A systematic study of gene mutations in urothelial carcinoma; inactivating mutations in TSC2 and PIK3R1

Abstract

Background: Urothelial carcinoma (UC) is characterized by frequent gene mutations of which activating mutations in FGFR3 are the most frequent. Several downstream targets of FGFR3 are also mutated in UC, e.g., PIK3CA, AKT1, and RAS. Most mutation studies of UCs have been focused on single or a few genes at the time or been performed on small sample series. This has limited the possibility to investigate co-occurrence of mutations.

Methodology/principal findings: We performed mutation analyses of 16 genes, FGFR3, PIK3CA, PIK3R1 PTEN, AKT1, KRAS, HRAS, NRAS, BRAF, ARAF, RAF1, TSC1, TSC2, APC, CTNNB1, and TP53, in 145 cases of UC. We show that FGFR3 and PIK3CA mutations are positively associated. In addition, we identified PIK3R1 as a target for mutations. We demonstrate a negative association at borderline significance between FGFR3 and RAS mutations, and show that these mutations are not strictly mutually exclusive. We show that mutations in BRAF, ARAF, RAF1 rarely occurs in UC. Our data emphasize the possible importance of APC signaling as 6% of the investigated tumors either showed inactivating APC or activating CTNNB1 mutations. TSC1, as well as TSC2, that constitute the mTOR regulatory tuberous sclerosis complex were found to be mutated at a combined frequency of 15%.

Conclusions/significance: Our data demonstrate a significant association between FGFR3 and PIK3CA mutations in UC. Moreover, the identification of mutations in PIK3R1 further emphasizes the importance of the PI3-kinase pathway in UC. The presence of TSC2 mutations, in addition to TSC1 mutations, underlines the involvement of mTOR signaling in UC.

Figure 1. Distribution of identified mutations.

In A) low grade (G1/G2) tumors and in B), high grade (G3) tumors. Red squares indicate inactivating mutation. Green squares indicate activating mutation. For PIK3CA, dark green squares indicate kinase domain mutations and light green helical domain mutations. At the right, mutation frequencies are given for each gene in the respective tumor grades.

Figure 2. Schematic representation of relationships and mutation frequencies among the investigated genes.

Arrowheads, positive regulation; filled circles, negative regulation; gene names in green, genes showing activating mutations; gene names in red, genes showing inactivating mutations; gene names in black, genes with no detected mutations in the present investigation; gene names in gray, genes not investigated. TP53 is not included in the graph. The mutation frequencies (%) given are based on the 145 samples investigated for each gene.