Integrated single-cell analysis characterizes malignant epithelial programs and context-dependent immune associations of MP7/SERINC2 in colorectal cancer

Introduction Colorectal cancer (CRC) comprises heterogeneous malignant epithelial states, but it remains unclear which transcriptional programs recur across patients and how these programs relate to the immune context. Methods We integrated five public single-cell RNA-sequencing datasets comprising 425,402 cells from 119 patients using scVI, defined malignant epithelial cells with inferCNV, and characterized their states and transcriptional programs using cNMF, pySCENIC, and CytoTRACE2. Program recurrence was assessed by rerunning cNMF separately for individual patients. Metaprogram associations were subsequently evaluated in bulk cohorts, CRC cell lines, spatial transcriptomic datasets, and an immune-checkpoint inhibitor (ICI) cohort. Results We identified five malignant epithelial states and eight metaprograms. MP7, a secretory/goblet-lineage program, was independently recovered in 9 of 26 evaluable patients across three datasets, with reciprocal-best matches in five. Although its top-100 gene profile closely resembled that of normal goblet cells (Spearman r = 0.834), 92.2–94.2% of MP7-dominant cells were retained as malignant under stricter classification criteria. Bulk MP7 scores were sensitive to epithelial composition, and an exploratory 17-gene survival score derived from MP7 showed limited discrimination in nested cross-validation and external cohorts. SERINC2 was prioritized from this gene set for functional testing. SERINC2-targeting shRNAs increased wound closure and Transwell invasion in SW480 and RKO cells, with RNA-level knockdown confirmed in SW480 cells. MP7 and SERINC2 showed context-dependent associations with immune features at the patient and spatial levels, but neither distinguished response in the examined ICI cohort. Discussion MP7 represents a secretory/goblet-lineage program that recurs in a subset of CRC tumors rather than a broadly shared malignant state. The findings also identify SERINC2 as a candidate regulator of CRC cell motility and invasion, although its mechanism and clinical relevance require further validation.