背景:跨物种水平基因转移(HGT)涉及遗传物质在不同物种之间的转移。近年来,越来越多的证据表明,跨物种HGT确实发生,并且可能在疾病的发展和进展中发挥作用。
方法:对从胆囊癌(GBC)患者获得的转录组数据评估反义RNA(asRNA)的差异表达。基本局部比对搜索工具(BLAST)用于跨物种分析与病毒,细菌,真菌,和古代人类基因组来阐明这些差异asRNAs的进化跨物种起源。进行了功能富集分析和文本挖掘,并构建了靶向mRNAs的asRNAs网络,以更好地了解差异asRNAs的功能。
结果:与正常胆囊相比,在胆囊癌组织中鉴定出总共17种差异表达的反义RNA(asRNA)。BLAST分析15种asRNA(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和MAGI2-AS)显示出与细菌和病毒基因组不同程度的相似性,除了UNC5B-AS1和SOX21-AS1,它们在进化过程中是保守的。这15个asRNA中的两个,(VPS9D1-AS1和SLC2A1-AS1)与病毒基因组(基孔肯雅病毒,人类免疫缺陷病毒1,隐形病毒1和寨卡病毒)和细菌基因组,包括(葡萄球菌。,缓生根瘤菌sp.,多杀巴斯德氏菌。,and,肺炎克雷伯菌。),表明进化过程中潜在的HGT。
结论:结果提供了新的证据,支持GBC中差异表达的asRNA与细菌表现出不同的序列相似性的假设。病毒,和古老的人类基因组,表明潜在的共同进化起源。这些非编码基因富含甲基化,并被发现与癌症相关通路有关。包括P53和PI3K-AKT信号通路,提示他们可能参与肿瘤的发展。
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.
CONCLUSIONS: 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.