Near universal detection of alterations in CTNNB1 and Wnt pathway regulators in desmoid-type fibromatosis by whole-exome sequencing and genomic analysis

Abstract

CTNNB1 mutations or APC abnormalities have been observed in ∼85% of desmoids examined by Sanger sequencing and are associated with Wnt/β-catenin activation. We sought to identify molecular aberrations in "wild-type" tumors (those without CTNNB1 or APC alteration) and to determine their prognostic relevance. CTNNB1 was examined by Sanger sequencing in 117 desmoids; a mutation was observed in 101 (86%) and 16 were wild type. Wild-type status did not associate with tumor recurrence. Moreover, in unsupervised clustering based on U133A-derived gene expression profiles, wild-type and mutated tumors clustered together. Whole-exome sequencing of eight of the wild-type desmoids revealed that three had a CTNNB1 mutation that had been undetected by Sanger sequencing. The mutation was found in a mean 16% of reads (vs. 37% for mutations identified by Sanger). Of the other five wild-type tumors sequenced, two had APC loss, two had chromosome 6 loss, and one had mutation of BMI1. The finding of low-frequency CTNNB1 mutation or APC loss in wild-type desmoids was validated in the remaining eight wild-type desmoids; directed miSeq identified low-frequency CTNNB1 mutation in four and comparative genomic hybridization identified APC loss in one. These results demonstrate that mutations affecting CTNNB1 or APC occur more frequently in desmoids than previously recognized (111 of 117; 95%), and designation of wild-type genotype is largely determined by sensitivity of detection methods. Even true CTNNB1 wild-type tumors (determined by next-generation sequencing) may have genomic alterations associated with Wnt activation (chromosome 6 loss/BMI1 mutation), supporting Wnt/β-catenin activation as the common pathway governing desmoid initiation.

Figure 1

Unsupervised clustering of desmoid-type fibromatoses based on the 1% of genes whose expression was most variable between tumors. ‘Wild-type’ tumors are indicated with black text; tumors with CTNNB1 detected by Sanger sequencing are indicated with colored text.

Figure 2

Somatically mutated genes in desmoid tumors reaching statistical significance. Desmoids designated ‘wild-type’ by Sanger sequencing are annotated (*). The bar chart at the left shows the number of mutations found and the percentage of tumors affected; blue indicates non-silent mutations and green denotes the one silent mutation found in these genes (in NBPF9). For ZNF844, six mutations were found in three tumors. The center panel shows the types of non-silent mutations in each tumor. The bar graph at right shows the statistical significance of each mutated gene (derived from MutSig), with the red line indicating the threshold for significance (q<0.1).

Figure 3

Copy number alterations in desmoid tumors as identified from array CGH results by the R-package algorithm copynumber. Desmoids designated ‘wild-type’ by Sanger sequencing are annotated (*). Blue indicates copy number loss and red indicates gain. Chromosome 6 loss was found in two tumors with no identifiable abnormality in CTNNB1 or APC (DES955, DES999; see arrows) as well as in two tumors with CTNNB1 mutation.