Single-cell transcriptional signature-based drug repurposing and in vitro evaluation in colorectal cancer

Background: The need for intelligent and effective treatment of diseases and the increase in drug design costs have raised drug repurposing as one of the effective strategies in biomedicine. There are various computational methods for drug repurposing, one of which is using transcription signatures, especially single-cell RNA Sequencing (scRNA-seq) data, which show us a clear and comprehensive view of the inside of the cell to compare the state of disease and health.

Methods: In this study, we used 91,103 scRNA-seq samples from 29 patients with colorectal Cancer (GSE144735 and GSE132465). First, differential gene expression (DGE) analysis was done using the ASAP website. Then we reached a list of drugs that can reverse the gene signature pattern from Cancer to normal using the iLINCS website. Further, by searching various databases and articles, we found 12 drugs that have FDA approval, and so far, no one has reported them as a drug in the treatment of any Cancer. Then, to evaluate the cytotoxicity and performance of these drugs, the MTT assay and Real-Time PCR were performed on two colorectal Cancer cell lines (HT29 and HCT116).

Results: According to our approach, 12 drugs were suggested for the treatment of colorectal Cancer. Four drugs were selected for biological evaluation. The results of the cytotoxicity analysis of these drugs are as follows: tezacaftor (IC10 = 19 µM for HCT-116 and IC10 = 2 µM for HT-29), fenticonazole (IC10 = 17 µM for HCT-116 and IC10 = 7 µM for HT-29), bempedoic acid (IC10 = 78 µM for HCT-116 and IC10 = 65 µM for HT-29), and famciclovir (IC10 = 422 µM for HCT-116 and IC10 = 959 µM for HT-29).

Conclusions: Cost, time, and effectiveness are the main challenges in finding new drugs for diseases. Computational approaches such as transcriptional signature-based drug repurposing methods open new horizons to solve these challenges. In this study, tezacaftor, fenticonazole, and bempedoic acid can be introduced as promising drug candidates for the treatment of colorectal Cancer. These drugs were evaluated in silico and in vitro, but it is necessary to evaluate them in vivo.

Colorectal cancer; Drug repurposing; Single-cell sequencing; Transcriptional signature; iLINCS (Integrative LINCS).