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A microfluidic multiwell chip for enzyme-free detection of mRNA from few cells

Haider, Michaela, Ji, Bozhi, Haselgrübler, Thomas, Sonnleitner, Alois, Aberger, Fritz, Hesse, Jan
Biosensors & bioelectronics 2016 v.86 pp. 20-26
nucleic acid hybridization, messenger RNA, gene overexpression, complementary DNA, pancreatic neoplasms, light microscopy, stem cells, reverse transcription, genes, gene expression regulation, biosensors
Isogenic cell populations possess heterogeneous gene expression patterns. Most methods for mRNA expression analysis start with the reverse transcription of mRNA into cDNA, a process that can introduce strong signal variations not related to the actual mRNA levels. Miniaturized lab-on-a-chip systems offer properties – e.g. low sample dilution, low contamination – that enable new reaction schemes for molecular analyses. To enable transcription-free mRNA expression analysis of few single cells, a one-step cell lysis, target labelling and hybridisation approach as well as a corresponding passive multiwell chip with a volume of 25.5 nL/well were developed. The method enabled the parallel analysis of up to 96 samples and 6 target genes per sample. Preceding light microscopy of the living cells allowed correlating mRNA levels and cell number. As a proof-of-principle, the pancreatic cancer cell line Panc-1 was investigated for expression heterogeneity of a reference gene plus 5 genes reported to be overexpressed in cancer stem cells (CSCs). A good correlation (r(51)=0.739, p<0.001; rs(51)=0.744, p<0.001) between the cell number per well and the number of detected reference gene mRNA confirmed the proper function of the device. Moreover, a heterogeneous expression of the CSC-associated target genes was found which matched well with reports on the presence of CSCs in the Panc-1 cell line.