once at Dana-Farber Cancer Institute have been offered the option of tumor sequencing using multiplexed copy number variation (CNV) and mts detection across the full coding regions of a total of 447 cancer genes and 191 regions across 60 genes for rearrangement detection (Oncopanel; OP). For our primary analysis, we selected the ongoing multi-center phase II trial (NCT01670877) activated at our site on Sep 30, 2013, evaluating neratinib in ERBB-2 mutated pts, as the study provided a clear delineation of eligible mts, and timing of slot availability was retrievable retrospectively over an extended time frame. Our primary aim was to describe the proportion of pts with a qualifying ERBB-2 mt detected by OP who enrolled on the selected trial. Secondary objectives included median time from OP result to trial registration and description of ERBB-2 mts spectrum within each subtype. Associations were calculated by Fisher's test.

Results

We identified a total of 1,046 pts with HER-2 negative MBC and who had OP results between Sep 1, 2013 and Jun 1, 2017. A total of 43 pts (4.1%) were found to have ERBB-2 mts. Of these, 20 (1.9%) had activating eligible mts. The proportion of these pts who enrolled in the trial was 30% (6/20). Of the remaining 14 pts, 5 screen-failed and 2 were enrolled with known ERBB-2 mt through other testing modalities. Seven of 20 (35%) molecularly eligible pts were not approached (3 pts lost to follow-up, 3 enrolled in other clinical trials and 1 pt chose standard treatment). The median time from OP result to trial enrollment was 85 days (34-554). A significantly higher frequency of ERBB2 activating mts was found in ER+ compared to ER- primary tumors (2.5% vs. 0.3%, p =0.036), and in lobular tumors compared with ductal (5.5% vs. 1.25%, p=0.003). Frequency of eligible mts in primary tumors were similar to metastatic site (1.9% and 1.8%, respectively p=1.0)

Discussion

In this cohort, activating ERBB-2 mts were present in 20 of 1046 (1.9%) pts tested. Although over half of pts with eligible mts on OP testing were approached for NCT01670877, only 0.5% of the total tested population were enrolled (6/1046). Our data illustrate the substantial challenges in screening and enrolling to trials of rare subsets, even within a large academic institution, and point to the need for creative and novel approaches to leverage pts and community- and academic-based providers to more effectively support the success of such studies.

Citation Format: Exman P, Garrido-Castro A, Hughes ME, Freedman RA, Ma C, Bose R, Cerami E, Wagle N, Barroso-Sousa R, Fitz CD, Lindeman NI, MacConaill L, Bychkovsky BL, Lloyd MR, Mackichan CR, Kumari P, Tolaney SM, Krop IE, Winer EP, Dillon DA, Lin NU. Identifying ERBB-2 activating mutations (mts) in HER2 negative tumors for clinical trials – Impact of institute-wide genomic testing and trial matching on trial enrollment in clinical practice [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-04-02.

Abstract PD9-02: Evolutionary analysis of 462 serial metastatic biopsies from 208 patients with estrogen receptor-positive (ER+) metastatic breast cancer (MBC) using whole exome sequencing (WES)

Background: While great strides have been made in the treatment of ER+ MBC, therapeutic resistance is nearly universal. The genomic evolution of ER+ breast cancer in the metastatic setting under the selective pressure of multiple lines of therapies is not well understood. To address this, we analyzed the clonal dynamics of serial metastatic samples (mets) to evaluate how tumors evolve and to identify acquired resistance mechanisms.

Methods: We performed WES on 462 clinically annotated samples from 208 patients (pts) with ER+ MBC, including 67 primary tumor biopsies, 229 metastatic biopsies and 160 blood samples (cfDNA). Pts with multiple mets included cases with temporally concordant metastatic tumor and blood samples (48 pts) and cases with serial mets obtained over the course of treatment in the metastatic setting (69 pts). Treatments given between the serial mets included CDK4/6 inhibitors (23 pts), and selective estrogen receptor degraders (19 pts), among others.

Results: In the temporally-concordant mets, we found that cfDNA mutations (muts) largely overlap with muts found in tumor biopsies, capturing >85% of clonal tumor muts. However, we observed a higher level of heterogeneity in cfDNA compared to biopsies (p.value< 1.05e-19, Welch test) and a subset of high-confidence muts that were only detected in cfDNA, including in clinically important genes such as ESR1, PIK3CA, KRAS, and ERBB2. Analysis of serial mets was used to elucidate the evolutionary dynamics within the metastatic setting under the selective pressure of treatment. The median duration between mets was 112 days and the median number of inter-biopsy unique treatments was two. Most tumors continued to evolve within the metastatic setting, with 50 out of 69 pts (72%) acquiring a meaningful sub-clone (50% increase in relative cancer cell fraction) and 31 out of 69 (45%) acquiring muts in known cancer genes, including a subset acquiring a plausible resistance alteration such as alterations that dysregulate ER (5 out of 69 pts, 7%; ESR1 mut, FOXA1 amplification (amp), NCOR1 bi-allelic deletion (del)), ERBB (4%; ERBB2 amp, ERBB3 mut), RAS (4%; KRAS mut, NRAS amp, NF1 del), FGF/FGFR (12%; FGFR2 mut, FGFR1/2 amp, FGF3 amp), and cell cycle (13%; RB1 del, CDK4 amp, AURKA amp, CDKN2A del). Finally, in pts who had multiple mets, we observed several cases of evolutionary convergence toward equivalent resistance mechanisms including convergent RB1 loss as a mechanism of resistance to a CDK4/6 inhibitor and convergent BRCA2 reversion following resistance to a PARP inhibitor.

Conclusions: This study demonstrates that ER+ MBC continues to evolve under the selective pressure of treatments in the metastatic setting. These findings elucidate the challenge of studying high complexity and heavily treated tumors, while also highlighting some commonalities in the evolutionary trajectories selected by these treatments. The multiplicity of clinically relevant genomic alterations acquired in these advanced stages highlights the need for serial biopsies and the potential to inform post-progression therapeutic choices through targeting the acquired dependencies in post-progression tumors.

Citation Format: Cohen O, Buendia-Buendia J, Wander S, Nayar U, Mao P, Waks A, Kim D, Freeman S, Adalsteinsson V, Helvie K, Livitz D, Rosebrock D, Leshchiner I, Dellostritto L, Garrido-Castro A, Jain E, Periyasamy S, Mackichan C, Lloyd M, Marini L, Krop I, Garraway L, Getz G, Winer E, Lin N, Wagle N. Evolutionary analysis of 462 serial metastatic biopsies from 208 patients with estrogen receptor-positive (ER+) metastatic breast cancer (MBC) using whole exome sequencing (WES) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-02.