Abstract P1-01-04: Mutational profiling of breast cancer brain metastases – matched pair analysis of next generation sequencing between primary breast cancer and later developed brain metastases
Authors: A Thulin, C Andersson, E Werner Rönnerman, S De Lara, C Chamalidou, A Schoenfeld, A Kovacs, F Enlund, BK Linderholm
Journal: Cancer Research (2018)

Abstract Background: Despite increased survival in patients with advanced breast cancer, breast cancer brain metastases (BCBM), remains a final frontier with a mean survival of 3-12 months. The biology facilitating BCBM is not fully understood. Aims: To compare gene expression profiles in primary BC, and later diagnosed, surgically removed BCBM. Material and Methods: A total of 58 BCBM and 46 breast tumors were analyzed with next generation sequencing (NGS). DNA was isolated from FFPE sectionsand then the Cancer Hotspot Panel v2 (ThermoFisher Scientific) covering 207-targeted regions in 50 cancer related genes was used. Template preparation and enrichment were performed with the IonChefTM Instrument (ThermoFisher Scientific). Eight barcoded samples were pooled per Ion 318 TM v2 BC chip and sequenced on the Ion PGMTM System (ThermoFisher Scientific).Alignment to the hg19 human reference genome and variant calling was performed by the Torrent Suite Software v5.2.0 (ThermoFisher Scientific) also IonReporterTM System (ThermoFisher Scientific) was used. Results: 46 of the BCBM were matched with a primary breast cancer tumor. All but 12 tumors had the same IHC characteristic in the matched pairs. The most common transformation was Luminal A to Luminal B in 8 tumors. The other changes were triple negative subtype (TNBC) to Luminal B, HER2+ to Luminal B, Luminal A to TNBC and Luminal A to HER2+ with one case respectively. The BCBM had the following IHC profile: one tumor was luminal A (1%), 15 tumors were Luminal B (25%), 29 were TNBC (50%) and 14 HER2 overexpressing (24%). The preliminary NGS data shows that the most common mutation in BCBM was found in the tumor suppressor gene p53 (22/58, 38 %). Other common mutations were PIK3CA (17/58, 29%); KDR (16/58, 28%), KIT (9/58, 16%) and PTEN (2/58, 3%). The corresponding figures in the primary BC were p53 (15/46, 33%), PIK3CA (16/46, 35%), KDR (17/46, 37%), KIT (7/46, 15%) and no tumors with PTEN. The mutational spectra in the 50 cancer related genes were similar in the primary BC as in the BCBM with 1-5 different driver mutations but additional mutations were registered in 6/46 matched cases (13%). We fail to identify any specific differences in mutations between the different morphological subtypes (LumA/LumB/TNBC/HER2+) in the metastatic sample. In the NGS analysis of the metastases and primary tumors 3 different variations of p53 was detected. Conclusions: In this large matched pairs of primary breast tumors and BCBM we show that the majority of BCBM have a similar gene profile as the primary BC. The most common aberrations were found in TP53, PIK3CA and KDR. Additional post analyses are under investigation and will be added to the results. It appears that brain metastases are not different from other metastases in that they remain fairly stable in their driver mutational profile. When the mutational profile changes there is addition of mutation rather than deletion. A clinical implication of these results could be to treat BCBM according to the mutational profile of the primary tumor which decreases the need for sampling of BCBM; something that if the patient is not eligible for surgery might otherwise prove complex. Citation Format: Thulin A, Andersson C, Werner Rönnerman E, De Lara S, Chamalidou C, Schoenfeld A, Kovacs A, Enlund F, Linderholm BK. Mutational profiling of breast cancer brain metastases – matched pair analysis of next generation sequencing between primary breast cancer and later developed brain metastases [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-01-04.