Replication error deficient and proficient colorectal cancer gene expression differences caused by 3'UTR polyT sequence deletions

Abstract

Replication error deficient (RER+) colorectal cancers are a distinct subset of colorectal cancers, characterized by inactivation of the DNA mismatch repair system. These cancers are typically pseudodiploid, accumulate mutations in repetitive sequences as a result of their mismatch repair deficiency, and have distinct pathologies. Regulatory sequences controlling all aspects of mRNA processing, especially including message stability, are found in the 3'UTR sequence of most genes. The relevant sequences are typically A/U-rich elements or U repeats. Microarray analysis of 14 RER+ (deficient) and 16 RER- (proficient) colorectal cancer cell lines confirms a striking difference in expression profiles. Analysis of the incidence of mononucleotide repeat sequences in the 3'UTRs, 5'UTRs, and coding sequences of those genes most differentially expressed in RER+ versus RER- cell lines has shown that much of this differential expression can be explained by the occurrence of a massive enrichment of genes with 3'UTR T repeats longer than 11 base pairs in the most differentially expressed genes. This enrichment was confirmed by analysis of two published consensus sets of RER differentially expressed probesets for a large number of primary colorectal cancers. Sequence analysis of the 3'UTRs of a selection of the most differentially expressed genes shows that they all contain deletions in these repeats in all RER+ cell lines studied. These data strongly imply that deregulation of mRNA stability through accumulation of mutations in repetitive regulatory 3'UTR sequences underlies the striking difference in expression profiles between RER+ and RER- colorectal cancers.

Fig. 1.

Enrichment for sequences containing 3′UTR mononucleotide T repeats [corresponding to the third tercile (T21 to T32) as analyzed in Tables 2 and 3]. Fold-changes for individual repeat lengths between T21 and T32 are shown in the three RER differentially expressed gene datasets. The actual numbers of genes containing all 3′UTR repeat lengths analyzed in all of the datasets are given in Dataset S2. (A) Fold-increase in 3′UTR mononucleotide repeats in top differentially expressed genes in CRC cell lines versus the overall incidence in all protein coding genes (n = 19,497). (B) Fold-increase in 3′UTR mononucleotide repeats in the top differentially expressed genes in primary CRC samples from published data versus the overall incidence in all protein coding genes (n = 19,497). Datasets are labeled by the first author from the corresponding publication (21, 22). Note that the scale for the fold increase (y axis) differs between the two graphs.

Fig. 2.

Mean deletion size in base pairs of 3′UTR mononucleotide repeat sequences of selected RER differentially expressed genes. Error bars indicate SEM. n = number of cell lines sequenced; see SI Materials and Methods for details. P values are based on two-tailed t test for mean deletion size differences between RER+ and RER− cell lines.