19-Aug-2022 - Eidgenössische Technische Hochschule Zürich (ETH Zürich)

Monitoring gene activities in living cells

Cell Biopsy instead of cell lysis

Researchers from ETH Zurich and EPFL are expanding the emerging field of single-​cell analysis with a ground-​breaking method: Live-​seq makes it possible to measure the activity of thousands of genes in a single cell without having to isolate and destroy it.

Modern biology is increasingly seeking to understand why individual cells behave differently. Various highly sensitive measurement methods have been available in basic research for a few years that allow specific analysis of single cells. This single-​cell analysis enables researchers to detect differences between cells in a group, find rare cell types and identify diseased cells – which is not possible with samples from mixed cell populations.

Scientists increasingly want to find out which genes in a specific cell are turned on or off. This can be examined by using single-​cell RNA sequencing (scRNA-​seq). As many messenger RNA molecules in the cell fluid as possible are decoded and matched with their respective active gene sequences. In this way, scRNA-​seq can measure the activity of thousands of genes in a cell.

The new field of scRNA-​seq has quickly grown into an important tool in biomedical research and today comprises numerous techniques for analysis of the entire messenger RNA, known as the transcriptome. "All these techniques have one limitation in common that was long considered unavoidable," says Julia Vorholt, Professor of Microbiology at ETH Zurich, "namely, that the cells to be studied have to be isolated and lysed – and thus killed."

Cell Biopsy instead of cell lysis

A team of researchers led by Vorholt and EPFL Professor of Systems Biology Bart Deplancke has now come up with an alternative to scRNA-​seq: the team is also analysing the transcriptome, but in a minimally invasive manner by cellular biopsy, thus keeping the cell alive and functionally intact – which is unique. The scientists have presented their "Live-​seq" technique in the journal Nature.

According to the researchers, the fact that the cell under analysis does not die is an advantage in itself: "Our strength is that we can continue to observe the sampled cells under the microscope to see how they develop and behave," Vorholt explains.

In addition, Live-​seq leaves the cells in their physiological context. "The micro-​environment and cell-​cell interactions remain intact," says Orane Guillaume-​Gentil, a postdoc in Vorholt's group. Together with Wanze Chen from EPFL, she developed the method in the laboratory.

Based on a cell suction microsystem

The researchers laid the groundwork for recording the transcriptome of living cells some time ago at ETH Zurich. The basis is the FluidFM micro-​injection system developed at ETH Zurich, which can manipulate minuscule quantities of fluid under a microscope. Vorholt and her group turned the "smallest injection needle in the world" into a cell extraction method in order to prick individual living cells with the micro-​injection needle and extract their content (see ETH News article).

The teams led by Vorholt and Deplancke are now showing that the full transcriptome can be recorded from such cell biopsies. The decisive breakthrough happened when the researchers succeeded in reading RNA out of these tiny quantities of cell fluid.

To validate Live-​seq, the EPFL-​ETH research team demonstrated that their analytical tool can accurately identify different cell types and cell states without disturbing them. The researchers also used their platform to directly map the changes in individual immune cells before and after they became active and in adipose stromal cells – a type of stem cell – before and after they differentiated into fat cells.

Tracking gene activity over time

Live-​seq can now help investigate new biomedical questions. Deplancke explains in more detail: "For example, why certain cells differentiate and their sister cells don't, or why certain cells are resistant to a cancer medication and their sister cells aren't."

Live-​seq is able to track the activity of thousands of genes in a single cell over time through repeated measurements. "Single-​cell analysis is transforming from a single endpoint into a temporal and spatial analytical method," says Vorholt.

Eidgenössische Technische Hochschule Zürich (ETH Zürich)

Recommend news PDF version / Print

Share on

Facts, background information, dossiers
  • single cell analysis
  • cells
  • cell analysis
  • RNA sequencing
  • transcriptome analysis
  • transcriptome
  • gene activity
More about ETH Zürich
  • News

    Where do toxins from tobacco attack DNA?

    It is known that toxins in tobacco smoke can change our DNA – but where exactly in the genome they do this has been a mystery. A new approach developed by researchers at ETH Zurich now brings light into the darkness. In the future, this could make it easier than ever to determine the safety ... more

    Hydrogen peroxide as a target in the fight against cancer?

    Reactive oxygen species (ROS) are reputed for their involvement in carcinogenesis. Results from a study published in the journal Angewandte Chemie have now shown that the level of one such ROS, hydrogen peroxide, is significantly higher in pancreatic cancer cells, unlike the level of other ... more

    Hope for patients with a severe rare disease

    New research offers potential benefits for those affected by the hereditary metabolic disease methylmalonic aciduria. By combining the results of multiple molecular analyses, scientists can better diagnose this rare and severe disease. In the future, an improved understanding of the disease ... more

More about Ecole Polytechnique Fédérale de Lausanne
  • News

    Tracking chirality in real time

    Scientists at EPFL have developed a new laser-based technique that can measure ultrafast changes in the structural symmetry of molecules, called chirality, tracking their conformational shifts in real time. In a collaboration with researchers from the Universities of Geneva and Pisa, the br ... more

    Molecular device turns infrared into visible light

    Light is an electromagnetic wave: it consists of oscillating electric and magnetic fields propagating through space. Every wave is characterized by its frequency, which refers to the number of oscillations per second, measured in Hertz (Hz). Our eyes can detect frequencies between 400 and 7 ... more

    Carbyne – an unusual form of carbon

    Which photophysical properties does carbyne have? This was the subject of research carried out by scientists at FAU, the University of Alberta, Canada, and the Ecole Polytechnique Fédérale de Lausanne in Switzerland, which has led to a greater understanding of the properties of this unusual ... more

  • Videos

    The Gates of Serotonin

    EPFL scientists have elucidated for the first time how a notoriously elusive serotonin receptor functions with atom-level detail. The receptor transmits electrical signals in neurons and is involved in various disorders, meaning that the discovery opens the way for new treatments. The recep ... more