Integrating single-cell and spatial transcriptomics reveals glycolysis heterogeneity and NEK6-mediated progression in colorectal cancer

BackgroundMetabolic reprogramming is a pivotal driver of tumor microenvironment (TME) remodeling and colorectal cancer (CRC) progression. However, the spatial organization of glycolysis heterogeneity and the molecular drivers maintaining the malignant high-glycolytic state remain poorly understood.MethodsSingle-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and Mendelian randomization (MR) analysis were integrated.

Glycolytic malignant subtypes were identified using AUCell and Non-negative Matrix Factorization (NMF). Cell-cell communication networks were inferred via CellChat.

Pseudotime trajectory analysis and spatial deconvolution were utilized to resolve the developmental dynamics and spatial architecture of subtypes. Finally, key pathogenic regulator genes were screened by integrating large-scale GWAS data with the TCGA cohort, and candidate gene NEK6 was validated through in vitro functional assays.ResultsThree distinct malignant subtypes were identified; the Glycolysis-C1 subtype exhibited a high-glycolytic state.

Cell-cell communication analysis revealed that Glycolysis-C1 cells function as a dominant signaling hub, secreting MIF ligands that target Macrophages and B cells via the CD74/CD44 receptor complex. Pseudotime analysis traced a lineage trajectory from low-glycolytic C3 to high-glycolytic C1.