A DNA-peptide probe coupled mass spectrometry-based method for the detection of LncRNA in hepatocyte and serum samples

Abstract

Liver cancer, a prominent contributor to cancer-related deaths, necessitates timely identification for successful intervention. In recent years, long non-coding RNAs (lncRNAs) have gained attention as potential biomarkers for liver cancer, and accurate quantification of lncRNA is essential for early diagnosis of liver cancer. However, existing methods for lncRNA detection rely on amplification and labeling techniques, resulting in semi-quantitative or qualitative outcomes. DNA-peptide technology offers a promising alternative. It has successfully translated nucleic acid quantification into peptide quantification, particularly in the context of miRNA analysis. However, the intricate structure of long-chain lncRNAs presents a challenge not encountered with miRNAs, making the design and acquisition of specific DNA-peptide probes for direct quantification more difficult. In this study, a strategy for lncRNA quantification was developed using a DNA-peptide probe coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based quasi-targeted proteomics. The inherent structural complexity of long-chain lncRNAs was overcome by designing DNA-peptide probes based on their unique sequence segments, enabling direct quantification without the need for amplification. Highly upregulated in liver cancer (HULC) was identified as a target lncRNA through bioinformatics analysis using GEO2R online software. Subsequently, the target lncRNA (i.e., HULC), which had been biotinylated and bound to streptavidin agarose beforehand, was hybridized with the probe. Following trypsin digestion, the reporter peptide was released and quantified using LC-MS/MS. Finally, this method was applied to analyze HULC levels in liver cancer cell lines and serum samples, enabling quantitative assessment and early diagnosis. The results demonstrated that liver cancer diagnostics could be enhanced through the integration of mass spectrometry and DNA-peptide probe technology for lncRNA quantification.