MyCTC chip: microfluidic-based drug screen with patient-derived tumour cells from liquid biopsies

Abstract

Cancer patients with advanced disease are characterized by intrinsic challenges in predicting drug response patterns, often leading to ineffective treatment. Current clinical practice for treatment decision-making is commonly based on primary or secondary tumour biopsies, yet when disease progression accelerates, tissue biopsies are not performed on a regular basis. It is in this context that liquid biopsies may offer a unique window to uncover key vulnerabilities, providing valuable information about previously underappreciated treatment opportunities. Here, we present MyCTC chip, a novel microfluidic device enabling the isolation, culture and drug susceptibility testing of cancer cells derived from liquid biopsies. Cancer cell capture is achieved through a label-free, antigen-agnostic enrichment method, and it is followed by cultivation in dedicated conditions, allowing on-chip expansion of captured cells. Upon growth, cancer cells are then transferred to drug screen chambers located within the same device, where multiple compounds can be tested simultaneously. We demonstrate MyCTC chip performance by means of spike-in experiments with patient-derived breast circulating tumour cells, enabling >95% capture rates, as well as prospective processing of blood from breast cancer patients and ascites fluid from patients with ovarian, tubal and endometrial cancer, where sensitivity to specific chemotherapeutic agents was identified. Together, we provide evidence that MyCTC chip may be used to identify personalized drug response patterns in patients with advanced metastatic disease and with limited treatment opportunities.

Keywords: Engineering; Materials science.

Fig. 1

MyCTC chip design. a Design of the MyCTC chip, containing a PDMS layer (top) and COC layer including the microfluidic structures (bottom). b Image showing the MyCTC chip, including a detailed view of the capture and culture section (red) and drug screen chamber (blue). c Focus stacked images showing the capture and culture chamber and drug screen chamber. d Schematic representation of the CTC capture process of the MyCTC chip

Fig. 2

Capture, release and translocation efficiency. a Fluidic dynamic simulation showing the distribution of shear rates (left) and pressure drop (right) within the culture and capture section at a constant flow rate of 50 µL min⁻¹. The viscosity of blood was set to 1–3 mPa∙s. b Size distribution of CTC-derived cell lines BR16, Brx50 and Brx07. Violin plots show the 25th, 50th and 75th percentiles. c Representation of the experimental design (left). Dot plots show the capture efficiency of single CTCs and CTC clusters from GFP- or RFP-tagged BR16, Brx50 and Brx07 cells spiked in healthy donor blood (right); n = 5 for BR16 and Brx50, n = 4 for Brx07; error bars represent s.e.m. d Representative brightfield and fluorescence images of single CTCs and homotypic and heterotypic CTC clusters isolated from the peripheral blood of a metastatic breast cancer patient using a MyCTC chip. Captured cells were stained with anti-EpCAM/EGFR/HER2 (green) and CD45 (red) antibodies. e Pie chart showing the percentages of single CTCs and homotypic and heterotypic CTC clusters isolated in d. f Representation of the experimental design (left). Dot plot showing the release efficiency from captured single and clustered CTCs of GFP- or RFP-tagged BR16, Brx50 and Brx07 cells (right); n = 5; error bars represent s.e.m. g A representation of the experimental design (left). Bar plot showing translocation efficiency from captured single and clustered CTCs of GFP- or RFP-tagged BR16, Brx50 and Brx07 cells into the six drug screening chambers (right); n = 3; error bars represent s.e.m

Fig. 3

MyCTC chip culture and drug screening. a Brightfield and fluorescence images at different time points (days 0, 7, 14, 21) showing the growth of the GFP-tagged Brx50 CTC line inside the culture chamber of the MyCTC chip. b Heatmap representing the average relative survival rate (n = 2) of Brx50 cells at the endpoint measurement after two days of chemotherapeutic agent (I–VI) treatment. c Schematic representation of the workflow for patient-derived ascites fluid processing with the MyCTC chip. Red squares (d, e) represent the position on the chip that was used for imaging cell growth shown in d, e. d Representative brightfield and immunofluorescence images of captured patient-derived ascites fluid cancer cells in the capture and culture chamber stained for EpCAM/EGFR/HER2 (green) and CD45 (red). e Representative brightfield images of patient-derived ascites fluid cells in the drug screen chambers at different time points after translocation (days 1, 2, 4). Red arrows indicate the imaging reference point. f Representative images showing the bioluminescence signal of the drug screen chambers containing cancer cells from patient-derived ascites fluid samples (Table S1; Patient four) treated with (VI) carboplatin, (V) gemcitabine, (IV) capecitabine, (III) topotecan, (II) navelbine and (I) DMSO control before (day 0) and 2 days after drug treatment. Bioluminescence levels indicate the viability of cancer cells from patient-derived ascites fluid samples. g Heatmap representing the average relative survival rate (n = 2) of cancer cells from patient-derived ascites fluid at the endpoint measurement