Clonal and intrinsic heterogeneity of somatic variants in microsatellite-stable colorectal carcinomas and their metastases
In order to test the traditional model of tumour progression, Darwinian-type evolution, against the more recent Big Bang model, we selected six treatment-naive microsatellite-stable colorectal standard-type adenocarcinomas and their synchronous lymph node and liver metastasis. Somatic genomic variants were identified by whole exome sequencing of large tumour fragments from the primaries and one liver metastasis each and used to design targeted resequencing NGS panels, one per case. Targeted deep resequencing (mean coverage 2725/median 2222) was done with DNA from punch samples (1 mm tissue microarrayer needles) obtained from different regions of the primaries and their metastases. In total, 255 genomic variants were interrogated in 108 punch samples. Clonal heterogeneity was infrequent: in fact, a pattern of clonal heterogeneity consistent with a role in metastasis formation was seen but in one case in a single gene (p.Asp604Tyr of the PTPRT gene). However, when comparing variant allele frequencies (VAF) of genomic variants in adjacent positions on chromosomes (matched genomic variant loci) across punch samples, there were seen differences that exceeded 2 SD of the NGS assays' variations (ad hoc dubbed VAF dysbalance) in 7.1% of the punch samples (2.6% to 12.0% per case) which indicates an intricate intermixing of mutated and non-mutated tumour cells (intrinsic heterogeneity). Additional OncoScan array analyses on a subset of the punch samples (31 in total) showed gross genomic aberrations as a possible explanation in only some (39.2%) of the matched genomic variant loci with VAF dysbalance. Taken together, our study provides a fairly direct (statistical model-free) view into the genomic states of microsatellite-stable colorectal carcinomas and their metastases and suggests that, at least in a pre-chemotherapy setting, Darwinian-type tumour evolution is not the key pathway to metastasizing disease; instead, we recorded an intrinsic genomic heterogeneity which may echo an initial Big Bang-like event.