Identification of frequently mutated genes with relevance to nonsense mediated mRNA decay in the high microsatellite instability cancers

Abstract

Frameshift mutations at coding mononucleotide repeats (cMNR) are frequent in high‐microsatellite instability (MSI‐H) cancers. Frameshift mutations in cMNR result in the formation of a premature termination codon (PTC) in the transcribed mRNA, and these abnormal mRNAs are generally degraded by nonsense mediated mRNA decay (NMD). We have identified novel genes that are frequently mutated at their cMNR by blocking NMD in two MSI‐H cancer cell lines. After blocking NMD, we screened for differentially expressed genes using DNA microarrays, and then used database analysis to select 28 candidate genes containing cMNR with more than 9 nucleotide repeats. cMNR mutations have not been previously reported in MSI‐H cancers for 15 of the 28 genes. We analyzed the cMNR mutation of each of the 15 genes in 10 MSI‐H cell lines and 21 MSI‐H cancers, and found frequent mutations of 12 genes in MSI‐H cell lines and cancers, but not in microsatellite stable (MSS) cancers. Among these genes, the most frequently mutated in MSI‐H cell lines were MLL3 (70%), PHACTR4 (70%), RUFY2 (50%) and TBC1D23 (50%). MLL3, which has already been implicated in cancer, had the highest mutation frequency in MSI‐H cancers (48%). Our combined approach of NMD block, database search, and mutation analysis has identified a large number of genes mutated in their cMNR in MSI‐H cancers. The identified mutations are expected to contribute to MSI‐H tumorigenesis by causing an absence of gene expression or low gene dosage effects.

Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers

“…MSs with longer repeat lengths exhibited a higher instability rate, which led to multiple nucleotide deletions (Suraweera et al 2001). Taken together, these results demonstrate that the number of candidate genes with MS mutations is markedly greater than had been previously known (Suraweera et al 2001;Kim et al 2002;Woerner et al 2003;Royrvik et al 2007;Shin et al 2011). …”

“…MSI is a key factor in several cancers, including colorectal, endometrial, and gastric cancers. MS mutations found in these cancers are expected to contribute to MSI-H (high levels of MSI) tumorigenesis (Menoyo et al 2001;Duval et al 2002;Mori et al 2002;Woerner et al 2003;Karamurzin and Rutgers 2009;Shin et al 2011).…”

Distribution of somatic mutations of cancer-related genes according to microsatellite instability status in Korean gastric cancer

“…Microsatellite mutations found in these cancers are expected to contribute to MSI-H tumorigenesis. [33] Depending on the type and number of MSI markers analyzed, widely variable results have been reported for the frequency of MSI-H in GC: 11.7% to 33.8% in Asian [34–36] and 16.3% to 25.2% in European [37–40] population. Recent exome sequencing of gastric adenocarcinoma showed that samples with unstable MSI had an average of 31.61 somatic mutations per megabase of DNA, whereas MSS GCs had an average of 3.29, a difference of approximately 10-fold.…”

Mutated tumor alleles are expressed according to their DNA frequency

“…Nonsense-mediated decay (NMD) surveillance, for example, scans transcripts for the presence of a premature termination codons (PTCs) before the last exon and, when found, initiates degradation of such transcripts4. NMD surveillance has been extensively studied in RNA splicing5, where it removes aberrantly spliced transcripts, and in microsatellite instability colorectal cells, where NMD blockage up-regulates genes containing somatic mononucleotide repeat mutations causing frameshift open reading frames6. If and to which extent this happens has not been systematically analyzed.…”