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Exploring the transcriptomic and m6a landscape of human chromosome 17 in breast cancer: A combined RNA-seq and MeRIP-Seq analysis
- 1 Xi’an Jiaotong-Liverpool University
* Author to whom correspondence should be addressed.
Abstract
N6-methyladenosine (m6A), recognized as the most prevalent post-transcriptional modification in organisms, has been substantiated to exert a significant influence on the genetic mechanisms underlying breast cancer. To delve deeper into the disparities in expression, modification, and interactions between mRNA and m6A in breast cancer (BC), we conducted RNA-seq and MeRIP-Seq analyses on eight human breast tissue transcriptome samples acquired from the GEO database. combining two single omics and integrated analysis, the study unveiled the mRNA and m6A expression patterns, differential genes, and enriched pathway functional disparities in BC (on Chromosome 17): (1) A confidence list comprised of 53 differential genes was derived by intersecting the 72 identified differentially expressed mRNA genes and the 781 differentially modified m6A genes; (2) The three-way analysis revealed two distinct types of pathways related to BC: “ABC transporter activity” and “Response to epidermal growth factor.” Among these, the EGF pathways exhibited the closest association with the differential m6A modifications. Meanwhile, all three BC subtypes enriched in DisGeNET were all linked to EGF; (3) By integrating PPI and enrichment analysis, we selected target genes from the confidence gene list, which included ABCA6, ABCA8, and ABCA10, known to be involved in regulating ABC transporters, and ERBB2, a central hub gene in PPI with a pivotal role in the EGF pathway and Her2-positive BC subtype under m6A differential modification. Subsequent research may uncover RNA-binding proteins for these target genes and offer effective drug design targets for BC.
Keywords
Breast Cancer, m6A, MeRIP-Seq, RNA-seq, Chromosome 17
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Cite this article
Wang,M. (2024). Exploring the transcriptomic and m6a landscape of human chromosome 17 in breast cancer: A combined RNA-seq and MeRIP-Seq analysis. Theoretical and Natural Science,40,117-138.
Data availability
The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.
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