Kong Peng-Fei, Yan Yong-Hao, Duan Yan-Tao, Fang Yan-Tian, Dou Yi, Xu Yong-Hu, Xu Da-Zhi
Department of Gastric Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.
BMC Cancer. 2025 Apr 7;25(1):628. doi: 10.1186/s12885-025-13493-6.
This study aimed to explore and compare the genomic characteristics and pathogenicity of Helicobacter pylori (H. pylori) strains derived from the gastric cancer (GC) and gastritis in the Chinese population.
We performed whole genome sequencing on 12 H. pylori strains obtained from GC and gastritis patients in China. Additionally, we retrieved sequencing data for 20 H. pylori strains from various regions worldwide from public databases to serve as reference genomes. An evolutionary tree was constructed based on comparative genomics, and we analyzed the differences in virulence factors (VFs) and gene functions.
In the GC strains, we identified 1,544 to 1,640 coding genes, with a total length ranging from 1,549,790 to 1,605,249 bp. In the gastritis strains, we found 1,552 to 1,668 coding genes, with a total length spanning from 1,552,426 to 1,665,981 bp. The average length of coding genes was approximately 1,594 (90.91%) for GC strains and 1,589 (90.81%) for gastritis strains. We observed a high degree of consistency in the VFs predicted for both cohorts; however, there was a significant difference in their cagA status. Clustering analysis showed significant core single nucleotide polymorphisms (SNPs) differences between GC and gastritis strains, but no major differences in homologous proteins or gene islands. Subsequent pan-genomic and Average Nucleotide Identity (ANI) analyses indicated high homology among GC, gastritis, and other reference H. pylori strains. Furthermore, gene function annotation results showed substantial similarity in gene functions between the H. pylori strains from GC and gastritis patients, with specific functions primarily concentrated in metabolic processes, transcription, and DNA repair.
H. pylori strains derived from GC and gastritis patients exhibit differences in virulence factors and SNPs, yet they demonstrate high genomic homology across other levels in the Chinese population.
本研究旨在探索并比较中国人群中源自胃癌（GC）和胃炎的幽门螺杆菌（H. pylori）菌株的基因组特征及致病性。
我们对从中国GC和胃炎患者中获取的12株H. pylori菌株进行了全基因组测序。此外，我们从公共数据库中检索了来自全球不同地区的20株H. pylori菌株的测序数据作为参考基因组。基于比较基因组学构建了进化树，并分析了毒力因子（VFs）和基因功能的差异。
在GC菌株中，我们鉴定出1544至1640个编码基因，总长度在1549790至1605249 bp之间。在胃炎菌株中，我们发现1552至1668个编码基因，总长度在1552426至1665981 bp之间。GC菌株编码基因的平均长度约为1594（90.91%），胃炎菌株为1589（90.81%）。我们观察到两个队列预测的VFs具有高度一致性；然而，它们的cagA状态存在显著差异。聚类分析显示GC和胃炎菌株之间存在显著的核心单核苷酸多态性（SNPs）差异，但同源蛋白或基因岛没有主要差异。随后的泛基因组和平均核苷酸同一性（ANI）分析表明GC、胃炎和其他参考H. pylori菌株之间具有高度同源性。此外，基因功能注释结果显示来自GC和胃炎患者的H. pylori菌株在基因功能上有很大相似性，特定功能主要集中在代谢过程、转录和DNA修复。
源自GC和胃炎患者的H. pylori菌株在毒力因子和SNPs方面存在差异，但在中国人群的其他层面上表现出高度的基因组同源性。
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