Clinical Implications of Sub-grouping HER2 Positive Tumors by Amplicon Structure and Co-amplified Genes

Myriam Maoz ¹ Michal Devir ¹ Aviad Zick Michal Inbar ¹ Ziva Inbar-Daniel ¹ Dana Sherill-Rofe ¹ Idit Bloch ¹ Karen Meir ² David Edelman ¹ Salah Azzam ¹ Karen Meir Hovav Nechushtan ¹ Ofra Maimon ¹ Beatrice Uziely ¹ Luna Kaduri ¹ Amir Sonnenblick ³ Amir Eden ⁴ Tamar Peretz ¹ Aviad Zick ¹

¹Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Israel
²Department of Pathology, Hebrew University-Hadassah Medical Center, Israel
³The Oncology Division, Tel Aviv Sourasky Medical Center, Israel
⁴Department of Cell & Developmental Biology, Institute of Life Sciences, the Hebrew University of Jerusalem, Israel

Background

ERBB2 amplification is a prognostic marker for aggressive tumors and a predictive marker for prolonged survival following treatment with HER2 inhibitors. We attempt to sub-group HER2+ tumors based on amplicon structures and co-amplified genes.

Methods

We extracted DNA from five HER2+ cell lines, three HER2+ xenographs and 57 HER2+ tumor tissues. ERBB2 amplification was analyzed using digital droplet PCR and low coverage whole genome sequencing. Copy number and structural variations were detected using Control FREEC and BreakDancer algorithms and further analyzed using FindAmpliconSTructure: FAST, a tool we developed. In some HER2+ tumors PPM1D, that encodes WIP1, is co-amplified. Cell lines were treated with a HER2 and WIP1 inhibitor.

Results

We find that inverted duplication is the amplicon structure in the majority of HER2+ tumors. In patients suffering from an early stage disease the ERBB2 amplicon is composed of a single segment while in patients suffering from advanced cancer the amplicon is composed of several different segments. We test inhibition of HER2 and WIP1 in HER2+ cell lines and find robust WIP1 inhibition in some HER2+ PPM1D amplified cell lines.

Conclusions

Sub-grouping HER2+ tumors using low coverage whole genome sequencing identifies inverted duplications as the main amplicon structure and based on the number of segments, differentiates between local and advanced tumors. In addition, we found that characterizing HER2+ tumors by amplicon structure could help determine if a tumor is a recurrent tumor or second primary tumor and identify co-amplified oncogenes that may serve as targets for therapy.