Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation DOI Creative Commons
Amandine Amalric,

Aurore Attina,

Amandine Bastide

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(5), P. 1825 - 1833

Published: Jan. 26, 2024

Cancer onset and progression are known to be regulated by genetic epigenetic events, including RNA modifications (a.k.a. epitranscriptomics). So far, more than 150 chemical have been described in all subtypes, messenger, ribosomal, transfer RNAs. their regulators implicated steps of post-transcriptional regulation. The dysregulation this complex yet delicate balance can contribute disease evolution, particularly the context carcinogenesis, where cells subjected various stresses. We sought discover involved cancer cell adaptation inhospitable environments, a peculiar feature stem (CSCs). were interested marks that help suspension culture, which is often used as surrogate evaluate tumorigenic potential. For purpose, we designed an experimental pipeline consisting four steps: (1) culture different growth conditions favor CSC survival; (2) simultaneous subtype (mRNA, rRNA, tRNA) enrichment hydrolysis; (3) multiplex analysis nucleosides LC-MS/MS followed statistical/bioinformatic analysis; (4) functional validation identified marks. This study demonstrates modification landscape evolves along with phenotype under constraints. Remarkably, discovered short epitranscriptomic signature, conserved across colorectal lines associated CSCs. Functional tests confirmed importance selected process confirming validity our approach opening up interesting prospects field.

Language: Английский

Regulations of m6A and other RNA modifications and their roles in cancer DOI
Xinhui Chen,

Kunxiong Guo,

Jing Li

et al.

Frontiers of Medicine, Journal Year: 2024, Volume and Issue: 18(4), P. 622 - 648

Published: June 22, 2024

Language: Английский

Citations

5
HCV 5-Methylcytosine Enhances Viral RNA Replication through Interaction with m5C Reader YBX1 DOI
Zhu-Li Li, Yan Xie, Yuke Xie

et al.

ACS Chemical Biology, Journal Year: 2024, Volume and Issue: 19(7), P. 1648 - 1660

Published: July 2, 2024

Hepatitis C virus (HCV) is a positive-stranded RNA that mainly causes chronic hepatitis, cirrhosis and hepatocellular carcinoma. Recently we confirmed m5C modifications within NS5A gene of HCV genome. However, the roles modification its interaction with host proteins in regulating HCV's life cycle, remain unexplored. Here, demonstrate infection enhances expression reader YBX1 through transcription factor MAX. acts as an reader, recognizing m5C-modified C7525 site genome significantly enhancing stability. This m5C-modification also required for colocalization lipid droplets Core protein. Moreover, facilitates replication, well viral assembly/budding. The tryptophan residue at position 65 (W65) critical these functions. Knockout or application inhibitor SU056 suppresses replication protein translation. To our knowledge, this first report demonstrating between methylation replication. Therefore, hepatic-YBX1 knockdown holds promise potential host-directed strategy therapy.

Language: Английский

Citations

5
RNA methyltransferase NSUN2-mediated m5C methylation promotes Cr(VI)-induced malignant transformation and lung cancer by accelerating metabolism reprogramming DOI Creative Commons

Rui-Ke Zhang,

Yan Li,

Fan-Li Sun

et al.

Environment International, Journal Year: 2024, Volume and Issue: 192, P. 109055 - 109055

Published: Oct. 1, 2024

Language: Английский

Citations

5
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia DOI Creative Commons

Yuhong Ding,

Akhilesh Kumar Bajpai,

Fengxia Wu

et al.

Aging, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 25, 2024

Acute myeloid leukemia (AML) is a highly heterogeneous malignant disease of the blood cell. The current therapies for AML are unsatisfactory and molecular mechanisms underlying unclear. 5-methylcytosine (m5C) an important posttranscriptional modification mRNA, involved in regulation mRNA stability, translation, other aspects RNA metabolism. However, based on our knowledge published literature, role m5C regulators has not been explored till date. In this study, we clarified expression gene variants found that most were differentially expressed correlated with prognosis. We also methylation status certain (e.g., DNMT3A, DNMT3B) affects survival patients. Two subtypes, high- low-risk subgroups identified showed significant differences prognosis as well immune cell infiltration. addition, to be miRNA AML, IC50 values many drugs. GSVA analysis used identify different miRNAs KEGG or hallmark pathways between subgroups. built prognostic model regulators, which was validated by two GSE databases. To verify reliability conclusions, qPCR expressions normal AML. summary, comprehensively characteristics proposed new mechanistic insights into multiple databases clinical data, may pave novel ways development therapeutic strategies.

Language: Английский

Citations

4
Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation DOI Creative Commons
Amandine Amalric,

Aurore Attina,

Amandine Bastide

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(5), P. 1825 - 1833

Published: Jan. 26, 2024

Cancer onset and progression are known to be regulated by genetic epigenetic events, including RNA modifications (a.k.a. epitranscriptomics). So far, more than 150 chemical have been described in all subtypes, messenger, ribosomal, transfer RNAs. their regulators implicated steps of post-transcriptional regulation. The dysregulation this complex yet delicate balance can contribute disease evolution, particularly the context carcinogenesis, where cells subjected various stresses. We sought discover involved cancer cell adaptation inhospitable environments, a peculiar feature stem (CSCs). were interested marks that help suspension culture, which is often used as surrogate evaluate tumorigenic potential. For purpose, we designed an experimental pipeline consisting four steps: (1) culture different growth conditions favor CSC survival; (2) simultaneous subtype (mRNA, rRNA, tRNA) enrichment hydrolysis; (3) multiplex analysis nucleosides LC-MS/MS followed statistical/bioinformatic analysis; (4) functional validation identified marks. This study demonstrates modification landscape evolves along with phenotype under constraints. Remarkably, discovered short epitranscriptomic signature, conserved across colorectal lines associated CSCs. Functional tests confirmed importance selected process confirming validity our approach opening up interesting prospects field.

Language: Английский

Citations

4