Targeted NGS, array-CGH, and patient-derived tumor xenografts for precision medicine in advanced breast cancer: a single-center prospective study

Abstract

Background: Routine feasibility and clinical impact of genomics-based tumor profiling in advanced breast cancer (aBC) remains to be determined. We conducted a pilot study to evaluate whether precision medicine could be prospectively implemented for aBC patients in a single center and to examine whether patient-derived tumor xenografts (PDX) could be obtained in this population.

Results: Thirty-four aBC patients were included. Actionable targets were found in 28 patients (82%). A targeted therapy could be proposed to 22 patients (64%), either through a clinical trial (n=15) and/or using already registered drugs (n=21). Ten patients (29%) eventually received targeted treatment, 2 of them deriving clinical benefit. Of 22 patients subjected to mouse implantation, 10 had successful xenografting (45%), mostly in triple-negative aBC.

Methods: aBC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials.gov, NCT01521676). Genomic profiling was established by whole-genome array comparative genomic hybridization (aCGH) and targeted next-generation sequencing (NGS) of 365 candidate cancer genes. For a subset of patients, a sample of fresh tumor was orthotopically implanted in humanized cleared fat pads of NSG mice for establishing PDX.

Conclusions: Precision medicine can be implemented in a single center in the context of clinical practice and may allow genomic-driven treatment in approximately 30% of aBC patients. PDX may be obtained in a significant fraction of cases.

Keywords: CGH; NGS; advanced breast cancer; patient-derived xenograft; precision medicine.

Conflict of interest statement

CONFLICTS OF INTEREST

Authors declare no potential conflicts of interest

Figures

Figure 1. Distribution of molecular alterations identified by CGH arrays and NGS in all 32 samples

A. Upper, mid and lower panels indicate the percentage of altered genomes, the mutation rate and the depth of sequencing for each sample, respectively (dot lines indicate mean percentage of altered genome, median mutation rate and median depth of sequencing, respectively). Gain, amplification, loss and deletion as well as neutral, damaging, hot spot and indel mutations were defined as indicated in the material and methods section. B. The distribution of molecular alterations (blue, mutation; red, amplification; green, deletion) was shown by decreasing frequency across samples (unique and anonymized patient number). Only alterations present in more than 1 sample are shown. Sample subtypes (HR-positive/HER2-negative, blue; HER2-positive, pink; triple-negative, red) are indicated. Patients with PDX engraftment (“PDX”) and genomic-driven treatment (therapeutic) are also shown. Asterisks indicate patients without germline sequencing.

Figure 2. Impact of germline sequencing on the number of retained mutations

Patients with available normal samples (N=27) were subjected to constitutional sequencing and somatic mutations were identified as indicated in the Material and methods section. Results are shown on a Venn diagram.

Figure 3. Correlations between molecular alterations and clinical features

The mutation rate A. and the fraction of altered genome B. were calculated as indicated in the material and method section and compared across molecular subtypes. C. The fraction of altered genome was compared according to the presence of visceral or non-visceral metastases. D. Overall survival was compared according to the fraction of altered genome. The median value of the overall population (0.2) was selected as threshold. * ANOVA ** student's t-test *** Log-rank test.

Figure 4. Actionable alterations retained by molecular tumor board

Actionable alterations were selected according to rules defined in the material and methods section. Mutations, amplifications and deletions are shown across the samples analyzed (N=32) in red, yellow and blue, respectively.