RNA-seq reveals determinants for irinotecan sensitivity/resistance in colorectal cancer cell lines

Abstract

Irinotecan is a topoisomerase I inhibitor approved worldwide as a first- and second-line chemotherapy for advanced or recurrent colorectal cancer (CRC). Although irinotecan showed significant survival advantage for patients, a relatively low response rate and severe adverse effects demonstrated the urgent need for biomarkers searching to select the suitable patients who can benefit from irinotecan-based therapy and avoid the adverse effects. In present work, the irinotecan response (IC50 doses) of 20 CRC cell lines were correlated with the basal expression profiles investigated by RNA-seq to figure out genes responsible for irinotecan sensitivity/resistance. Genes negatively or positively correlated to irinotecan sensitivity were given after biocomputation, and 7 (CDC20, CTNNAL1, FZD7, CITED2, ABR, ARHGEF7, and RNMT) of them were validated in two CRC cell lines by quantitative real-time PCR, several of these 7 genes has been proposed to promote cancer cells proliferation and hence may confer CRC cells resistance to irinotecan. Our work might provide potential biomarkers and therapeutic targets for irinotecan sensitivity in CRC cells.

Keywords: CITED2; CTNNAL1; Colorectal cancer; FZD7; RNA-seq; irinotecan.

Figure 1

Determination of IC50 doses for 21 CRC cell lines. 21 CRC cell lines were treated with nine doses of irinotecan for 144 h, and then the cell viability was detected by MTS assay. The IC50 doses of these cell lines were calculated with the aid of GraphPad Prism 5.0 software via nonlinear regression.

Figure 2

Identification of genes correlated with compound response. A: In upper panel, we showed that genes with expression counter-correlated with compound response (FDR < 20%); in lower panel we showed that genes with expression correlated with compound response (FDR < 30%). B: The correlation/counter-correlation was improved when gene expression were accumulated, where we are able to estimate the size of gene panel in the predictor.

Figure 3

qPCR validation. 7 genes were validated in two CRC cell lines (COLO205 and LS174T) by qPCR. The gene expression was calculated relative to that in COLO205 cells.