Circulating tumor DNA to monitor clonal subpopulation responses to different treatments in a pancreatic cancer model

Cancer cells are subjected to evolutionary selection of clonal populations by immune editing, distinct microenvironment at the local and metastatic sites as well as in response to drug treatment. Here we evaluate how treatment responses of clonal subpopulations are reflected in circulating cell-free DNA.

Methods: We established a model of tumor heterogeneity from syngeneic, clonal primary cancer cells isolated from a mutant Kras/P53 mouse pancreatic cancer (KPC). The clones were characterized molecularly for signature mutations and tumors reconstituted as allografts from mixes of the clonal cell lines.

Results and Discussion: Clonal cells formed invasive and metastatic lesions when grafted into syngeneic hosts. The original tumor and clonal cell lines harbored common mutations in ~100 genes suggesting their common ancestry. Unique mutations in each clonal cell line were used to identify and quantitate the clones in heterogeneous cell pools. The clones showed different levels of MAP kinase signaling, unique morphologies, different growth rates in vitro and tumor growth rates in immune competent mice. Moreover, the sensitivity to ~200 anticancer drugs revealed an up to 25-fold varying in vitro sensitivity of the clones to signal transduction inhibitors and cytotoxic drugs.

To our surprise, drug sensitivity of individual clones when included in a heterogeneous cell population was strikingly different from their drug sensitivity when growing on their own. In particular, the sensitivity of clones to an anti-PD1 checkpoint inhibitor was distinct across the clonal cells growing in the heterogeneous mixture. Some clones were resistant and others highly sensitive to the checkpoint inhibition.

We will discuss changes in clone-specific circulating cell free DNA as an indicator of treatment sensitivity and resistance to different treatments and on clonal subpopulations present in the tumors.