Comprehensive Multi-omics Integration of Bulk, Single cell and Spatial Transcriptomics Reveals Temporal and Spatial Gene Expression to Cisplatin and 5-Fluorouracil in Colorectal Cancer

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, mainly as outcomes of varying treatment responses and an increase of drug resistance. Although cisplatin and 5-fluorouracil (5-FU) are used in medical treatment widely, it remains unknown exactly molecular pathways explain numerous therapeutic responses. This study aimed to identify genes responsive to these two drugs and to characterize their expression patterns and associated cell populations using an integrative multi-omics approach. We first analyzed bulk RNA-seq datasets from CRC cell lines (HCT116, HT29, and SW480) treated with 5-FU and cisplatin to identify differentially expressed genes (DEGs) and pathways. Next, we assessed the expression levels and cell-type specificity of these DEGs in single-cell RNA-seq data from ten colorectal tissue samples (five tumors and five normal tissues). Finally, spatial transcriptomics from four CRC tumor slides were examined to map the localization of treatment-responsive genes within the tumor microenvironment. Our results revealed that epithelial and fibroblast populations exhibited distinct transcriptional adaptations to chemotherapy. Pseudotime trajectories showed fibroblast enrichment at later transition states and suggesting a role in remodeling during treatment adaptation. Spatial mapping demonstrated that fibroblast-associated genes (SPARC, COL12A1, VCAN) were localized to stromal-rich peripheral regions, while epithelial markers (IFIT3, MYH9, KMT2E-AS1) were concentrated in tumor cores, particularly under high-dose cisplatin. Collectively, these findings demonstrate that epithelial plasticity and fibroblast-mediated remodeling contribute to drug resistance, highlighting possible targets to enhance cancer therapy sensitivity because chemotherapy induces considerable cellular and spatial modifications in the landscape of colorectal tumors.