Currently, clinical characterization of metastatic breast cancer is based on tissue samples taken at time of diagnosis. However, tissue biopsies are invasive and tumors are continuously evolving, which indicates the need for minimally invasive longitudinal assessment of the tumor. Blood-based liquid biopsies provide minimal invasive means for serial sampling over the course of treatment and the opportunity to adjust therapies based on molecular markers. Here, we aim to identify cellular changes that occur in breast cancer over the lifespan of an affected patient through single-cell proteomic and genomic analysis of longitudinally sampled solid and liquid biopsies. Three solid and 17 liquid biopsies from peripheral blood of an ER+/HER2− metastatic breast cancer patient collected over 4 years and eight treatment regimens were analyzed for morphology, protein expression, copy-number alterations, and single-nucleotide variations. Analysis of 563 single morphometrically similar circulating tumor cells (CTCs) and 13 cell-free DNA (cfDNA) samples along with biopsies of the primary and metastatic tumor revealed progressive genomic evolution away from the primary tumor profiles, along with changes in ER expression and the appearance of resistance mutations. Both the abundance and the genomic alterations of CTCs and cfDNA were highly correlated and consistent with genomic alterations in the tissue samples. We demonstrate that genomic evolution and acquisition of drug resistance can be detected in real time and at single-cell resolution through liquid biopsy analytes and highlight the utility of liquid biopsies to guide treatment decisions.

The liquid biopsy has the potential to improve current clinical practice in oncology by providing real-time personalized information about a patient’s disease status and response to treatment. In this study, we evaluated 161 peripheral blood (PB) samples that were collected around surgical resection from 47 metastatic colorectal cancer (mCRC) patients using the High-Definition Single Cell Assay (HDSCA) workflow. In conjunction with the standard circulating tumor cell (CTC) enumeration, cellular morphology and kinetics between time-points of collection were considered in the survival analysis. CTCs, CTC-Apoptotic, and CTC clusters were found to indicate poor survival with an increase in cell count from pre-resection to post-resection. This study demonstrates that CTC subcategorization based on morphological differences leads to nuanced results between the subtypes, emphasizing the heterogeneity within the CTC classification. Furthermore, we show that factoring in the time-point of each blood collection is critical, both for its static enumeration and for the change in cell populations between draws. By integrating morphology and time-based analysis alongside standard CTC enumeration, liquid biopsy platforms can provide greater insight into the pathophysiology of mCRC by highlighting the complexity of the disease across a patient’s treatment.

Background: It is established that tumors evolve over time due to treatment pressure or physiological constraints. Tissue biopsies give a one-time window into the characteristics of a primary tumor or metastatic nodule. Their main pitfall is procedure risk, pain, and cost, which is why they are rarely repeated. Liquid biopsies, however, are performed with minimal discomfort and risk, providing an easier way to monitor disease. Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have proven to be of high prognostic and diagnostic value. Here we evaluate 17 longitudinal blood draws collected from a metastatic breast cancer patient over 4 years and assess the power of single-cell analysis relative to analysis of tissue biopsies and cfDNA. Methods: CTCs were enumerated using the high-definition single-cell assay (HD-SCA) and single CTCs were isolated by micromanipulation. DNA of single cells underwent whole genome amplification and Illumina library construction for copy number variation (CNV) analysis. Genomic DNA from microdissected FFPE tissue and cfDNA extracted from plasma were converted into Illumina sequencing libraries for CNV analysis. CA27.29 levels were reported by the clinic. Results: Levels of CTCs and circulating tumor DNA (ctDNA) fractions were positively correlated with CA27.29. CNV analysis of single tumor cells at time of enrollment revealed 3 morphometrically indistinguishable clones that persisted during the 4-year follow-up. Genomic analysis of primary breast tissue and bone metastasis detected at time of diagnosis matched CNV data of the evolutionary first clone, while a later liver metastasis was comprised solely of clone 2. Remarkably, CTCs in clone 2 were identified years before discovery of the liver metastasis. To date, we have not detected a metastatic site harboring clone 3. We found that CNV profiles from cfDNA represented the aggregate of CTC clones. Conclusion: Longitudinal blood sampling enabled tracing of tumor evolution robustly and less invasively than solid tumor biopsies. Metastasis associated clones were identified years before measureable disease, providing an opportunity for earlier interventions. While plasma-based assays detected the presence of tumor-derived DNA, the single-cell high-content resolution of the HD-SCA workflow was required to deconvolute 3 genomically distinct clones present in this patient. We propose that enumeration of CTCs and analysis of ctDNA could be used as additional clinical markers to monitor disease recurrence, adding valuable morphogenomic information about the primary tumor and metastatic sites. Additionally, we are currently analyzing the results of single nucleotide variation analysis of single CTCs, cfDNA and FFPE tissue from this patient. Citation Format: Lisa Welter, Liya Xu, Dillon McKinley, Sara Restrepo-Vassalli, Angel Dago, Mariam Rodriguez Lee, Anand Kolatkar, James Hicks, Jorge Nieva, Peter Kuhn. Characterization of disease evolution in sequential sampled metastatic breast cancer using liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2963.