Messenger RNA in the crosshairs – The Nano Argovia project “ecamist” aims to improve single-cell analysis

Cells are separated in single droplets of a water in oil emulsion. Afterwards, the cell are lysated and the mRNA is purified (Image: Georg Lipps, FHNW)

The aim of the Nano Argovia project “ecamist” is to develop an effective method for working up messenger RNA from single cells. A team of scientists from the School of Life Sciences at the University of Applied Sciences Northwestern Switzerland (FHNW), the Department of Biosystems Science and Engineering at the Federal Institute of Technology (ETH) Zurich in Basel (D-BSSE), and the company Memo Therapeutics AG (Basel) wants to improve the yield and quality of isolated messenger RNA compared with existing methods. Among other applications, the information about the messenger RNA present in a cell can be used to derive conclusions about the development of diseases. It is also important for studying cell lines used in antibody production, for example.

Analysis of individual cells
Nowadays, messenger RNA (mRNA) is often analyzed to determine which genes are active in cells. Inside a cell, the mRNA acts as a mediator between the hereditary information stored in the DNA and the ribosomal RNA, which is needed for protein synthesis in cell ribosomes. When examining various research questions, scientists now increasingly opt to analyze the mRNA in single cells instead of analyzing mixtures of an entire cell culture. Single-cell analysis is particularly useful for understanding the development of diseases, as defective processes often begin in individual cells.

Bound to tiny beads
In the Nano Argovia project “ecamist”, the team led by Professor Dr. Georg Lipps from the FHNW is developing a new method that is intended to make the workup of mRNA from single cells more effective. Before a cell’s mRNA can be analyzed, it must first be separated from the cell lysate and preserved. Until now, this has been done using tiny microbeads fitted with a short segment of DNA, which binds to the mRNA in order to separate it from the lysate. This binding, known as hybridization, is based on purely physical processes and produces an equilibrium between hybridized and free binding sites on the microbeads. However, the free mRNA segments still present in the lysate contaminate the sample in the subsequent steps.

Enzyme selection is crucial
The researchers led by Professor Georg Lipps and Dr. Martin Held from the Department of Biosystems Science and Engineering (D-BSSE) therefore want to immobilize the hybridized mRNA segments by establishing a covalent, more thermally stable bond to the microbeads’ surface. They hope that this will lead to a greater yield of bound mRNA on the microbeads, as well as fewer impurities and therefore a higher-quality mRNA yield. The project hinges on selecting a suitable enzyme that catalyzes the formation of covalent bonds to the microbeads and that works reliably even in high salt and detergent concentrations, as these conditions are necessary for lysing the cells. “For Memo Therapeutics, the Nano Argovia project is a good opportunity to extend single-cell analytics with additional protocols and hence to further expand our activities in the area of antibody development,” says Dr. Simone Schmitt, Senior Scientist at Memo Therapeutics and an industrial partner within the Nano Argovia project “ecamist”.