Multiregion whole-exome sequencing of matched primary and metastatic tumors revealed genomic heterogeneity and suggested polyclonal seeding in colorectal cancer metastasis

Abstract

Background: Distant metastasis accounts for 90% of deaths from colorectal cancer (CRC). Genomic heterogeneity has been reported in various solid malignancies, but remains largely under-explored in metastatic CRC tumors, especially in primary to metastatic tumor evolution.

Patients and methods: We conducted high-depth whole-exome sequencing in multiple regions of matched primary and metastatic CRC tumors. Using a total of 28 tumor, normal, and lymph node tissues, we analyzed inter- and intra-individual heterogeneity, inferred the tumor subclonal architectures, and depicted the subclonal evolutionary routes from primary to metastatic tumors.

Results: CRC has significant inter-individual but relatively limited intra-individual heterogeneity. Genomic landscapes were more similar within primary, metastatic, or lymph node tumors than across these types. Metastatic tumors exhibited less intratumor heterogeneity than primary tumors, indicating that single-region sequencing may be adequate to identify important metastasis mutations to guide treatment. Remarkably, all metastatic tumors inherited multiple genetically distinct subclones from primary tumors, supporting a possible polyclonal seeding mechanism for metastasis. Analysis of one patient with the trio samples of primary, metastatic, and lymph node tumors supported a mechanism of synchronous parallel dissemination from the primary to metastatic tumors that was not mediated through lymph nodes.

Conclusions: In CRC, metastatic tumors have different but less heterogeneous genomic landscapes than primary tumors. It is possible that CRC metastasis is, at least partly, mediated through a polyclonal seeding mechanism. These findings demonstrated the rationale and feasibility for identifying and targeting primary tumor-derived metastasis-potent subclones for the prediction, prevention, and treatment of CRC metastasis.

Keywords: colorectal cancer; heterogeneity; metastasis; whole-exome sequencing.

Figure 1.

Phylogenetic trees showing the relationships of tumor samples in each patient based on mutation sharing and CCFs. The gray line represents trunk mutations that are clonal in all samples. The black line represents leaf mutations that are subclonal and private to the corresponding tumor samples. All other colored lines represent branch mutations that are subclonal and shared by at least two tumor samples. The lengths of the trunk and the branches of the tree are proportional to the number of corresponding mutations.

Figure 2.

Subclonal architecture for all patients. Each panel represents a patient and each row in one panel represents a tumor sample from the corresponding patient. The area of the ovals is proportional to the estimated CCF. For each patient, the most left panel shows the constructed subclonal architecture. Cluster 1 shows the clonal trunk mutations in all tumor regions, the last cluster shows the subclonal leaf mutations observed in only one tumor region, and clusters in between shows subclonal trunk and branch mutations that are shared by two or more tumor regions.

Figure 3.

Subclonal evolutionary routes from primary to metastatic/lymph node tumors for all patients. The color scheme is the same as that in Figure 2. The length of the branches in the tree represents the number of somatic mutations in the corresponding subclone, and the thickness of the branches represents the proportion of the tumor cells occupied by the corresponding subclone. The dashed link between subclones indicates that the relationship is not definitive. Mutated genes and CNAs derived in each subclone are labeled along the branches.