Experimental and meta-analytic validation of RNAseq signatures for predicting status of microsatellite instability

Microsatellite instability (MSI) is important diagnostic and prognostic cancer biomarker. In colorectal, cervical, ovarian and gastric cancers, it can guide prescription of chemotherapy and immunotherapy. In laboratory diagnostics of susceptible tumors, MSI is routinely screened by size of marker PCR products encompassing frequent microsatellite expansion regions. Alternatively, MSI status is screened indirectly by immunohistochemical (IHC) interrogation of microsatellite binding proteins. RNA sequencing (RNAseq) profiling is emerging source of data for wide spectrum of cancer biomarkers. In one test, it can interrogate IHC biomarkers, expressions of all cancer drug target genes, and activities of molecular pathways. Recently, three RNAseq-based gene signatures were deduced for establishing MSI status in tumor samples. These signatures had 25, 15, and 14 gene products with only one common gene. However, they were developed and validated on the same literature sampling of The Cancer Genome Atlas (TCGA) project database and never validated experimentally. In this study, we for the first time systematically validated three RNAseq MSI signatures on both literature (n=620) and experimental (n=36) samples of colorectal, cervical, ovarian and gastric cancers. As the gold standard for the current experimental sampling, we used seven PCR MSI biomarkers. We found that all three signatures performed well with area under the curve (AUC) range within 0.84-0.96 for the experimental, and 0.94-0.95 for the literature TCGA samples. We conclude that RNAseq profiles may be used to interrogate MSI statuses of tumors using any of the above signatures. In addition, current experimental data can be used to validate further MSI gene signatures.