Patient-Specific Pharmacogenomics demonstrates xCT as Predictive Therapeutic Target in Colon Cancer with Possible Implications in Tumor Connectivity

Colorectal cancer (CRC) represents the third-leading cause of cancer-related deaths. Knowledge covering diverse cellular and molecular data from individual patients has become valuable for diagnosis, prognosis, and treatment selection. Here, we present an in-depth comparative mRNA-seq analysis of tissue samples from 32 CRC patients, pairing tumors with adjacent healthy tissues. The differential expression gene (DEG) analysis revealed apparently dysregulated metabolic programs,in what we focused on the impact of overexpressed SLC7A11 (xCT) and SLC3A2 genes which compose the cystine/glutamate transporter (Xc-) system. To assess the oncogenic potency of the Xc- system in a cellular setting, we applied a knowledge-based approach for analyzing gene perturbations from CRISPR screens across various cell types as well as using a variety of functional assays in five primary patient-derived organoid cell models to functionally verify our hypothesis. We identified a previously undescribed cell surface protein signature predicting chemotherapy resistance and further highlighted the causality and potential of pharmacological blockage of ferroptosis as promising avenue for cancer therapy. Biological processes such as redox homeostasis, ion/amino acid transporters and regulators of neuronal survival and differentiation were associated with these co-dependent genes in patient specimens. This study highlights a number of potential clinical targets for CRC and promotes patient-individual in vitro model systems as functionally validate in silico predictions. Overall design: The mRNA expression levels of all genes (coding and non-coding) were determined by pairwise analysis of cancerous and healthy tissues obtained from the same patient. Healthy tissue samples were harvested from the aboral margin of the colectomy specimen, at least 5–7 cm distal to the primary tumor, in accordance with national and international guidelines for oncologic resection safety. These normal adjacent tissue samples were macroscopically examined, approved by the pathologist and underwent extensive washing procedures prior to sequencing to ensure the absence of tumor cell contamination. Total of 32 patients were analyzed with 73 deep sequencing results. Altogether, there were 36 samples marked as tumor (T) and 37 samples marked as healthy (H). Each participant provided at least one sample for T and H. For four participants the number of samples was higher. Each sample was studied by partition total RNA by size to support mRNA and miRNA transcriptomics.