Chemotherapy resistance in colorectal cancer (CRC) is a multifaceted process driven by the diverse contributions of individual cancer cell clones. The presence of cancer cell clone subpopulations with varying sensitivities to therapy allow resistant clones to survive and expand, ultimately reducing treatment efficacy and contributing to disease progression or recurrence. To investigate the mechanisms underlying this resistance, we established oxaliplatin-resistant SW480 cells and employed cellular DNA barcoding technology to track their clonal evolution. Our approach also aimed to identify drivers of oxaliplatin resistance and to uncover secondary drug vulnerabilities to counteract resistance.

We used cellular DNA barcoding technology to track SW480 individual clones during the resistance process. All analyses were performed in three drug resistant replicates and control groups. Using amplicon sequencing, we analyzed the barcode distributions across oxaliplatin-resistant and control groups. Whole-exome sequencing (WES) was employed to uncover genomic alterations that may have a pivotal role in resistance mechanisms. Additionally, a secondary drug screen of a 50-compound library was performed to explore therapeutic possibilities.

We used amplicon sequencing to identify barcode distributions, and the pre-existing vs de novo nature of clones selected through the resistance generation process. Whole-Exome Sequencing (WES) was employed to uncover the genomic make-up of oxaliplatin resistance, highlighting the differences in mutational landscapes of the resistant groups. Finally, a secondary drug screening was performed using a 50-compound drug library, for an ultimate aim to exploit therapeutic vulnerabilities arising from oxaliplatin resistance.

To conclude, this study underscores the utility of cellular DNA barcoding as a powerful tool for dissecting the complex evolution of chemotherapy resistance in cancer. Our findings provide critical insights into the clonal dynamics and molecular drivers of CRC drug resistance, paving the way for targeted approaches to overcome resistance and improve treatment outcomes.