IGF::OT::IGF Developing Novel Tools for Site-Specific Quantitative Analysis of RNA ModificationsPeriod Performance: September 19, 2017 through June 16, 2018

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Although recent developments in highly sensitive technologies have revolutionized research on RNA modifications, the available quantitative methods can be further improved. Current methods include liquid chromatography-tandem mass spectroscopy (LC-MS/MS) and next-generation sequencing coupled with modification-specific antibodies. The LC-MS/MS method is not accessible to many researcher scientists due to its high cost and specialization. Deep sequencing is only useful for research on specific RNA modifications if high quality antibodies are commercially available. We found there are at least a dozen RNA modifications that are not commercially available, but have been suggested to be related to cancer, suggesting a gap in the antibody market. Furthermore, though antibody pull-down followed by RT-qPCR can be used to evaluate the modification of a specific RNA, this method is not site-specific, and will not work well when there are multiple modification sites in one targeted RNA. There is a need for a simpler method to quantitatively analyze site-specific RNA modifications beyond the current options available. Here, we propose to 1) fill the gap in next-generation sequencing approach by developing high-affinity antibodies for cancer-related modifications with no commercially available antibodies, and 2) develop simpler alternative methods for the site-specific quantification of RNA modifications using Mediomics’ PINCER technology.