Figure 3

PTEN loss in HGSOC mainly occurs through copy number alteration (CNA). (A) Western blot showing the quantification of PTEN, TP53 and GAPDH (loading control) from extracts of the ovarian cancer SKOV3 cell line and complemented with wild-type and mutated TP53. (B) Box plot showing distribution of methylation levels according to PTEN expression levels in TCGA samples. A small increase in DNA methylation is observed in samples with lower PTEN expression (Wilcoxon test P≪0.001). (C) Pie chart showing distribution of PTEN ploidy within the TCGA data set. (D) Box plot showing distribution of PTEN mRNA expression according to PTEN ploidy, suggesting that CNA influences mRNA expression (t-test, diploid vs hetloss P≪0.001). (E) Example of IHC staining for PTEN scored as positive in [14], but reclassified here as weak staining, as staining in tumour cells is markedly reduced in comparison to stromal cells. (F) Table showing differences between scoring for PTEN IHC staining used [14] and reclassified score. Of the original 36 positive samples, 21 have been reclassified as heterogeneous or weakly positive. (G) Box plot showing distribution of PTEN mRNA expression within each scoring group for PTEN IHC staining, according to the Hanrahan score [14] and the reclassified score. There is a significant difference between PTEN expression in tumours classified as weak positives and positives (t-test, P=0.002). (H) Contingency table showing significant correlation between scores for PTEN IHC staining and PTEN CNA (Fisher’s exact test, P≪0.001). CNA, copy number alteration; IF, immunofluorescence; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; hetero, heterogeneous; IHC, immunohistochemistry; TCGA, The Cancer Genome Atlas.