Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product
Abstract
AbstractCirculating 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.
Article Details
Authors (33)
Avanish Mishra
Center for Engineering in Medicine and Surgery, Massachusetts General Hospital and Harvard Medical School
Shih-Bo Huang
Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center and Harvard Medical School
Taronish Dubash
Risa Burr
Krantz Family Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School
Jon F. Edd
Center for Engineering in Medicine and Surgery, Massachusetts General Hospital and Harvard Medical School
Ben S. Wittner
Quinn E. Cunneely
Victor R. Putaturo
Akansha Deshpande
Ezgi Antmen
Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center and Harvard Medical School
Kaustav A. Gopinathan
Center for Engineering in Medicine and Surgery, Massachusetts General Hospital and Harvard Medical School
Keisuke Otani
Yoshiyuki Miyazawa
Ji Eun Kwak
Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center and Harvard Medical School
Sara Y. Guay
Justin Kelly
Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center and Harvard Medical School
John Walsh
Center for Engineering in Medicine and Surgery, Massachusetts General Hospital and Harvard Medical School
Linda T. Nieman
Isabella Galler
PuiYee Chan
Michael S. Lawrence
Ryan J. Sullivan
Massachusetts General Hospital Cancer Center Boston Massachusetts USA
Aditya Bardia
Douglas S. Micalizzi
Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center and Harvard Medical School
Lecia V. Sequist
Richard J. Lee
Joseph W. Franses
David T. Ting
Patricia A. R. Brunker
Shyamala Maheswaran
David T. Miyamoto
Daniel A. Haber
Mehmet Toner