Experimental and Meta-Analytic Validation of RNA Sequencing Signatures for Predicting Status of Microsatellite Instability

Maksim Sorokin; Elizaveta Rabushko; Victor Efimov; Elena Poddubskaya; Marina Sekacheva; Alexander Simonov; Daniil Nikitin; Aleksey Drobyshev; Maria Suntsova; Anton Buzdin

doi:10.3389/fmolb.2021.737821

Experimental and Meta-Analytic Validation of RNA Sequencing Signatures for Predicting Status of Microsatellite Instability

Front Mol Biosci. 2021 Nov 23:8:737821. doi: 10.3389/fmolb.2021.737821. eCollection 2021.

Authors

Maksim Sorokin^{1

2

3}, Elizaveta Rabushko^{1

4}, Victor Efimov^{2

5

6}, Elena Poddubskaya⁵, Marina Sekacheva⁵, Alexander Simonov^{5

6}, Daniil Nikitin^{6

7}, Aleksey Drobyshev¹, Maria Suntsova^{2

5}, Anton Buzdin^{2

3

5

7}

Affiliations

¹ Laboratory For Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
² Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
³ OmicsWay Corp., Walnut, CA, United States.
⁴ Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
⁵ World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, Russia.
⁶ Oncobox Ltd., Moscow, Russia.
⁷ Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.

Abstract

Microsatellite instability (MSI) is an important diagnostic and prognostic cancer biomarker. In colorectal, cervical, ovarian, and gastric cancers, it can guide the prescription of chemotherapy and immunotherapy. In laboratory diagnostics of susceptible tumors, MSI is routinely detected by the size of marker polymerase chain reaction products encompassing frequent microsatellite expansion regions. Alternatively, MSI status is screened indirectly by immunohistochemical interrogation of microsatellite binding proteins. RNA sequencing (RNAseq) profiling is an emerging source of data for a wide spectrum of cancer biomarkers. Recently, three RNAseq-based gene signatures were deduced for establishing MSI status in tumor samples. They had 25, 15, and 14 gene products with only one common gene. However, they were developed and tested on the incomplete literature of The Cancer Genome Atlas (TCGA) sampling and never validated experimentally on independent RNAseq samples. In this study, we, for the first time, systematically validated these three RNAseq MSI signatures on the literature colorectal cancer (CRC) (n = 619), endometrial carcinoma (n = 533), gastric cancer (n = 380), uterine carcinosarcoma (n = 55), and esophageal cancer (n = 83) samples and on the set of experimental CRC RNAseq samples (n = 23) for tumors with known MSI status. We found that all three signatures performed well with area under the curve (AUC) ranges of 0.94-1 for the experimental CRCs and 0.94-1 for the TCGA CRC, esophageal cancer, and uterine carcinosarcoma samples. However, for the TCGA endometrial carcinoma and gastric cancer samples, only two signatures were effective with AUC 0.91-0.97, whereas the third signature showed a significantly lower AUC of 0.69-0.88. Software for calculating these MSI signatures using RNAseq data is included.

Keywords: NGS; RNA sequencing; RNAseq; experimental validation; gene signatures; microsatellite instability.