Genetic and epigenetic alterations in colorectal cancer (CRC) have been extensively investigated. Small depressed-type colorectal tumors (DCs) constitute a highly invasive CRC subtype. We characterized the mutational profiles of 22 DC samples, seven of which were subjected to whole exome sequencing (WES). This revealed frequent mutations (7 of 22 cases, 31.8%) in PTPRK, with most of these mutations located in the D1 domain-encoding region. To further quantify the incidence of PTPRK mutations, we analyzed 567 CRCs cases from two public databases (The Cancer Genome Atlas and the Catalogue of Somatic Mutations in Cancer). Mutations were more frequently observed in proximal colon tumors and were highly associated with the CpG island methylator phenotype-positive (CIMP-P) subtype (76.2%) and microsatellite instability (MSI; 66.7%). PTPRK mutant proteins (particularly those with D1 domain) retained the ability to bind integrin beta-4 (ITGB4). In addition, CRC cells expressing PTPRK mutants exhibited increased ITGB4 phosphorylation, suggesting that the mutations impair the phosphatase activity of PTPRK. Consistent with this, tumors with PTPRK mutations proliferated significantly more rapidly than their wild type counterparts in vivo. These findings suggest that PTPRK mutations contribute to DC development by dysregulating phosphorylation-mediated signaling pathways.
Tojo et al. (2026) studied this question.