Single cell capture and molecular analysis of live CTCs using integrated microwells and single cell aspirator

Resistance to targeted therapies can be caused by acquired genomic alterations in genes that code for the targeted protein. Circulating tumor cells (CTCs) provide an accessible source of tumor cells from diverse metastatic lesions from which to evaluate the frequency of genomic alterations that can be matched to distinct phenotypes, including therapeutic resistance. Successful analysis of the diversity of molecular mechanisms of therapeutic resistance requires isolation of live tumor cells for nucleic acid extraction. We have developed a semi-automated single cell aspirating platform to enrich and isolate live, rare cell populations for downstream molecular analysis. Using immortalized cell lines, we were able to enrich a target population of cells from a mixed population resulting a high purity sample (71.7-83.8%) to interrogate. Target cells were captured for nucleic acid extraction for downstream gene expression to validate enrichment. We demonstrate the ability to achieve high quality whole genome and transcriptome endpoints from low cell numbers in cell lines: the lower threshold for cellular input required to attain whole genome amplification (WGA) products reliable for downstream sequencing applications is now being validated. We also isolated CTCs from patient blood samples and showed phenotypic heterogeneity of EpCAM expression among individual CTCs. EpCAMhigh and EpCAMlow CTCs were detected, with a broad range of fluorescent intensities (141.2-5804.56 MFI). Using the phenotypic characterization of EpCAM expression, individual live CTCs were identified and captured for evaluation of their genomic heterogeneity. We have identified molecular heterogeneity in these cells that may reflect heterogeneity driving treatment resistance in CRPC. Early identification of treatment resistant clones may help develop intervention strategies that prolong the efficacy of molecular targeted therapies. Citation Format: Charlotte N. Stahlfeld, Jake J. Tokar, David Quigley, David Niles, Jamie M. Sperger, Felix Feng, Joshua M. Lang. Single cell capture and molecular analysis of live CTCs using integrated microwells and single cell aspirator [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2291.