Identification of PLXNC1 as a novel biomarker for Consensus Molecular Subtype 4 in colorectal cancer

Colorectal cancer (CRC) is the third most diagnosed cancer worldwide. Tumor heterogeneity often causes inconsistent outcomes and drug responses among patients with CRC. Although a recent unified transcriptomic classification categorizes most CRC into four consensus molecular subtypes (CMSs) with clear clinical interpretability, it has not been translated to a routine clinical examination due to the lack of biomarkers. Therefore, it is urgent to find new biomarkers for CMS subtypes. We compared the expression of PLXNC1 in CRC and adjacent tissues using public databases and immunohistochemistry. We then analyzed the impact of PLXNC1 on survival probability by the Kaplan-Meier plot, Cox proportional risk model, and Nomogram diagram. Then we evaluated the accuracy of PLXNC1 in distinguishing CMS4 colorectal cancer. The microenvironment of tumor was investigated by deconvolution algorithms and single cell RNA-seq. We subsequently used siRNA interference and plasmid transfection techniques to detect the effects of PLXNC1 knockdown or overexpression on the proliferation, migration, and invasion of colorectal cells. We further established subcutaneously transplanted tumor models and liver metastasis models to investigate the key role of PLXNC1 in the growth and metastasis of colon cancer. We also verified the essential role of PLXNC1 in maintaining the CMS4-related phenotypes of CRC. PLXNC1 was distinctly upregulated in CRC compared to adjacent tissues. Patients with high PLXNC1 expression tend to have poor prognoses. The expression of PLXNC1 was capable to distinguish the CMS4 subtype from other subtypes. CRC with high expression of PLXNC1 exhibit a distinct mesenchymal phenotype, usually accompanied by high infiltration of stromal components, angiogenesis, complement activation, and immunosuppressive microenvironment. PLXNC1 promotes CRC growth and metastasis by regulating epithelial-mesenchymal transformation and immune escape. Knockdown of PLXNC1 reduced CMS4-related phenotypes in CRC. For the first time, we demonstrated that PLXNC1 can predict the poor prognosis of patients with CRC and accurately distinguish patients with CMS4 CRC. PLXNC1 contributes to the growth and metastasis of CRC by promoting the biological features associated with CMS4 CRC such as epithelial-mesenchymal transformation and immune escape.