Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells

Abstract

Microsatellite instability (MSI) caused by deficient DNA mismatch-repair functions is a hallmark of cancers associated with the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome but is also found in about 15% of all sporadic tumors. Most affected microsatellites reside in untranslated intergenic or intronic sequences. However, recently few genes with coding microsatellites were also shown to be mutational targets in MSI-positive cancers and might represent important mutation targets in their pathogenesis. The systematic identification of such genes and the analysis of their mutation frequency in MSI-positive cancers might thus reveal major clues to their functional role in MSI-associated carcinogenesis. We therefore initiated a systematic database search in 33,595 distinctly annotated human genes and identified 17,654 potentially coding mononucleotide repeats (cMNRs) and 2,028 coding dinucleotide repeats (cDNRs), which consist of n > 6 and n > 4 repeat units, respectively. Expression pattern and mutation frequency of 19 of these genes with the longest repeats were compared between DNA mismatch repair-deficient (MSI ؉ ) and proficient (MSS) cancer cells. Instability frequencies in these coding microsatellite genes ranged from 10% to 100% in MSI-H tumor cells, whereas MSS cancer cells did not show mutations. RT-PCR analysis further showed that most of the affected genes (10/15) were highly expressed in tumor cells. The approach outlined here identified a new set of genes frequently affected by mutations in MSI-positive tumor cells. It will lead to novel and highly specific diagnostic and therapeutic targets for microsatellite unstable cancers.

Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers

“…Only three of these genes were highlighted by the TCGA as frequent targets for mutation, ACVR2A, MSH3 , and BRAF (V600E). Of the 21 genes with the same location mutated, all but four were frameshift mutations occurring at mononucleotide repeats as others have seen in mismatch repair deficient MSI tumors 24. The four genes with recurrent missense mutations were NEK4, KRT3 , BRAF , and MAP4K1 .…”

Identification of MARCKS, FLJ11383 and TAF1B as putative novel target genes in colorectal carcinomas with microsatellite instability

“…Of the remaining 28 genes, 27 contained (A)10 and one contained (T)10 in their coding regions (Table 1). These sequences encompassed all of the previously identified 11 candidate target genes (TGF-b RII, AIM2, SEC63, Caspase 5, OGT, ATR, MBD4, SYCP1, GART, PRKDC and MAC30) in MSI-H tumors Bader et al, 1999;Schwartz et al, 1999;Woerner et al, 2001;Mori et al, 2001), the remaining 22 genes had not been identified before.…”

“…Among the 33 genes evaluated, frequent frameshift mutations (440%) in MSI-H colorectal carcinomas were found in 11 genes ( Figure 3). Five of these 11 genes, TGF-b RII, AIM2, SEC63, Caspase 5 and OGT have been previously reported to show frameshift mutations Schwartz et al, 1999;Woerner et al, 2001;Mori et al, 2001), but the other six genes had not been evaluated before. The mutational frequencies of the five known genes in our MSI-H colorectal carcinomas were 85% in TGF-b RII, 67% in AIM2, 56% in SEC63, 49% in Caspase 5 and 41% in OGT.…”

“…Currently, three studies are available, and these studies reported several additional candidate target genes (Woerner et al, 2001;Mori et al, 2001;Park et al, 2002). In the present study, we searched a number of genes containing cMNR with a length of 10 or more nucleotides, and analysed frameshift mutations in these repetitive sequences in our 39 MSI-H colorectal carcinomas and eight MMR-deficient cell lines.…”

Microsatellite instability of selective target genes in HNPCC-associated colon adenomas

“…Several studies identified additional cancer relevant genes like IGF2R, MSH3, MSH6, BAX, CASP5, TCF4, RIZ, AIM2, ACVR2, and TAF1B, which contain cMS and are mutated in MSI-H cancers (Malkhosyan et al, 1996;Souza et al, 1996;Akiyama et al, 1997;Rampino et al, 1997;Duval et al, 1999;Schwartz Jr et al, 1999;Mori et al, 2001;Kim et al, 2002). It is also known that different genes with cMS of identical type and length show major differences in frameshift mutation frequencies in MSI-H tumors (Duval and Hamelin 2002;Woerner et al, 2001Woerner et al, , 2003. In addition, MSI-H tumors of different organs displayed significant differences in frameshift mutation frequencies for a given cMS gene (Schwartz Jr et al, 1999).…”