Gene

Metastasis

Liquid biopsy

Ecology

Biology

Massive parallel sequencing

Telecommunications

Cancer research

Computer science

DNA sequencing

Computational biology

Genetics

Exome sequencing

Transcriptome

Contamination

RNA-Seq

Circulating tumor cell

Single cell sequencing

Cell

Wireless

Throughput

Single-cell analysis

Breast cancer

Cancer

Gene expression

Cancer cell

Phenotype

Nature Communications

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.

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