A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome

Wang, Jin; Chew, Bing Liang Alvin; Lai, Yong; Dong, Hansong; Xu, Luang; Liu, Yu; Fu, Xin-Yuan; Zhang, Lin; Shi, Pei–Yong; Lu, Timothy K.; Luo, Dahai; Jaffrey, Samie R.; Dedon, Peter C.

doi:10.1038/s41596-023-00857-0

Cited by 4 publications

(2 citation statements)

References 50 publications

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“…Chu et al reported that PDE1 released m 7 G fully, both in mRNA sequence and in the 5′ cap; contrarily, S1 nuclease released the internal m 7 G with high activity but released m 7 G from the 5′ cap with much lower activity [ 50 ]. Different digestion methods were recommended for studies of 2′- O -methylated ribonucleosides [ 51 ], RNA 5′ caps [ 52 ], et al Besides the base structure, sequence specificity also needs to be considered; for instance, the formation of G-quadruplex (G4) inhibits the cleavage efficiency of nuclease [ 53 , 54 ]. Caution also needs to be used regarding digestion conditions during special modification quantification.…”

Section: Qualitative and Quantitative Analysismentioning

confidence: 99%

Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery

Liu,

Dong,

Shen

et al. 2024

IJMS

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Nucleic acid modifications play important roles in biological activities and disease occurrences, and have been considered as cancer biomarkers. Due to the relatively low amount of nucleic acid modifications in biological samples, it is necessary to develop sensitive and reliable qualitative and quantitative methods to reveal the content of any modifications. In this review, the key processes affecting the qualitative and quantitative analyses are discussed, such as sample digestion, nucleoside extraction, chemical labeling, chromatographic separation, mass spectrometry detection, and data processing. The improvement of the detection sensitivity and specificity of analytical methods based on mass spectrometry makes it possible to study low-abundance modifications and their biological functions. Some typical nucleic acid modifications and their potential as biomarkers are displayed, and efforts to improve diagnostic accuracy are discussed. Future perspectives are raised for this research field.

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Section: Qualitative and Quantitative Analysismentioning

confidence: 99%

Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery

Liu,

Dong,

Shen

et al. 2024

IJMS

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“…Current research on the role of m 5 C methylation in the innate immune pathways of HCC largely relies on RNA methylation sequencing technologies and bioinformatics analysis ( 28 ). Therefore, it is imperative to develop more precise high-throughput detection technologies, such as Nanopore Sequencing ( 91 ), Chemical Labeling Coupled with Mass Spectrometry ( 92 ), Single-Molecule Real-Time Sequencing ( 93 ), and Selective Chemical Labeling Followed by Sequencing ( 94 ), for accurately quantifying and localizing m 5 C methylation. With the ongoing advancements in nanomedicine technology ( 95 , 96 ), we can anticipate the application prospects of nanocarriers in the regulation of immune pathways by m 5 C methylation.…”

Section: Challenges and Prospectsmentioning

confidence: 99%

RNA m5C methylation: a potential modulator of innate immune pathways in hepatocellular carcinoma

Meng,

Jiangtao,

Haisong

et al. 2024

Front. Immunol.

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RNA 5-methylcytosine (m5C) methylation plays a crucial role in hepatocellular carcinoma (HCC). As reported, aberrant m5C methylation is closely associated with the progression, therapeutic efficacy, and prognosis of HCC. The innate immune system functions as the primary defense mechanism in the body against pathogenic infections and tumors since it can activate innate immune pathways through pattern recognition receptors to exert anti-infection and anti-tumor effects. Recently, m5C methylation has been demonstrated to affect the activation of innate immune pathways including TLR, cGAS-STING, and RIG-I pathways by modulating RNA function, unveiling new mechanisms underlying the regulation of innate immune responses by tumor cells. However, research on m5C methylation and its interplay with innate immune pathways is still in its infancy. Therefore, this review details the biological significance of RNA m5C methylation in HCC and discusses its potential regulatory relationship with TLR, cGAS-STING, and RIG-I pathways, thereby providing fresh insights into the role of RNA methylation in the innate immune mechanisms and treatment of HCC.

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The P(III)‐Amidite Based Synthesis of Stable Isotope Labeled mRNA‐Cap‐Structures Enables their Sensitive Quantitation from Brain Tissue

Ripp,

Krämer,

Barth

et al. 2024

Angewandte Chemie

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The 5’ cap structure is crucial to mRNA function, with its diverse methylation patterns depending on the cellular state. Sensitive analytical methods are sought after to quantify this cap variety also referred to as cap epitranscriptome. To address a bottleneck for accurate and precise quantitation, we report a facile and fast access to high‐quality synthetic standards via a new route, involving P(III)‐amidite chemistry. A range of cap nucleotides and their stable heavy isotopic labeled analogues were derived from nucleoside diphosphates, which themselves were directly prepared in a one‐step reaction sequence starting from unprotected nucleosides using a triphosphorylating reagent in combination with ethylenediamine. Considering a wider scope, the route also enables direct access to magic spot nucleotides and diphosphates of isoprenyl‐alcohols. Stable‐isotope labeled cap nucleotides derived from this route paved the way for the development of a highly sensitive LC‐MS/MS method, applied to the characterization of mouse brain cap epitranscriptomes, which turned out to be very different from those of cultured cell lines of widespread use in the life sciences.

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A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome

Cited by 4 publications

References 50 publications

Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery

Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery

RNA m5C methylation: a potential modulator of innate immune pathways in hepatocellular carcinoma

The P(III)‐Amidite Based Synthesis of Stable Isotope Labeled mRNA‐Cap‐Structures Enables their Sensitive Quantitation from Brain Tissue

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