Zeng Xi, Peng Fang, Wang Ziying, Teng Qiuli, Sha Ying, Leung Ross Ka-Kit, Christopher L A I Koon Chi, Li Guoliang, Huang Xiaoyuan, Lin Shitong
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan 430070, China.
Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xilu, Jinan, Shandong 250012, PR China.
Hum Mol Genet. 2025 May 17;34(11):920-933. doi: 10.1093/hmg/ddaf027.
HPV infection is common among women and can result in serious illnesses. This research utilizes single-cell RNA-sequencing (scRNA-seq) to study the connection between cellular heterogeneity and HPV integrations in cervical histopathology. scRNA-seq was used to examine heterogeneity among normal patients and those in three disease stages: high-grade squamous intraepithelial lesions (HSIL), microinvasive carcinoma (MIC), and cervical squamous epithelium carcinoma cancer (CSCC) tissues. A method was developed to identify HPV integration events from scRNA-seq data. Our results indicated an increase in squamous epithelial cells and a decrease in columnar epithelial cells as the disease progressed from normal to CSCC. We discovered HPV genes that were differentially expressed across normal patients and those in the three disease stages. Notably, HPV integration events were more common in squamous epithelial cells at the single-cell level. The ratio of HPV-integrated cells increased as the disease progressed from normal tissue to CSCC, eventually stabilizing. Several genes, such as EGR1, S100A11, S100A8, KRT5, RPL34, ATP1B1, RPS4X and EEF2, were frequently integrated by HPV across patients. In contrast, genes like PAN3, BABAM2, SPEN, TCIM-SIRLNT, TEX41-PABPC1P2 and KCNV1-LINC01608 showed frequent integration events across cells. KRT5, ATP1B1, RPS4X, PAN3 and SPEN were novel recurrent HPV-integrated genes we observed at the patient or cell level in this study. Additionally, we found that HPV genes from various HPV types exhibited integration preferences in various samples and disease stages. This provides a valuable insight into the mechanism of HPV-induced cervical cancer from a single-cell standpoint, highlighting its clinical relevance.
人乳头瘤病毒（HPV）感染在女性中很常见，可导致严重疾病。本研究利用单细胞RNA测序（scRNA-seq）来研究宫颈组织病理学中细胞异质性与HPV整合之间的联系。scRNA-seq用于检查正常患者以及处于三个疾病阶段的患者之间的异质性，这三个疾病阶段分别为：高级别鳞状上皮内病变（HSIL）、微浸润癌（MIC）和宫颈鳞状上皮癌（CSCC）组织。开发了一种从scRNA-seq数据中识别HPV整合事件的方法。我们的结果表明，随着疾病从正常发展到CSCC，鳞状上皮细胞增加，柱状上皮细胞减少。我们发现了在正常患者和三个疾病阶段的患者中差异表达的HPV基因。值得注意的是，在单细胞水平上，HPV整合事件在鳞状上皮细胞中更为常见。随着疾病从正常组织发展到CSCC，HPV整合细胞的比例增加，最终趋于稳定。在患者中，HPV经常整合几个基因，如EGR1、S100A11、S100A8、KRT5、RPL34、ATP1B1、RPS4X和EEF2。相比之下，PAN3、BABAM2、SPEN、TCIM-SIRLNT、TEX41-PABPC1P2和KCNV1-LINC01608等基因在细胞中显示出频繁的整合事件。KRT5、ATP1B1、RPS4X、PAN3和SPEN是我们在本研究中在患者或细胞水平观察到的新的复发性HPV整合基因。此外，我们发现来自不同HPV类型的HPV基因在不同样本和疾病阶段表现出整合偏好。这从单细胞角度为HPV诱导宫颈癌的机制提供了有价值的见解，突出了其临床相关性。
