CyTOF-based profiling of circulating tumor cells predicts aggressiveness and therapy response in SCLC liquid biopsies at a personalized level

Bose, M.; Ruoff, C. J.; Ehsan, S. F.; Stewart, C. A.; Duarte, A.; Bhattacharyya, S.; Li, J.; Anchang, B.; Welte, T.; Victorian, A.; Lujan, F. E.; Diao, L.; Wang, J.; Chen, K.; Zhang, B.; Wang, R.; Solis Soto, L. M.; Serrano, A. G.; Cardnell, R.; Gay, C. M.; Byers, L.; Karacosta, L. G.

doi:10.64898/2025.12.16.694669

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bioRxiv · 10.64898/2025.12.16.694669

CyTOF-based profiling of circulating tumor cells predicts aggressiveness and therapy response in SCLC liquid biopsies at a personalized level

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Abstract

Small-cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma characterized by high numbers of circulating tumor cells (CTCs). We applied CyTOF and a 20-marker antibody panel to detect and phenotype CTCs directly in liquid biopsies of 51 SCLC patients (treatment-naive, chemotherapy and immunotherapy-treated, and tarlatamab-treated), of which a subset were longitudinally tracked. Unsupervised clustering revealed distinct cell populations enriched in patient liquid biopsies compared to those from healthy donors. Further analysis identified CTC populations of the three established SCLC subtypes driven by the high expression of ASCL1, NeuroD1, and POU2F3 transcription factors respectively. Significant differences in CTC EMT markers, established therapeutic targets (e.g. DLL3), and subtype heterogeneity were observed between naive versus treated samples. Changes in subtype proportions were observed in longitudinally tracked samples in both treatment modalities. Our study demonstrates the utility of CyTOF for high-resolution CTC profiling, offering dynamic insights into CTC heterogeneity, treatment response, and resistance mechanisms. HighlightsO_LICTCs can be detected, subtyped and phenotyped in SCLC liquid biopsies using CyTOF C_LIO_LICTC subtypes and EMT states are differentially associated with treatment modality C_LIO_LICTC DLL3 levels and epithelial features increase following anti-DLL3 BiTE therapy C_LIO_LICyTOF CTC subtyping can predict disease aggressiveness C_LIO_LILongitudinal tracking reveals CTC plasticity and therapy response correlations C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/694669v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@384cbcorg.highwire.dtl.DTLVardef@35dd37org.highwire.dtl.DTLVardef@4e7d61org.highwire.dtl.DTLVardef@1098e4f_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Bose, M., Ruoff, C. J., Ehsan, S. F., Stewart, C. A., Duarte, A., Bhattacharyya, S., Li, J., Anchang, B., Welte, T., Victorian, A., Lujan, F. E., Diao, L., Wang, J., Chen, K., Zhang, B., Wang, R., Solis Soto, L. M., Serrano, A. G., Cardnell, R., Gay, C. M., Byers, L., Karacosta, L. G.. 2025-12-19. CyTOF-based profiling of circulating tumor cells predicts aggressiveness and therapy response in SCLC liquid biopsies at a personalized level. https://doi.org/10.64898/2025.12.16.694669

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