Molecular Archive Lets Scientists Look Back at Past Gene Activity in Cells

Researchers can usually measure only what a cell is doing right now. What it was doing hours or days earlier stays out of view. That limitation makes it harder to understand how immune responses develop or why certain cancer cells survive treatment.

Knowing which genes in a cell are active gives scientists important clues about how cells and the body function. To get this information, they measure RNA molecules, which are transcripts of active genes, but each measurement captures only a single moment. Collecting the RNA also destroys the cell, so each cell can be measured only once.

A team from ETH Zurich in Basel has now developed a way to archive RNA molecules inside cells. For the first time, this makes it possible to see a cell’s present state and also reconstruct which of its genes were active earlier.

“Among other reasons, this glimpse into the past is of interest because it tells you about a cell’s short-lived responses—of which there are many. Immune and stress responses are just a few examples,” explains Christopher Reinkemeier, co-first authof of the study published in Nature Biotechnology. In such responses, an outside stimulus switches on particular genes, and the cell turns them off again once the stimulus is gone.

In one study, the team showed how cultured human cells react to an immune system signaling molecule. “If you measure too late with the conventional method, you no longer see that the response has even taken place,” says Marcos Manero Carranza, co-first author of the study with Reinkemeier.

Building the archive meant capturing RNA molecules, which normally don’t last long, and protecting them from natural breakdown. One component is a protein found naturally in stress granules. These are clusters of RNA that cells form under stress, such as during an infection, when they temporarily shut down parts of their metabolism and save RNA for later.

The researchers optimized this protein and two others. The resulting system gathers a cell’s RNA into a film around its mitochondria, where the molecules are shielded from the cell’s own RNA-degrading enzymes. Plasmids deliver the blueprints for the three proteins, and the cells then assemble the archiving system themselves. Each cell can store several thousand RNA molecules over several days.

The method can capture rare events, which is especially helpful when researchers only learn later which cells interest them. They can then select those cells and use the archive to see which genes had been active. 

The team has applied for a patent and plans to develop the technology further for future use in animals and in cancer research. One possible use involves tumor cells that survive chemotherapy and can later contribute to a cancer’s recurrence. At present, it is very difficult to study which cells will survive treatment and how they developed beforehand. 

“Which cells will develop into these persister cells is something that is not known in advance and is poorly understood,” says Reinkemeier. “If we can put our system to use in cancer research, we’ll be able to isolate persister cells and look into their past. This will allow us to research how these cells form and develop and could pave the way for decisive advances in cancer research.”