The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy

Abstract

Early-onset colorectal cancers (EOCRCs) may have biological or genomic features distinct from late-onset CRCs (LOCRCs). Previous studies have mostly focused on the germline predisposition conditions of EOCRCs, but we hypothesized that EOCRCs may have distinct somatic aberrations that accelerate cancer development. To identify the somatic aberrations that accelerate cancer development at an early age, we conducted whole exome sequencing for 28 polyposis-unrelated, microsatellite stable (MSS) EOCRCs with no known germline predisposition conditions. Surprisingly, we found two distinct groups in the context of mutational burden: 6 hypermutated cases with 2325 to 10973 mutations and 22 nonhypermutated cases with 47 to 154 mutations. Further analysis revealed that four of the six hypermutated cases had the same POLE P286R mutation. We validated this finding in 83 MSS EOCRCs and 27 MSS LOCRCs, which revealed that 7.2% of EOCRCs (6/83) had the POLE P286R mutation, which was not found in LOCRCs. Clinicopathologically, EOCRCs with POLE mutations occurred far more frequently in the right colon than in the left colon, affecting men more frequently than women. In summary, we have identified a unique subclass of colon cancer characterized by a hypermutation associated with the POLE mutation. The acquisition of the POLE mutation leading to hypermutation can accelerate cancer development. Clinically, this subset with hypermutation may be susceptible to immune checkpoint blockade.

Keywords: PD-1 blockade; POLE; early-onset colorectal cancer; hypermutation; immunotherapy.

Figure 1. Mutational frequency and patterns

A. The prevalence of somatic mutations in the 28 MSS EOCRCs. Here, somatic mutations are represented by nonsynonymous mutations, stop-gain mutations, stop-loss mutations, splicing variants, and indels that lead to changes in the primary structure of proteins. B. Mutation patterns of the 28 MSS EOCRCs. The mutation patterns were different between the hypermutated and the nonhypermutated cases. C. Mutation patterns of 224 CRCs in the TCGA study. Of note, the mutation patterns of the hypermutated MSI CRCs were different from those of the hypermutated MSS CRCs, which is characterized by a high C:G>A:T peak. This peak was also characteristic of the hypermutated MSS EOCRCs in our study (B).

Figure 2. Highly mutated signaling pathways

In general, the hypermutated group had higher mutational frequencies in most genes in the affected pathways. One exception is the P53 mutation, a late-stage event in CRC carcinogenesis. The hypermutated group had low mutational frequency in P53, indicating that this group may have a carcinogenic mechanism distinct from the nonhypermutated group. A. WNT and TGF-β pathways. B. P53 pathway. C. PI3K and RTK-RAS pathways. Alteration frequencies are expressed as a percentage of all cases. HM: hypermutated group; nHM: nonhypermutated group.

Figure 3. A representative immunohistochemistry image of POLE-mutated colorectal cancer

Tumor cells form cribriform architectures that contain apoptotic debris in their lumen (arrow). (Hematoxylin and eosin, ×20 objective lens, scale bar = 120 μm).

Figure 4. Representative immunohistochemical results

Immunohistochemical analyses of immune-related marker expression in tumor cells and tumor-infiltrating lymphocytes (TILs) using five cytotoxic T cell markers and immune checkpoint molecules. TILs were mostly positive for CD45ro and/or CD3, and some TILs were positive for PD-1.