Delayed processing of CPT-collected blood preserves transcriptomic and genomic features of propagated circulating tumor cells

Circulating tumor cells (CTCs) provide a minimally invasive window into metastatic disease but are constrained by the need for rapid specimen processing after blood collection. We evaluated whether a workflow utilizing BD Vacutainer CPT-based blood collection could support delayed processing while preserving molecular features of propagated CTC-derived material. In a pilot cohort of four patients, paired CPT tubes were collected; one tube was processed within 2 hours of phlebotomy, whereas the second was stored at 4°C and processed 24 hours later. Both tubes were then harvested for CTCs, which were propagated ex vivo and analyzed by bulk RNA sequencing and whole-exome sequencing. Transcriptomic analyses showed that paired CPT-derived samples demonstrated phenotypes consistent with CTCs, including reduced immune-associated signatures and enrichment of epithelial-mesenchymal transition and KRAS signaling pathways. Direct comparison of paired early- and delayed-processed CPT samples demonstrated strong within-patient gene expression concordance. Whole-exome sequencing further revealed preservation of patient-specific oncogenic alterations and high overlap of detected variants across paired processing conditions. These findings altogether support the feasibility of a CPT-based delayed processing workflow for propagating and studying CTCs, thereby reducing a key logistical barrier to broader CTC research.