Hypermutable DNA chronicles the evolution of human colon cancer

Abstract

Intratumor genetic heterogeneity reflects the evolutionary history of a cancer and is thought to influence treatment outcomes. Here we report that a simple PCR-based assay interrogating somatic variation in hypermutable polyguanine (poly-G) repeats can provide a rapid and reliable assessment of mitotic history and clonal architecture in human cancer. We use poly-G repeat genotyping to study the evolution of colon carcinoma. In a cohort of 22 patients, we detect poly-G variants in 91% of tumors. Patient age is positively correlated with somatic mutation frequency, suggesting that some poly-G variants accumulate before the onset of carcinogenesis during normal division in colonic stem cells. Poorly differentiated tumors have fewer mutations than well-differentiated tumors, possibly indicating a shorter mitotic history of the founder cell in these cancers. We generate poly-G mutation profiles of spatially separated samples from primary carcinomas and matched metastases to build well-supported phylogenetic trees that illuminate individual patients' path of metastatic progression. Our results show varying degrees of intratumor heterogeneity among patients. Finally, we show that poly-G mutations can be found in other cancers than colon carcinoma. Our approach can generate reliable maps of intratumor heterogeneity in large numbers of patients with minimal time and cost expenditure.lineage tracing | microsatellites | tumor phylogenetics H uman cancers are composed of a continually evolving population of genetically and phenotypically divergent cells (1). This reservoir of diversity feeds the natural selection process that fundamentally drives disease progression through acquisition of metastatic properties and emergence of therapy-resistant clones (2-4). In recent years, characterization of intratumor heterogeneity has received increased attention as advanced sequencing technologies have enabled more detailed analysis of tumor cell populations (5-8).Depending on the context, the term "intratumor heterogeneity" refers either to differences between cells that coexist in one localized tumor region or to variation in clonal composition between spatially separated parts, most notably between a primary tumor and its metastases (in the latter case, "intracancer heterogeneity" is a more appropriate terminology). The extent of genetic divergence between primary and metastatic tumors (and the history of dissemination encoded therein) is beginning to be investigated, but relatively few patient data are currently available. The canonical "linear progression" model of metastasis states that a genetically advanced cell metastasizes late in primary tumor development (9-11). This aggressive clone generates new metastases in a so-called "metastasis shower" (12). Linear progression predicts that metastases will be genetically similar to the primary tumor and to each other. The alternative "parallel progression" model (9) posits that metastasis occurs early in tumor evolution and consequently expects metastases to be substantially differe...

The evolution of tumour phylogenetics: principles and practice

“…After some specific methods are used in hundreds of studies, we hope that the results will be sufficiently robust and interpretable to aid in patient prognosis and treatment planning. Similarly, clinicians interpreting phylogenetic analyses should insist that different methods be tried and that results are actionable only when different methods of analysis lead to the same qualitative understanding of a patient’s tumour 68,106 .…”

“…For example, the studies that concluded that there was little selection in some tumours looked mostly at SNVs and CNVs, but perhaps there is selection in those tumours via evolutionary mechanisms that would be apparent only when looking at other marker types, such as karyotypes or methylation patterns. Few studies have tested whether the phylogenetic inferences made are robust to a change of methods, with notable exceptions 68,106 .…”

The influence of subclonal resistance mutations on targeted cancer therapy

“…11–13 These subclones carry distinct sets of oncogenic driver mutations and other phylogenetic signatures of their unique, and ongoing, evolutionary history. 14,15 Subclonal mutations arise initially in a single cell; this cell can then expand to become a detectable minority population within the tumour. The mutations that confer a growth advantage—frequently referred to as ‘driver mutations’—can occur in concert with additional unselected mutations.…”

Genetic Profiling of Cancers of the Digestive System: Biological Insights and Clinical Implications

“…Several groups have even suggested that genetic tumor heterogeneity might explain why the success stories of biomarker discovery and identification of drug targets are modestly small to date [78][79][80] . The emerging picture is now that almost every major cancer of the digestive system, including CRC [81] , PDAC [56] , esophageal carcinoma and its precursors [82,83] , CC [84] , and HCC [85] , is composed of more than one tumor cell clone. The degree of genetic heterogeneity, however, appears to be quite variable.…”