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Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis - PubMed

  • ️Mon Jan 01 2024

Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis

Monika Rajput et al. World J Surg Oncol. 2024.

Abstract

Background: Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.

Methods: Transcriptomic data obtained from patients with gallbladder cancer (GBC) was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.

Results: A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15 asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.

Conclusion: The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.

Keywords: Antisense RNA (asRNAs); Cross-species horizontal gene transfer (CS-HGT); Gallbladder cancer; Gene regulatory network; Transcriptomic profiling; asRNAs targeting mRNAs.

© 2024. The Author(s).

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1

Neighbour-joining phylogenetic tree of significant asRNAs showing 5 clusters

Fig. 2
Fig. 2

Phylogenetic tree analysis showing ancestry with bacterial, viruses, fungi, Homo neanderthalensis, and Homo heidelbergensis DNA (A-O). Highlighted asRNAs indicate our DEGs, different colour nodes represent different species

Fig. 3
Fig. 3

asRNA targeted mRNA interaction network. Nodes in the network are represented by dots with various colors and shapes. The link between the two nodes is represented by the edge. Seeds (circle yellow), complex (Circle light blue), miRNA (circle dark pink), chemical (circle dark green), protein family (circle peach), small molecule (circle purple), stimulus (circle brown), phenotype (circle orange), and protein (circle pink)

Fig. 4
Fig. 4

Crosstalk between the significant asRNAs and the targeted mRNAs. Yellow color circle – Significant asRNAs, blue rectangular box—targeted mRNAs

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