Quantitative Label‐Free Surface‐Enhanced Raman Spectroscopic Transcriptome‐Wide Profiling of RNA Adenosine Methylation

Abstract RNA N 6 ‐methyladenosine (m 6 A) modification plays critical roles in diverse biological processes and human diseases, but its functional studies are greatly impeded by the inability to quantify the m 6 A methylation in whole‐transcriptomes. Here, An integrated label‐free surface‐enhanced Raman spectroscopy (SERS) profiling strategy, named m 6 A‐SERS‐profiler, is developed for quantitative transcriptome‐wide m 6 A detection of cellular and serum RNA. The m 6 A‐SERS‐profiler is rationally designed through coupling the plasmonic liquid microparticle‐based label‐free SERS biosensing with the custom deep learning‐assisted spectral analysis of m 6 A methylation signatures. With this m 6 A‐SERS‐profiler, direct identification of SERS spectral signatures of canonical nucleoside monophosphates and N 6 ‐methyladenosine 5′‐monophosphate is achieved. The applicability of the m 6 A‐SERS‐profiler is verified by quantifying the m 6 A methylation status of microRNA and natural RNA in total RNA isolated from cancer cells and clinical serums. The results reveal a significant difference in the m 6 A RNA methylation among breast cancer cells of different subtypes and between clinical serums from healthy individuals and breast cancer patients. Moreover, the method can quantitatively track the m 6 A dynamics in cancer cells caused by pharmacological inhibition of the m 6 A methyltransferase. Thus, this m 6 A‐SERS‐profiler holds great promise for transcriptome‐wide quantitative detection of m 6 A RNA methylation to investigate biological functions and dynamics of m 6 A methylation in human diseases.