IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [RNA-seq Tumoroid]

We have previously shown that IKKa coordinates the activation of several oncogenic and therapy-resistant pathways, including ATM/DDR, BRD4, and JAK/STAT3, independently of canonical NF-kB signaling. Here, we found that IKKa suppression, either genetically or pharmacologically, led to stabilization of ZO-1 protein and increased CLDN2 expression, resulting in altered tight junction distribution. IKKa KO cells showed a shift in their migratory mode towards collective migration, which is associated with superior metastatic capacity in vivo. Analysis of single-cell (sc)RNA-seq data from a mouse model of CRC revealed an accumulation of the tight junction signature, including ZO-1 and CLND2, in the metastatic populations. scRNA-seq analysis of patient-derived organoid (PDO5) identified three distinct epithelial cell clusters (C2, C4 and C8) that show a significant enrichment for the metastasis-specific EpiHR signature and the tight junction signature. In particular, C2 and C8 display unique genetic signatures that are significantly upregulated in IKKa KO cells and enriched in the PDO5 IKKa KO-derived metastases. Analysis of human paraffin-embedded CRC specimens led to the identification of vascular tumor infiltrates with ZO-1 and CLDN2-positive cluster-like or glandular phenotypes. The concomitant presence of low CHUCK (IKKa) and high TJP1 (ZO-1) RNA levels is sufficient to predict poor prognosis in CRC patients. These results suggest that the presence of collectively migrating cancer cells in the vascular infiltrates, characterized by high levels of tight junction proteins, could be standardized as a prognostic tool to predict metastasis. We anticipate the use of drugs targeting tight junction elements for metastasis prevention.