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Table 3 Microfluidics technologies for CTCs isolation and single cell sequencing

From: Microfluidics applications for high-throughput single cell sequencing

Sample type

Microfluidics device

Markers

Capture (%)

Sequencing technique

Key findings

Refs.

Breast cancer

Single-cell RNA sequencing (SCR-Chip)

EpCAM

93

SMART-Seq II

The sequencing data showed significant genetic differences between tumor cells and white blood cells. Tumor cells maintained a high consistency in the RNA panel, while there were large variations in WBC genes panel, which might be due to the presence of different subtypes in WBCs

[157]

Pancreatic cancer

CTC-iChip

CK

CD45

95

ABI 5500XL

CTCs clustered separately from primary tumors and tumor-derived cell lines, showing enrichment for gene Aldh1a2 and Igfbp5. Pancreatic CTCs exhibit a very high expression of stromal-derived extracellular matrix proteins, including SPARC

[158]

Lung cancer

Deterministic lateral displacement (DLD chip)

CK

CD45

90

Illumina HiSeq

Six new somatic gene mutations in both single CTC and surgical specimen of this patient, namely HIVEP2, SPATA21A, TUBGCP2, KCNG1, MIR4756, and ASMTL

[159]

Breast cancer

ClearCell FX

CD45

CD31

80

Illumina MiSeq

Compared to peripheral blood mononuclear cell (PBMCs), CTCs showed elevated expression of breast cancer-specific markers BRCA1 and MDM2, and a canonical epithelial cell marker CDH1

[160]

Prostate cancer

CTC-iChip

EpCAM

CDH11

CD45

92

RNA-seq

A total of 711 genes were highly expressed in CTCs compared to primary tumors, with the most enriched being the molecular chaperone HSP90AA1 and the non-coding RNA transcript MALAT1

[161]

Ovarian/colorectal/prostate/breast/pancreatic cancer

Sinusoidal microfluidics chip

EpCAM

FAPα

80

Illumina HiSeq

KRAS mutational status in CTCs has been shown a high concordance with the primary tumor (~ 90%). KRAS mutations were detected in CTCFAPα and CTCEpCAM but not always in both CTC subpopulations

[162]

Lung cancer

Microfluidic chip with micropore arrayed filtration membrane

CK

CD45

85

Illumina HiSeq X

Four common mutation sites were found between tissue and ctDNA samples before treatment, including CREBBP, ROS1, TP53 and EGFR. Moreover, oncogene HRAS mutated both in single CTC sample and ctDNA sample after treatment, rather than samples before treatment

[163]

Breast cancer

ClearCell FX

CK

CD45

32.31

Single-cell whole-exome sequencing (WES)

There were a few hundreds of somatic mutations in the three CTCs, with only 16 overlapping mutations. Significantly mutated genes in pan-cancer BRCA1 and EPHA3 were found in CTC-1, and mutations in FGFR2 and ATM were found in CTC-3, indicating genomic heterogeneity among the CTCs

[164]

Prostate cancer

CTC-iChip

CD45

CD16

CD66b

93.8

Illumina NextSeq 500

No significant differences were evident between fresh and preserved blood for any of the 40 genes except for KRT18. Select genes in certain patients showed a trend toward increased expression

[165]

Prostate cancer

Celsee PREP100

CK

CD45

79

Sanger sequencing

The p.K139fs*3 deletion of TP53 and p.T877A mutation of AR could be detected in the captured PC3 and LNCaP cells, respectively

[166]