A new study, published in the March 9 issue of Science , reveals that by engineering cells to express a modified RNA called “Spinach”, researchers from the Weill Cornell Medical College have advanced in reproducing small-molecule metabolites, i.e. intermediates and products of individual cell metabolism in living cells and observed that metabolite levels changed with time.
The discovery of measuring a metabolite’s production rate is likely to transform scientists’ understanding of the metabolome and could prove beneficial in identifying whether a cell is metabolically dysfunctional like in cancer, or to help develop drugs that can restore a normal function in metabolites. A metabolome consists of thousands of metabolites that provide chemical fingerprints of dynamic activity within cells.
Dr. Samie R. Jaffrey, an associate professor of pharmacology at Weill Cornell Medical College explains:
“The ability to see metabolites in action will offer us new and powerful clues into how they are altered in disease and help us find treatments that can restore their levels to normal.”
Study leader, Dr. Jaffrey says:
“Metabolite levels in cells control so many aspects of their function, and because of this, they provide a powerful snapshot of what is going on inside a cell at a particular time.”
The fact that cancer cells have an abnormal metabolism is well known amongst biologists. The abnormal cells produce a distinct metabolic profile by changing their use of glucose for energy and produce a unique breakdown product like lactic acid. Dr. Jaffrey explains:
“The ability to see these metabolic abnormalities can tell you how the cancer might develop. But up until now, measuring metabolites has been very difficult in living cells.”
Dr. Jaffrey, and his colleagues proved that by using specific RNA sequences metabolite levels in cells could be sensed. These RNAs are fundamentally the same as the Spinach RNA that emits a green fluorescent glow in cells. The researchers modified Spinach RNAs so that they turn off until they come across the metabolite they are specifically designed to bind to, which causes the fluorescence of Spinach to be switched on.
They subsequently developed RNA sequences to trace five different cell metabolite levels; the cell’s energy molecule, the product of ATP, ADP and SAM or S-Adenosyl methionine which plays a role in methylation that controls gene activity. Jaffrey comments:
“Before this, no one has been able to watch how the levels of these metabolites change in real time in cells.”
Researchers can now measure levels of a specific metabolite in a single cell as it changes in real time by delivering the RNA into living cells. Dr. Jaffrey says:
“You could see how these levels change dynamically in response to signaling pathways or genetic changes. And you can screen drugs that normalize those genetic abnormalities. A major goal is to identify drugs that normalize cellular metabolism.”
This approach is preferable compared to the prevailing method of sensing molecules in living cells by using green fluorescent protein (GFP), as there are no obstacles to overcome. Even though researchers can use GFP and other proteins to sense metabolites if these are fused to naturally occurring proteins that bind the metabolite, however, in some instances, metabolite binding is able to twist the proteins in such a way that their fluorescence is impacted. Furthermore, for most metabolites there are no proteins available that can be fused to GFP to make sensors.
This obstacle can be tackled by using RNAs as metabolite sensors. Jaffrey explains: “The amazing thing about RNA is that you can make RNA sequences that bind to essentially any small molecule you want. They can be made in a couple of weeks.” Once produced, these artificial sequences are then fused to Spinach and expressed as a single strand of RNA in cells.
Jaffrey continues: “This approach would potentially allow you to take any small molecule metabolite you want to study and see it inside cells.” The team has expanded the technology to identify proteins and other molecules inside living cells.
Jaffrey indicates that scientists can gain a better knowledge of human biology by using this technology for numerous diseases and concludes:
“We are very interested in seeing how metabolic changes within brain neurons contribute to developmental disorders such as autism. There are a lot of opportunities, as far as this new tool is concerned.”
Written by Petra Rattue