New RNA archive lets scientists replay a cell's past days

Researchers at ETH Zurich have built an RNA archive that works inside living cells, storing copies of RNA molecules so scientists can reconstruct which genes were active days earlier rather than only at the moment of measurement. The work, from the university's Department of Biosystems Science and Engineering in Basel, was published in the journal Nature Biotechnology, according to ETH Zurich.

Gene activity is normally read by measuring RNA, the transcripts produced when genes switch on. That measurement gives only a snapshot of the cell at a given instant, and the cell is destroyed in the process, so each cell can be examined just once. Short-lived responses, such as the flare of immune or stress genes after a stimulus, can vanish before a researcher looks, leaving no trace that they happened at all.

That blind spot matters because gene activity is among the clearest windows into how cells and the body work. When a cell meets an infection, a drug, or another outside signal, specific genes switch on and then switch off again once the signal passes. Standard single-cell methods capture whatever is active at the time of sampling and nothing from before, which means brief responses are easy to miss entirely.

Christopher Reinkemeier, a postdoc in the group led by ETH professor Randall Platt, said the glimpse into the past is of interest because it reveals a cell's short-lived responses, of which there are many, with immune and stress responses among the examples. In the study, the researchers in Basel showed how human cells in a cell culture respond to a signaling molecule of the immune system. "If you measure too late with the conventional method, you no longer see that the response has even taken place," said Marcos Manero Carranza, a doctoral student in Platt's group and first author of the study alongside Reinkemeier.

How the archive protects RNA

RNA molecules are not built to last, so the team had to capture them and shield them from the enzymes that normally break them down. Their solution draws on a protein found in stress granules, the accumulations of RNA that form when a cell is under stress, for example during an infection, when the cell temporarily shuts down parts of its metabolism and saves RNA molecules for later. The researchers combined that protein with two more engineered proteins to form a system that gathers a cell's RNA molecules into a film around its mitochondria, where degrading enzymes cannot reach them.

The blueprints for the proteins are delivered into cells on plasmids, and the cells then assemble the archiving system themselves. Per cell, the system can store several thousand RNA molecules across multiple days, the researchers reported. The approach is called Recordanelles, and the full study appears in Nature Biotechnology.

Why cancer researchers are paying attention

The method could help detect rare events in cells that only become interesting in hindsight. When researchers learn later which cells matter, they can pick those cells out and read the stored RNA to investigate which genes had been active within them earlier. The researchers have applied for a patent on the technology, according to the university, and want to develop it further with a view to future applications in animals and cancer research.

A possible application is tumour cells that survive a course of chemotherapy and later contribute to a cancer's recurrence. At present, it is very difficult to investigate which cells will survive treatment and how they previously developed. Reinkemeier said which cells will develop into these persister cells "is something that is not known in advance and is poorly understood," and that the system could let researchers isolate persister cells and look into their past, which could help research into how these cells form and develop.

So far the method has been shown in human cells grown in culture. The team now plans to develop it for animal studies and cancer research, where reading a cell's history could show why some cells survive treatment while others do not.