Abstract 5380: An integrated platform for the clinical detection and molecular profiling of single circulating tumor cells

Abstract

Abstract Introduction: Detection of circulating tumor cells (CTCs) and characterization of CTCs at single-cell resolution may benefit the clinical management of cancer patients. To make the CTC analysis a “bench-to-bedside” technology, we developed an integrated platform named ChimeraX®-i120 system for the high-throughput, automated, and clinical applicable CTC sorting and downstream single-cell genomic profiling. Methods: ChimeraX®-i120 system is designed based on negative enrichment strategy, integrating blood sample pre-processing, immunofluorescence staining, artificial intelligence (AI)-assisted CTC identification. CTCs enriched by this system is compatible with downstream single-cell whole genome sequencing (WGS) analysis. Performance of CTCs detection was evaluated by a series of analytical experiments, clinical utility was further verified. We validated our downstream molecular profiling pipeline of single CTC. Results: Analytical experiments showed that this system was featured with high accuracy, repeatability, sensitivity and anti-interference capability for CTC detection, achieving an average recovery rate of the spiked cells in 71.3%-83.2% (R2= 0.99). In clinical samples, this system effectively detected CTCs and CTC clusters (CTM) in 5 mL blood from cancer patients. The proportion of patients that were positive for CTCs (EpCAM+/pan-CK++CD45-+DAPI+), was 59.3% (86/145, avg. cell count 1.38 ± 2.01) for hepatocellular carcinoma (HCC), 63.2% (24/38, 1.42 ± 1.75) for intrahepatic cholangiocarcinoma (ICC), 63.6% (28/44, avg. 2.52 ± 3.93) for breast cancer (BRC), 61.5% (24/39, avg. 1.62 ± 2.11) in colorectal cancer (CRC), 78.9% (15/19, avg. 2.74 ± 4.46) in lung cancer (LC). Only 1 of 125 (0.8%) healthy volunteers had detectable CTC. The prognostic value of the system was assessed in HCC. Preoperative CTC ≥1/5mL blood was significantly associated with a higher 1-year recurrence rate (38.9% vs. 27.6%, P=0.042) in HCC patients after curative surgery. Low-pass WGS analysis was performed on CTCs and paired tumor tissues of 3 ICC, 3 HCC and 4 BRC. We observed concordance in CNAs (10%-61%) between CTCs and tissues. CTC profiling identified diverse intra- and inter-patient heterogeneity in CNAs pattern. Exclusive CNA patterns were identified in CTCs but not tissue, and vice versa. Multiple well-known oncogenes (e.g., BRAF, EGFR, BRCA1/2, MYC and MET) and tumor suppressor genes (e.g., FOXA1 and TRAF3) could be identified from CNAs in CTCs. For example, in one BRC patient, potentially actionable alterations of BRC such as BRAF, EGFR, MET, ERBB2, PIK3CA and MYC were only identified in CTCs but not tissues. Conclusion: Our results highlight the potential clinical utility of ChimeraX®-i120 system in both CTC detection and downstream genomic profiling. Genomic sequencing of CTCs allows blood-based tumor profiling in greater fraction of patients for clinical decision making. Citation Format: Pengxiang Wang, Yunfan Sun, Weixiang Jin, Haixiang Peng, Jian Zhou, Jia Fan, Xinrong Yang. An integrated platform for the clinical detection and molecular profiling of single circulating tumor cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5380.