Comprehensive analysis of RNA-5-methylcytosine modification in breast cancer brain metastasis
Creators: name: Cai, Peiying
name: Li, Jichao
name: An, Meng
name: Li, Min
name: Guo, Jianran
name: Li, Jun
name: Li, Xuan
name: Chen, Shen
name: Zhang, Anqi
name: Li, Peng
name: Liu, Yan
name: Zhang, Wei
name: Fu, Bo
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: <b>Aim:</b> To delineate the RNA-5-methylcytosine (m5C) modification of breast cancer brain metastasis (BCBM). <b>Methods:</b> Methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) was performed to obtain RNA-m5C patterns of BCBM. <b>Results:</b> 1048 hypermethylation and 1866 hypomethylation m5C peaks were identified in BCBM compared with those in breast cancer. The most significant m5C hypermethylated genes included ENG, SHANK1, IGFN1, EVL and MMP9, whereas the most significant m5C hypomethylated genes included AREG, SAA2, TP53I11, KRT7 and LCN2. MeRIP-qPCR data were concordant with the corresponding MeRIP-seq results in terms of the observed m5C levels. Conjoint analysis identified 190 hyper-up genes characterized by concurrent m5C hypermethylation and up-regulation, alongside 284 hypo-down genes exhibiting both m5C hypomethylation and down-regulation. <b>Conclusion:</b> This study presents the first comprehensive analysis of RNA-m5C modification in BCBM. Breast cancer (BC) is the second most common solid malignancy to involve the brain. However, the underlying molecular mechanism of breast cancer brain metastasis (BCBM) remains largely unknown. We attempted to delineate the RNA 5-methylcytosine (m5C) modification landscape of BCBM to elucidate its underlying molecular mechanism. We employed methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) to obtain a comprehensive profile of m5C methylation patterns in the BCBM group (231-BR cells) in comparison to the BC group (MDA-MB-231 cells). A total of 1048 hypermethylation and 1866 hypomethylation m5C peaks were identified in the BCBM group compared with those in the BC group. The most significant m5C hypermethylated genes included ENG, SHANK1, IGFN1, EVL and MMP9, whereas the most significant m5C hypomethylated genes included AREG, SAA2, TP53I11, KRT7 and LCN2. MeRIP-qPCR results were consistent with the corresponding MeRIP-seq data regarding m5C methylation levels of the candidate molecules IGFN1, EVL, AREG and KRT7. Conjoint analysis identified 190 hyper-up genes characterized by concurrent m5C hypermethylation and up-regulation, alongside 284 hypo-down genes exhibiting both m5C hypomethylation and down-regulation. Protein-protein interaction (PPI) network analysis based on differentially m5C methylated and expressed genes identified MMP9, ICAM1, THBS1, LAMA5, PDGFRB, TGFB2, NOTCH1 and SAA2 as hub genes related to BCBM. The hub genes were associated with the positive regulation of cell migration, response to oxygen levels, regulation of epithelial cell migration and inflammatory response. An analysis of methylation regulators indicated that the methyltransferases NOP2, NSUN5, DNMT3A and DNMT3B and the demethylase TET2 may be implicated in the regulation of m5C RNA methylation related to BCBM. This study presents the first m5C modification profile of mRNAs in BCBM, providing a framework for a better understanding of the mechanisms that trigger brain metastasis and delineating innovative biomarkers and therapeutic targets for improving the diagnosis and treatment of BCBM.