Abstract 2312: Single-cell low pass whole genome sequencing for copy-number profiling in circulating tumor cells from prostate, non-small cell lung and breast cancers

Background: Circulating tumor cells (CTCs) have been considered as an alternative to tissue biopsy for providing both germline-specific and tumor-derived genetic variants. Copy number variations (CNVs) play an important role in molding the genomes of cancers and have been shown the clinical value for prognostic signature and therapeutic target. The current study aimed to evaluate CNVs at single-cell resolution and explore the potential clinical utility of tracking this key mechanism of cancer progression. Methods: Blood samples were collected in Streck tubes from 40 stage II-IV cancer patients (5 prostate cancer, 15 non-small lung cancer (NSCLC), 20 breast cancer (BC)) before treatment. CTCs was identified as cells containing an intact nucleus, without CD45 expression, and with cytokeratin expression. Genomic analysis of chromosomal CNVs by low pass whole genome sequencing (Lp-WGS) and number of large-scale transitions (LSTs) calculation was performed in the CTCs. Results: A total of 9 CTCs from 4 prostate cancer, 70 CTCs from 7 NSCLC, 22 CTCs from 9 breast cancer patients, representing a range of sizes, shapes, and protein expression levels of cytokeratin were identified. A total of 84 individual CTCs were successfully sequenced from 20 patients (1-6 CTCs/patient). The selected highlights for gene CNVs include: 1) CXCR4 and ATM were detected as loss on single cell CTC (scCTC) level in BC; 2) MED12, an important regulator for maintaining accurate cytokinesis and survival, was detected as loss on scCTC level in NSCLC. A wide range of LST scores were observed among the 20 patient samples. Cell morphology analysis, phenotypic heterogeneity biomarker analysis and homologous recombination deficiency (HRD) biomarker analysis using a previously developed HRD classifier1 trained on genomic markers is still ongoing. Conclusion: Our data demonstrated that Lp-WGS of DNA from CTCs can detect CNVs loss and assess disease heterogeneity at the single-cell level. Since genome-wide CNV profiles can be used to characterize genomic instability, it is anticipated that the integrative analysis of morphology and genomics in CTCs can potentially complement tissue and/or ctDNA analysis to determine HRD, enabling in-depth investigation of tumor heterogeneity and individualized clinical assessment. Citation Format: Danyi Wang, Giuseppe Locatelli, Ioannis Gounaris, Juergen Scheuenpflug, Zheng Feng. Single-cell low pass whole genome sequencing for copy-number profiling in circulating tumor cells from prostate, non-small cell lung and breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2312.