Comprehensive Analysis of PTEN Allelic Status Confirms Gross Genomic Rearrangement as the Main Mechanism of PTEN Inactivation in Sporadic Breast Carcinomas.

Background The PTEN tumour suppressor gene is frequently inactivated in a wide range of cancers and encodes a nonredundant phosphatase which antagonizes the PI3K signalling pathway. Previous IHC analysis and genomic characterization (through BAC CGH array) of a series of 135 sporadic breast carcinomas identified some tumours with decreased or absent PTEN levels and/or loss at 10q23.3, including the PTEN locus. Comprehensive molecular genetic analysis of PTEN , in addition to PI3KCA and TP53 point mutation screening were performed on this large homogenous series of breast carcinomas, giving a molecular portrait of key players of sporadic breast carcinogenesis. Materials and methods A series of 135 sporadic invasive ductal carcinomas resected between 1989 and 1992 at Institut Bergonie underwent PTEN molecular genetic screening through QMPSF to detect gross genomic rearrangements and the recently developed Enhanced Mismatch Mutation Analysis (EMMA) to detect point mutations and to confirm gross genomic rearrangements. Tumours with a suspected PTEN large deletion identified using these techniques, along with any additional tumours previously shown to have decreased or absent PTEN levels and/or loss at 10q23.3, were analyzed using Agilent 4x44K high density oligo CGH arrays. The TP53 status of all tumours was assessed through IHC and direct sequencing. In addition, molecular analysis of the recurrent point mutations of PI3KCA, the catalytic subunit of the PI3 kinase, was performed. Results Gross PTEN gene rearrangements were detected in 48 tumours through QMPSF ; 19 biallelic large deletions, 21 monoallelic large deletions and 8 large duplications. Variant EMMA profiles indicating a PTEN point mutation have been identified in approximately 15% of tumours which are confirmed by direct sequencing. High density oligo CGH array performed on 54 tumours demonstrates 7 monoallelic large deletions and 9 biallelic large deletions to date (analysis to be completed). A total of 39 tumours were shown to have mutant TP53 on IHC and/or a TP53 mutation, which interestingly only includes 8/19 tumours with a biallelic PTEN large deletion. Finally, an overall assessment of the above gene status, including results of the PI3KCA point mutation screen will be presented. Conclusion This study shows that the predominant mechanism of PTEN inactivation in sporadic breast carcinomas is through gross genomic rearrangements rather than deleterious point mutations, and that this is not restricted to BRCA1-mutated tumours. Furthermore, previous reports have suggested that biallelic inactivation of PTEN in tumours with wild-type TP53 would result in cell death and therefore not be advantageous for tumour growth. In this series, we did not observe a correlation between biallelic inactivation of PTEN and TP53 mutation status (p=0.31, chi-squared test). Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3151.