Somatic mutations and copy number variations in breast cancers with heterogeneous HER2 amplification

• Published in: Molecular oncology Vol. 14; no. 4; pp. 671 - 685
• Main Authors: Van Bockstal, Mieke R., Agahozo, Marie Colombe, van Marion, Ronald, Atmodimedjo, Peggy N., Sleddens, Hein F. B. M., Dinjens, Winand N. M., Visser, Lindy L., Lips, Esther H., Wesseling, Jelle, van Deurzen, Carolien H. M.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01-04-2020; John Wiley and Sons Inc; Wiley
• Subjects: Adult; Breast cancer; Breast Neoplasms - genetics; Cancer therapies; Carcinogenesis; Cell growth; Copy number; copy number variations; Deoxyribonucleic acid; DNA; DNA Copy Number Variations; Epidermal growth factor receptors; ErbB-2 protein; Female; Fibroblast growth factor receptor 1; Gene Amplification; HER2 amplification; Humans; Hybridization; intratumour heterogeneity; Invasiveness; Kinases; Middle Aged; Mutation; Myc protein; next‐generation sequencing; Paraffin; Receptor, ErbB-2 - genetics; Retrospective Studies; somatic mutation; Studies; Tumors; United States > US; Netherlands; Germany; breast cancer; intratumour heterogeneity; somatic mutation; next-generation sequencing; copy number variations; HER2 amplification
• ISSN: 1574-7891; 1878-0261; 1878-0261
• DOI: 10.1002/1878-0261.12650

Intratumour heterogeneity fuels carcinogenesis and allows circumventing specific targeted therapies. HER2 gene amplification is associated with poor outcome in invasive breast cancer. Heterogeneous HER2 amplification has been described in 5–41% of breast cancers. Here, we investigated the genetic differences between HER2‐positive and HER2‐negative admixed breast cancer components. We performed an in‐depth analysis to explore the potential heterogeneity in the somatic mutational landscape of each individual tumour component. Formalin‐fixed, paraffin‐embedded breast cancer tissue of ten patients with at least one HER2‐negative and at least one HER2‐positive component was microdissected. Targeted next‐generation sequencing was performed using a customized 53‐gene panel. Somatic mutations and copy number variations were analysed. Overall, the tumours showed a heterogeneous distribution of 12 deletions, 9 insertions, 32 missense variants and 7 nonsense variants in 26 different genes, which are (likely) pathogenic. Three splice site alterations were identified. One patient had an EGFR copy number gain restricted to a HER2‐negative in situ component, resulting in EGFR protein overexpression. Two patients had FGFR1 copy number gains in at least one tumour component. Two patients had an 8q24 gain in at least one tumour component, resulting in a copy number increase in MYC and PVT1. One patient had a CCND1 copy number gain restricted to a HER2‐negative tumour component. No common alternative drivers were identified in the HER2‐negative tumour components. This series of 10 breast cancers with heterogeneous HER2 gene amplification illustrates that HER2 positivity is not an unconditional prerequisite for the maintenance of tumour growth. Many other molecular aberrations are likely to act as alternative or collaborative drivers. This study demonstrates that breast carcinogenesis is a dynamically evolving process characterized by a versatile somatic mutational profile, of which some genetic aberrations will be crucial for cancer progression, and others will be mere ‘passenger’ molecular anomalies.
This in‐depth analysis of 10 breast cancers with heterogeneous HER2 gene amplification illustrates that HER2 positivity is not an unconditional prerequisite for the maintenance of tumour growth. This study demonstrates that breast carcinogenesis is a dynamically evolving process characterized by a versatile somatic mutational profile: some genetic aberrations will be crucial for cancer progression, and others will be mere ‘passenger’ molecular anomalies.