Scripps Research has unveiled a new software tool for studying RNA (ribonucleic acid) molecules, which has a host of critical applications in organisms. Pytheas, an open-source app developed by Nature Communications, has speeded up the process of characterizing and quantifying RNAs in basic research and drug development areas.
RNA molecules that are not simple chains of standard RNA nucleotides but rather modified in some way are identified and quantified. Pytheas can be used in order to swiftly identify and quantify modified RNA molecules like those used in the current Pfizer and Moderna COVID-19 vaccinations.
According to the study senior author, "We want Pytheas to bring the field to the 21st century" because to the lack of the tools previously used in other areas of biological research.
During the study, Luigi DAscenzo and Anna Popova were both a postdoctoral research associate and staff scientist.
RNA is very similar to DNA, and RNA molecules in cells are important in the process of translating genes into proteins as well as in fine-tuning gene activity. Moreover, RNA-based therapies, including the Pfizer and Moderna vaccines, are viewed as a highly promising new class of medicines, capable in principle of reaching their biological targets more powerful and selectively than traditional small-molecule medicines.
Mass spectrometry, which is usually used to recognize RNAs and their modifications based on their masses, is a common technique for tracking natural RNA molecules, which is often required for vaccinations and RNA-based drugs to perform artificially, to optimize their activity and reduce side effects. Up until now, methods for processing raw mass spectrometry data on modified RNAs have been relatively slow and manualthus, which is quite labor-intensive in contrast to previous methods in protein analysis.
Pytheas, which is based on the Python programming language, has helped Williamson and his team develop it, allowing for mass spec data on an RNA sample to be incorporated as the input, and allows for identification of specific RNA sequences and chemical modifications, in a manner that is also easy to quantify.
Pytheas'' speed, reliability, and versatility were demonstrated by mass spec data for important bacterial and yeast RNAs, as well as for SARS-CoV-2 spike protein messenger-RNAs, similar to those used in the Pfizer and Moderna COVID-19 vaccines.
Williamson cautions that companies involved in manufacturing RNA vaccinations and other RNA therapeutics will find Pytheas very helpful in monitoring their products.
Researchers are now using Pytheas in their natural RNA research, and they are continuing to improve the software.
Pytheas is freely available on the Github software repository.