Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells

Yu Heng Cheng, Yu Chih Chen, Eric Lin, Riley Brien, Seungwon Jung, Yu Ting Chen, Woncheol Lee, Zhijian Hao, Saswat Sahoo, Hyun Min Kang, Jason Cong, Monika Burness, Sunitha Nagrath, Max S. Wicha, Euisik Yoon

Research output: Contribution to journalArticlepeer-review

125 Citations (Scopus)


Molecular analysis of circulating tumor cells (CTCs) at single-cell resolution offers great promise for cancer diagnostics and therapeutics from simple liquid biopsy. Recent development of massively parallel single-cell RNA-sequencing (scRNA-seq) provides a powerful method to resolve the cellular heterogeneity from gene expression and pathway regulation analysis. However, the scarcity of CTCs and the massive contamination of blood cells limit the utility of currently available technologies. Here, we present Hydro-Seq, a scalable hydrodynamic scRNA-seq barcoding technique, for high-throughput CTC analysis. High cell-capture efficiency and contamination removal capability of Hydro-Seq enables successful scRNA-seq of 666 CTCs from 21 breast cancer patient samples at high throughput. We identify breast cancer drug targets for hormone and targeted therapies and tracked individual cells that express markers of cancer stem cells (CSCs) as well as of epithelial/mesenchymal cell state transitions. Transcriptome analysis of these cells provides insights into monitoring target therapeutics and processes underlying tumor metastasis.

Original languageEnglish
Article number2163
JournalNature communications
Issue number1
Publication statusPublished - 2019 Dec 1

Bibliographical note

Funding Information:
This work was supported in part by grants R35 CA 129765 from the NIH and from the Breast Cancer Research Foundation to M.S.W and in part by University of Michigan Coulter Translational Research Partnership Program, and in part by the grants R01 CA 203810 and R21 CA 195016 from NIH to E.Y. The support of Y.-C.C. from Forbes Institute for Cancer Discovery and the support of M.B. from FFANY (Fashion Footwear Charitable Foundation of New York/QVC Presents Shoes on Sale ™) are acknowledged. We thank the Lurie Nanofabrication Facility of the University of Michigan (Ann Arbor, MI) for device fabrication.

Publisher Copyright:
© 2019, The Author(s).

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • General
  • Physics and Astronomy(all)


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