Comprehensive profiling and evaluation of the alteration of RNA modifications in thyroid carcinoma by liquid chromatography-tandem mass spectrometry

RNA molecules contain diverse modifications that display important functions in a variety of physiological and pathological processes. So far over 150 chemical modifications have been characterized to be present in various RNA species, such as in messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Previous studies revealed that certain RNA modifications were correlated to specific human diseases, indicating RNA modifications could serve as the potential indicator of human diseases. However, systemic investigation of the alteration of RNA modifications in different RNA species of carcinoma tissues are still lacked. Herein, we carried out the comprehensive profiling and evaluation of the alteration of RNA modifications in thyroid carcinoma by liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS) analysis. The developed method allowed us to simultaneously detect 48 different types of RNA modifications. Using this method, we detected 10, 15, 14, and 25 modifications in mRNA, 18S rRNA, 28S rRNA and small RNA (< 200 nt), respectively. Compared to the normal tissues, we revealed a total of 14 RNA modification exhibited significant increase and 2 RNA modifications showed significant decrease in thyroid carcinoma tissues. Our study provided the first comprehensive profile as well as the alteration of modifications in different RNA species in thyroid carcinoma and matched tumor-adjacent normal tissues. The altered pattern RNA modifications may serve as the indicator of thyroid carcinoma. Moreover, this study may promote the in-depth understanding of the regulatory roles of RNA modifications in thyroid carcinoma.