Abstract 3140: Differential clonal selection in tumor tissue and cell-free DNA from a neratinib-treated refractory breast cancer patient harboring an activating ERBB2 (HER2) mutation

The ongoing Copenhagen Prospective Personalized Oncology (CoPPO) research program aims to offer patients with exhausted treatment options, targeted therapy against actionable driver mutations identified in freshly obtained biopsies by whole exome sequencing (WES). Mutations are tracked in circulating cell free DNA (cfDNA) to examine the clonal selection of tumor cells evoked by therapy. Here we report the results from a patient with metastasizing HER2 negative and estrogen receptor (ER) positive breast cancer (Luminal A) previously exposed to seven lines of chemotherapy as well as ER antagonists and aromatase inhibitors. After enrollment in the program, examination of liver metastases by whole exome sequencing, RNA-Seq and microarray expression analysis revealed high expression of the estrogen receptor 1 (ESR1) as well as a mutation in the ligand-binding domain of ESR1 (H524L). Moreover, somatic variants in ERBB2 and PIK3CA were identified, including an activating mutation in ERBB2 (S310Y), and consequently the patient treated with neratinib, an irreversible pan-HER (EGFR/ERBB2/ERBB4) tyrosine kinase inhibitor, through a compassionate use program (Puma Biotechnology Inc.). Neratinib caused a rapid decrease in the allelic frequency of ERBB2 (S310Y) cfDNA after 2 days with a continuous decline during the next 7 days. Consistent with this neratinib treatment effect, MRI scans showed regression of the liver metastases. In contrast, the PIK3CA mutation showed an increase in the allele frequency, indicating the existence of a subclone that was insensitive to neratinib. Two months later, the total amount of cfDNA increased and continued to do so. After 5 months on neratinib, the patient progressed with the appearance of brain metastases which were surgically removed and subject to WES. The vast majority of the mutations, including the ERBB2 mutation, observed in the liver metastasis could not be identified in the brain metastases, except for the PIK3CA mutation. More than 300 new variants were exclusively identified in the brain metastases, among these, ERBB3 as well as new PIK3CA, and ESR1 mutations, that were not present in the pre-treatment cfDNA samples. After 4 months of treatment, an increase in the mutation frequency of the liver metastasis specific ESR1 and ERBB2 mutations was observed. In conclusion, neratinib was able to suppress an activating ERBB2 mutation in a heavily pre-treated ER+ breast cancer patient. However, refractory tumor clones harboring E