3′-UTR Poly(T/U) Tract Deletions and Altered Expression of EWSR1 Are a Hallmark of Mismatch Repair–Deficient Cancers

Abstract

The genome-wide accumulation of DNA replication errors known as microsatellite instability (MSI) is the hallmark lesion of DNA mismatch repair (MMR)-deficient cancers. Although testing for MSI is widely used to guide clinical management, the contribution of MSI at distinct genic loci to the phenotype remains largely unexplored. Here, we report that a mononucleotide (T/U) 16 tract located in the 3 0 untranslated region (3 0 -UTR) of the Ewing sarcoma breakpoint region 1 (EWSR1) gene is a novel MSI target locus that shows perfect sensitivity and specificity in detecting mismatch repair-deficient cancers in two independent populations. We further found a striking relocalization of the EWSR1 protein from nucleus to cytoplasm in MMR-deficient cancers and that the nonprotein-coding MSI target locus itself has a modulatory effect on EWSR1 gene expression through alternative 3 0 end processing of the EWSR1 gene. Our results point to a MSI target gene-specific effect in MMRdeficient cancers. Cancer Res; 74(1); 224-34. Ó2013 AACR.

3′-UTR poly(T/U) repeat of EWSR1 is altered in microsatellite unstable colorectal cancer with nearly perfect sensitivity

“…All the 156 mutations seen in the Finnish MSI CRCs were deletions and of the 56 mutated Danish MSI CRCs all but one showed a deletion. Our results thus support the previously reported finding [8].…”

“…Therefore, similar to the previous study and as is typical for MSI, instability was driven mostly by deletion rather than insertion [8].…”

“…EWS16T, a mononucleotide tract consisting of 16 thymines in the 3 0 -UTR of the EWSR1 gene, was recently reported to represent a novel, quasimonomorphic MSI target gene locus, which identifies both hereditary and sporadic MSI colorectal, gastric, and endometrial cancers with perfect sensitivity and specificity [8]. In our study, the repeat was analyzed by fragment analysis in altogether 213 MSI (157 Finnish and 56 Danish) and 148 MSS samples.…”

“…ensembl.org) amplified by PCR with the following primers: 5 0 -AATGTTCATGGTTGTGATGT-3 0 (forward FAM-labeled) and 5 0 -GAAGGATGACTCTTTATAA-3 0 (reverse) [8]. The PCR mix contained 1.5 ll of 1 9 PCR-buffer (Applied Biosystems, Brachburg, NJ, USA), 0.2 ll of deoxynucleotide triphosphate (dNTP) (FINNZYMES, Espoo, Finland), 0.6 ll of forward and reverse primer (SIGMA Ò , GENOSYS, Helsinki, Finland), 0.15 ll of DNA polymerase enzyme AmpliTaqGold Ò (Applied Biosystems, Brachburg, NJ, USA), 9.95 ll of water, and 25 ng of DNA extracted from fresh-frozen colorectal tumor.…”

“…Recently, a quasimonomorphic mononucleotide T/U16 (EWST16) repeat at the 3 0 untranslated region (UTR) of Ewing sarcoma breakpoint region 1 (EWSR1) was reported by Kishore et al to show perfect sensitivity and specificity in detecting MMR deficient cancers in two independent populations [8]. The first sample set consisted of 85 Swiss Lynch syndrome-related cancers and 113 sporadic CRCs, and the second set of eight Finnish Lynch syndrome-related cancers, 50 sporadic CRCs as well as 64 sporadic gastric cancers.…”