Abstract LB179: Automated viable circulating tumor cell (CTC) isolation enables efficient single-cell multi-omics analysis in a clinical setting

Abstract

Abstract Circulating tumor cells (CTCs) are rare cells found in peripheral blood or other body fluids of cancer patients. Single-cell multi-omics analysis of CTCs can provide critical information and insights for tumor heterogeneity, early detection, residual disease, recurrence, and response and resistance to therapies. However, the adoption of single cell analysis in a clinical setting has been challenging due to complicated and lengthy workflows, lack of automation, low throughput, cell loss, inefficient cell picking, and nucleic acid degradation. To overcome these challenges, we have developed the fully automated LiquidScan liquid biopsy platform as a solution for CTC enrichment and single cell isolation. Whole blood samples were collected from breast, prostate, and lung cancer patients using BioFluidica blood collection tubes. CTCs were enriched with LiquidScan platform coupled with microfluidic affinity selection of rare cells with antibodies against cancer specific surface markers. Cell eluates released from microfluidic chips were further sorted and individual cells were placed into individual wells of PCR plates. The isolated single cells were processed with either whole genome amplification for DNA analysis or pre-amplification of RNA for transcriptome profiling. Cell viability and RNA integrity were assessed for enriched cells post LiquidScan processing. Whole blood samples were directly loaded to microfluidic chips and processed (capture, wash, release and elute) using Hamilton robot for automated processing with no require to red blood cell lysis. The sample processing time was approximately 3 hours with up to 8 samples processed simultaneously. Enriched cells were 70% viable on average post LiquidScan sample processing. The RNA RIN score for the enriched cells was 6 on average. Success rate of DNA amplifications and RNA pre-Amplifications were both over 90% across all samples processed. The LiquidScan platform provides a solution for fast, automated single viable cell isolation making downstream molecular analysis possible in a clinical setting. Protocols for RNA pre-amplification and DNA sequencing including copy number analysis and targeted resequencing have been developed. Single cell DNA methylation and proteomics assay development is in progress. Citation Format: Janet Dickerson, Dylan Dufek, Robbie Huff, Stephenie Jones, Jennifer Barber-Singh, Christopher Brandt, Judy Muller-Cohn, Rolf Muller, Yipeng Wang. Automated viable circulating tumor cell (CTC) isolation enables efficient single-cell multi-omics analysis in a clinical setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB179.