Abstract 2957: A novel circulating tumor DNA (ctDNA) assay enables monitoring of disease progression and treatment response in disseminated preclinical hematologic cancer models

We have established a novel assay to assess circulating tumor DNA (ctDNA) in mice engrafted with disseminated cell line and patient-derived xenografts (PDX) of hematologic malignancies. Disseminated models recapitulate many features of human disease, but engraftment in multiple tissues makes monitoring of disease and treatment response difficult. Existing assays also lack the sensitivity required to assess minimal residual disease (MRD). This novel ddPCR assay targets highly conserved human-specific regions of LINE-1 and HERV-K repeat elements resulting in exceptionally sensitive detection of shed human ctDNA. Initial data shows sensitivity of 0.8 haploid genome equivalents (one haploid genome is ~3.3pg of human DNA), whereas ctDNA monitoring assays currently on the market require 1,000 times more input DNA to reach a sensitivity of just 2-9 genome equivalents. Serial dilution experiments confirm this assay is suitable to detect increases in ctDNA over several orders of magnitude, while also establishing a minimum plasma input of 40uL. To validate the assay we assessed the ability of ctDNA to detect disease alongside traditional histology, bioluminescence imaging, and flow cytometry assays in 10 leukemia and lymphoma models. Levels of ctDNA correlated well with disease progression across models engrafting in bone marrow, spleen, liver, blood and other tissues. In all cases where early stage disease was analyzed, the ctDNA assay was able to detect disease earlier relative to other methods due to its increased sensitivity, and these data can be effectively used for randomization into treatment groups. We also assessed the utility of ctDNA for determining drug treatment response in mice engrafted with a disseminated mantle cell lymphoma PDX. Baseline ctDNA assessment was completed on day 11 post-engraftment confirming ctDNA levels above baseline, at which point mice were divided into 7 treatment groups: Vehicle, Acalabrutinib, and 5 combination arms of Acalabrutinib plus clinically used agents. After 4 weeks of treatment disease burden was assessed by flow cytometry of the bone marrow (femur) compared to ctDNA detected in plasma. Efficacy readouts from both assays agreed for all groups, while the ctDNA assay was able to identify a significant difference between the two best responding arms which appeared to have near complete responses when assessed by flow cytometry alone. The fold difference between the two best responding arms was 1.1 fold by flow cytometr