Journal Article

Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product

Sullivan, Ryan J., Cunneely, Quinn E., Putaturo, Victor R., Huang, Shih-Bo, Deshpande, Akansha, Burr, Risa, Lee, Richard J., Ting, David T., Franses, Joseph W., Maheswaran, Shyamala, Kelly, Justin, Wittner, Ben S., Nieman, Linda T., Otani, Keisuke, Edd, Jon F., Micalizzi, Douglas S., Gopinathan, Kaustav A., Sequist, Lecia V., Antmen, Ezgi, Toner, Mehmet, Walsh, John, Mishra, Avanish, Galler, Isabella, Kwak, Ji Eun, Lawrence, Michael S., Miyazawa, Yoshiyuki, Miyamoto, David T., Haber, Daniel A., Guay, Sara Y., Chan, PuiYee, Bardia, Aditya, Brunker, Patricia A. R., Dubash, Taronish

2025

Overview

Circulating Tumor Cells (CTCs) in blood encompass DNA, RNA, and protein biomarkers, but clinical utility is limited by their rarity. To enable tumor epitope-agnostic interrogation of large blood volumes, we developed a high-throughput microfluidic device, depleting hematopoietic cells through high-flow channels and force-amplifying magnetic lenses. Here, we apply this technology to analyze patient-derived leukapheresis products, interrogating a mean blood volume of 5.83 liters from seven patients with metastatic cancer. High CTC yields (mean 10,057 CTCs per patient; range 100 to 58,125) reveal considerable intra-patient heterogeneity. CTC size varies within patients, with 67% overlapping in diameter with WBCs. Paired single-cell DNA and RNA sequencing identifies subclonal patterns of aneuploidy and distinct signaling pathways within CTCs. In prostate cancers, a subpopulation of small aneuploid cells lacking epithelial markers is enriched for neuroendocrine signatures. Pooling of CNV-confirmed CTCs enables whole exome sequencing with high mutant allele fractions. High-throughput CTC enrichment thus enables cell-based liquid biopsy for comprehensive monitoring of cancer. Circulating tumor cells (CTCs) are clinically useful for detecting and monitoring cancer, but they are rare in blood. Here, the authors use a highthroughput microfluidic device to massively enrich CTCs from leukapheresis products to uncover single cell molecular features in prostate and other cancers.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 14 / 14/35 / 38 / 38/1 / 38/23 / 38/62 / 38/91 / 49 / 631/67/1857 / 639/166/985 / Aneuploidy / Biomarkers / Biomarkers, Tumor - genetics / Biomarkers, Tumor - metabolism / Biopsy / Blood / Blood circulation / Blood volume / Cancer / Deoxyribonucleic acid / DNA / DNA sequencing / Enrichment / Epitopes / Exome Sequencing / Female / Gene sequencing / Hematopoietic stem cells / Heterogeneity / High-Throughput Nucleotide Sequencing - methods / Humanities and Social Sciences / Humans / Interrogation / Leukapheresis / Leukapheresis - instrumentation / Leukapheresis - methods / Liquid Biopsy - methods / Magnetic lenses / Male / Metastases / Microfluidic Analytical Techniques - instrumentation / Microfluidic Analytical Techniques - methods / Microfluidic devices / Microfluidics / Microfluidics - instrumentation / Microfluidics - methods / Monitoring / multidisciplinary / Neoplasms - genetics / Neoplasms - pathology / Neoplastic Cells, Circulating - metabolism / Neoplastic Cells, Circulating - pathology / Prostate / Prostate cancer / Prostatic Neoplasms - genetics / Prostatic Neoplasms - pathology / Ribonucleic acid / RNA / Science / Science (multidisciplinary) / Single-Cell Analysis - methods / Technology assessment / Tumor cells / Tumors / Whole genome sequencing