Abstract 683: Evaluation of PTEN and PIK3CA status in breast cancer for patient selection: Cross-validation between institutions
Authors: Violeta Serra, Jordi Rodon, Ludmila Prudkin, Claudia Aura, Ana Vivancos, Yasir H. Ibrahim, Mathew Maurer, Hanina Hibshoosh, Katherine Stemke-Hale, José Jimenez, Yuker Wang, Vicente Peg, Javier Hernandez, Santiago Ramon y Cajal, Rodrigo Dienstmann, Cristina Saura, Gessami Sanchez, Josep Tabernero, Ramon Parsons, Gordon Mills, José Baselga
Journal: Cancer Research (2012)

Abstract PTEN and PIK3CA status are potential predictors of response to PI3K-pathway inhibitors. Therefore, we searched the most reliable platform to assess both PTEN expression and PIK3CA mutations in primary and metastatic breast cancer (BC). Cross-validation across platforms at SU2C sites was performed using three different sample sets: 18 formalin-fixed paraffin-embedded (FFPE) primary triple negative breast cancer (pTNBC) samples from VHUH/VHIO, 12 FFPE pTNBC samples from Columbia University and 21 FFPE all-comers BC from VHUH/VHIO. Moreover, we evaluated the transitions occurring between early and disseminated disease in 14 paired FFPE samples from VHUH/VHIO. PTEN alterations were genotyped in 18 triple pTNBCs by OncoscanTM platform (Affymetrix) and were correlated to immunohistochemistry (IHC, 138G6 CST antibody). PTEN loss of heterozygosity (LOH, n=4) or frameshift mutation (n=1) was concordant to PTEN protein loss (H-Score&amp;lt;50) by IHC in 4 samples; with the discordant LOH having an H-Score of 60. In the other two non-concordant samples (total of 3/18, 17% discordance), presence of non-tumor DNA, as assessed by genomic heterogeneity, impeded an accurate DNA copy number variation determination by OncoscanTM. PTEN protein loss by IHC was also cross-validated between two institutions (Columbia and VHIO). In a cohort of 12 pTNBCs containing eight PTEN low samples, only two samples were discordant (2/12, 17% discordance). Paired primary versus metastatic tumors were identified to transit either way, in the PTEN assessment by IHC (2/8 paired samples, 25% transition). PTEN IHC failed in most (3/5) metastatic bone samples due to Bouin's fixative required for handling of this tissue. PIK3CA mutations by OncoscanTM were concordant to MassARRAY (Sequenom) in 4 out of 5 mutated samples within the panel of 18 pTNBCs. The discrepancy (1/18, 6%) was most likely due to differences in the sensitivity of the two assays. In another cohort of 21 BC samples, PIK3CA mutational status was cross-validated by MassARRAY at two institutions (MDACC and VHIO). Using identical, customized panels we found that only two samples were discordant because of mutant allele frequency close to the sensitivity of the assay (10%). Manual review of the individual assays increased the concordance to 100%. Among 14 paired primary vs metastatic breast cancers we detected two transitions from wild type (WT) to H1047R mutation and one transition from E545K to WT (3/14, 21% transition), underscoring the need to determine PIK3CA status in metastatic lesions. The divergence evaluating both PTEN and PIK3CA status between institutions was due to cut-off and sensitivity of the assays respectively. For patient pre-screening purposes, MassARRAY and IHC can be performed at each SU2C site both in primary and metastatic breast cancer lesions. OncoscanTM is a valid, centralized platform for evaluation of PTEN and PIK3CA genomic alterations in BC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 683. doi:1538-7445.AM2012-683