Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling of Tissue and Blood in Metastatic Triple-Negative Breast Cancer

PURPOSE

The clinical utility of next-generation sequencing (NGS) in breast cancer has not been demonstrated. We hypothesized that we could perform NGS of a new biopsy from patients with metastatic triple-negative breast cancer (TNBC) in a clinically actionable timeframe.

EXPERIMENTAL DESIGN

We planned to enroll 40 patients onto a prospective study, Individualized Molecular Analyses Guide Efforts (IMAGE), to evaluate the feasibility of obtaining a new biopsy of a metastatic site, perform NGS (FoundationOne), and convene a molecular tumor board to formulate treatment recommendations within 28 days. We collected blood at baseline and at time of restaging to assess cell-free circulating plasma tumor DNA (ptDNA).

RESULTS

We enrolled 26 women with metastatic TNBC who had received ≥1 line of prior chemotherapy, and 20 (77%) underwent NGS of a metastatic site biopsy. Twelve (60%) evaluable patients received treatment recommendations within 28 days of consent. The study closed after 20 patients underwent NGS, based on protocol-specified interim futility analysis. Three patients went on to receive genomically directed therapies. Twenty-four of 26 patients had genetic alterations successfully detected in ptDNA. Among 5 patients, 4 mutations found in tumor tissues were not identified in blood, and 4 mutations found in blood were not found in corresponding tumors. In 9 patients, NGS of follow-up blood samples showed 100% concordance with baseline blood samples.

CONCLUSIONS

This study demonstrates challenges of performing NGS on prospective tissue biopsies in patients with metastatic TNBC within 28 days, while also highlighting the potential use of blood as a more time-efficient and less invasive method of mutational assessment. Clin Cancer Res; 23(2); 379-86. ©2016 AACR.

Abstract PD6-08: IMAGE: Individualized molecular analyses guide efforts in breast cancer with comprehensive genomic profiling of tissue and plasma tumor DNA

Background: Standard treatment options for patients with metastatic triple negative breast cancer (TNBC) are limited to chemotherapy. Molecular profiling of tumors may allow for novel treatment recommendations.

Methods: We initiated a prospective study designated IMAGE. Women with newly progressing metastatic TNBC who received at least one line of prior chemotherapy were eligible. New metastatic biopsies were obtained for molecular profiling at study entry. Archived metastatic biopsy specimens were allowed if patients had not commenced new systemic therapy. The specimens were reviewed by the study pathologist and stained for ER, PR, HER2, and androgen receptor (AR) by immunohistochemistry. Specimens underwent hybrid-capture based comprehensive genomic profiling (CGP) (Foundation Medicine Inc., Cambridge, MA). Clinical data and genomic profiling reports were reviewed by the GAITWAY (Genomic Alterations in Tumors with Actionable Yields) Molecular Profile Tumor Board. Recommendations were communicated to the treating oncologist and patients were followed for treatment decision and clinical outcomes. Peripheral blood was also analyzed by an investigational assay for circulating plasma tumor DNA (ptDNA) (Foundation Medicine Inc.) at study entry, and when obtainable, from serial blood draws at time of progression. The primary objective was to assess feasibility of completing the process from consent to GAITWAY recommendations within 28 days for at least 80% of patients.

Results: From September 2013 to April 2015, we enrolled 26 eligible women. Median age was 55 (range 25-67); patients identified as white 12 (46%), black 11 (42%), or other 3 (12%); median number of prior lines of treatment was 3; and 65.4% of patients had visceral disease. Twenty (77%) eligible patients received CGP of a metastatic site biopsy. Six patients did not undergo CGP due to either absence of a metastatic site amenable for biopsy or inadequate tissue for CGP. The study met the predefined statistical endpoint for futility and was closed after 20 patients had undergone CGP. Twelve (60%) evaluable patients received treatment recommendations within 28 days of study consent. Failure to meet this time frame was due to difficulties in accessing archival tumor tissue (N=5) and need for additional tissue for molecular analysis (N=3). Preliminary results demonstrate high concordance between mutations in metastatic biopsies and ptDNA in 15/17 patients.

Enrolled in IMAGE26Successful NGS20Potentially actionable mutation identified15GAITWAY recommended targeted therapy as possible next treatment13Received targeted therapy4

Conclusions: CGP of patients with metastatic TNBC can provide additional information that may help direct treatment. However, difficulties in obtaining adequate tumor tissue may hinder this approach. Use of a well-validated ptDNA profiling assay could be an alternative to overcome these limitations.

Citation Format: Parsons HA, Beaver JA, Cimino-Mathews A, Zorzi J, Slater S, Clark T, Lipson D, Ali SM, Kennedy M, Otto GA, Young LE, Jeter S, VanDenBerg DA, Rosner GL, Park BH, Stearns V. IMAGE: Individualized molecular analyses guide efforts in breast cancer with comprehensive genomic profiling of tissue and plasma tumor DNA. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD6-08.

ESR1 Mutations in Circulating Plasma Tumor DNA from Metastatic Breast Cancer Patients

PURPOSE

Mutations in the estrogen receptor (ER)α gene, ESR1, have been identified in breast cancer metastases after progression on endocrine therapies. Because of limitations of metastatic biopsies, the reported frequency of ESR1 mutations may be underestimated. Here, we show a high frequency of ESR1 mutations using circulating plasma tumor DNA (ptDNA) from patients with metastatic breast cancer.

EXPERIMENTAL DESIGN

We retrospectively obtained plasma samples from eight patients with known ESR1 mutations and three patients with wild-type ESR1 identified by next-generation sequencing (NGS) of biopsied metastatic tissues. Three common ESR1 mutations were queried for using droplet digital PCR (ddPCR). In a prospective cohort, metastatic tissue and plasma were collected contemporaneously from eight ER-positive and four ER-negative patients. Tissue biopsies were sequenced by NGS, and ptDNA ESR1 mutations were analyzed by ddPCR.

RESULTS

In the retrospective cohort, all corresponding mutations were detected in ptDNA, with two patients harboring additional ESR1 mutations not present in their metastatic tissues. In the prospective cohort, three ER-positive patients did not have adequate tissue for NGS, and no ESR1 mutations were identified in tissue biopsies from the other nine patients. In contrast, ddPCR detected seven ptDNA ESR1 mutations in 6 of 12 patients (50%).

CONCLUSIONS

We show that ESR1 mutations can occur at a high frequency and suggest that blood can be used to identify additional mutations not found by sequencing of a single metastatic lesion.

Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA

OBJECTIVES

Circulating plasma DNA is being increasingly used for biomedical and clinical research as a substrate for genetic testing. However, cell lysis can occur hours after venipuncture when using standard tubes for blood collection, leading to an increase in contaminating cellular DNA that may hinder analysis of circulating plasma DNA. Cell stabilization agents can prevent cellular lysis for several days, reducing the need for immediate plasma preparation after venipuncture, thereby facilitating the ease of blood collection and sample preparation for clinical research. However, the majority of cell stabilizing reagents have not been formally tested for their ability to preserve circulating plasma tumor DNA.

DESIGN & METHODS

In this study, we compared the properties of two cell stabilizing reagents, the cell-free DNA BCT tube and the PAXgene tube, by collecting blood samples from metastatic breast cancer patients and measuring genome equivalents of plasma DNA by droplet digital PCR. We compared wild type PIK3CA genome equivalents and also assayed for two PIK3CA hotspot mutations, E545K and H1047R.

RESULTS

Our results demonstrate that blood stored for 7 days in BCT tubes did not show evidence of cell lysis, whereas PAXgene tubes showed an order of magnitude increase in genome equivalents, indicative of considerable cellular lysis.

CONCLUSIONS

We conclude that BCT tubes can prevent lysis and cellular release of genomic DNA of blood samples from cancer patients when stored at room temperature, and could therefore be of benefit for blood specimen collections in clinical trials.