Prolonged hybridization with a cRNA probe improves the signal to noise ratio for in-tube in situ hybridization for quantification of mRNA after fluorescence-activated cell sorting

In tube immunocytochemistry for fluorescence-activated cell sorting that prevents RNA degradation in sorted cells

Fluorescence-activated cell sorting (FACS) is a powerful tool for analyzing stem cells. When using fixed cells, however, it is sometimes difficult to analyze RNA extracted from sorted cells due to RNA degradation. We established a protocol for immunocytochemistry before FACS to prevent RNA degradation. Cells were fixed with a methanol-based fixative (UM-Fix), then subjected to immunocytochemistry. The addition of RNase inhibitor and dithiothreitol (DTT) to some buffers used for immunocytochemistry increased RNA integrity after cell recovery. We found increased copy numbers of mRNA in recovered cells using quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis. When RNase inhibitor and DTT were added, amplification of mRNA using T7 promoter was possible with RNA extracted from recovered cells after FACS. Our protocol ensures high quality RNA in cells recovered by FACS; therefore, gene expression analysis with a smaller number of cells is possible using pre-amplification of mRNAs. Our protocol for immunocytochemistry also might be applicable to RNA recovery after immunostaining.

An improved protocol for mRNA quantification after fluorescence-activated cell sorting with an increased signal to noise ratio in flow cytometry

We established a method to analyze cells collected by fluorescence-activated cell sorting (FACS) named mRNA quantification after FACS (FACS-mQ), in which cells are labeled with a fluorescent dye in a manner that minimizes RNA degradation, and then cells sorted by FACS are examined by analyzing their gene expression profile. In this study, we established a modified protocol to analyze molecules with a low expression level, such as N-cadherin and thyroid transcription factor, by improving the signal to noise ratio in flow cytometry. Use of a fluorophore-conjugated second antibody and the appropriate choice of a fluorescence dye showed a marked increase in the signal to noise ratio. Use of the Can Get Signal Immunostain in diluting antibodies shortened the reaction time. In real-time reverse transcription-PCR, a significant decrease in the copy number of intracellular mRNAs was not observed after in-tube immunostaining. These results indicated that the present protocol is useful for separating and analyzing cells by FACS-mQ, targeting a molecule with a low expression level.

Preparation of thyroid follicular cells for mRNA quantification after fluorescence-activated cell sorting

We established a novel method to analyze cells collected by fluorescence-activated cell sorting (FACS) named mRNA quantification after FACS (FACS-mQ) in which cells are labeled with a fluorescence dye in a manner that minimizes RNA degradation, and then cells sorted by FACS are examined by analyzing their gene expression profile. In order to analyze cells using FACS-mQ, it is essential to prepare single-cell suspensions without RNA degradation. We found that a new tissue preservation medium, ThelioKeep™, which contains epigallocatechin-3-gallate (EGCG), was suitable for preservation of thyroid tissues. The aim of this study was to establish a cell dispersion method of thyroid follicular cells using ThelioKeep™. We compared the efficiency of cell dispersion between the two methods, the conventional cold pre-incubation method and the ThelioKeep™ method; then we determined if cells obtained by the ThelioKeep™ method were suitable for FACS-mQ analysis. We found that a larger number of cells were recovered using ThelioKeep™ than using the conventional cold pre-incubation method. Furthermore, cell viability was higher with the ThelioKeep™ method than with the cold pre-incubation method. Thyroid cells collected by this method were analyzed by FACS-mQ. A clear shift in flow cytometry analysis was observed when cells were stained with an anti-thyroglobulin or anti-thyroid transcription factor-1 antibody. After sorting, the same copy number of ACTB mRNA was detected in thyroid cells as in an anaplastic carcinoma cell line, 8305C. These findings imply that preparation of thyroid cells using the present method is suitable for FACS-mQ analysis.