Cell cycle gene expression and microbial profiles associated with HPV related cervical neoplasia and cervical microbiome shifts

Background and objectives The improper regulation of the cell cycle is a significant risk factor for cervical cancer (CC), which is a serious health concern for women worldwide. The interaction between viral pathogens and microbiota with host cells could be vital in this dysregulation. The research aimed to explore changes in the transcription levels of CDK2 and CCNE1, and how these changes relate to the HPV genotypes in women with cervical intraepithelial neoplasia (CIN) compared with non-infected healthy women. Additionally, microbiome and gene expression analyses were conducted in a subgroup of participants with HPV-16/18 infection in compare to non-infected healthy women. Materials and methods A cross-sectional study was conducted on women who attended cervical screenings at Yas Hospital in Tehran between March 2024 and May 2025. Three segments of exocervical biopsies were collected during examinations. Pathological analysis was performed to study histological changes, and gene expression analysis was conducted to detect relative transcriptional changes in CDK2 and CCNE1 levels using quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, 16S rDNA sequencing was performed using the Illumina MiSeq platform to characterize differences in bacterial composition among the samples. Statistical analysis was conducted to investigate the correlation between infection status, cell cycle dysregulation, and microbial diversity. Results A total of 220 women (mean age 36.1 ± 8.33 years) were enrolled. Of these, 206 (93.6%) tested positive for HPV, while 15 (6.81%) served as HPV-negative individuals by PCR. Among the HPV-positive patients, HPV-16 and HPV-18 were detected in 30.5% and 11.8%, respectively; the remaining high-risk genotypes accounted for 50.9%, with HPV-66 being the most common (12.4%). CCNE1 transcription was significantly higher in the infected group compared to the non-infected group (p-value = 0.001), in HPV-16-positive patients versus HPV-18-positive patients (p-value = 0.015), and in HPV-16-positive patients versus patients with other genotypes (p-value = 0.034). CDK2 transcription was elevated in HPV-18-positive patients compared to non-infected individuals (p-value = 0.009), in HPV-16-positive patients compared to HPV-18-positive patients (p-value = 0.019), and in patients with different HPV types compared to HPV-18-positive patients (p-value = 0.001). No significant differences were observed in alpha (p-value = 0.89) or beta (p-value = 0.46) diversity. HPV-16 and HPV-18 infections led to notable changes in the cervical microbiome compared to the non-infected group, showing increased levels of Prevotella_7, Megasphaera, Corynebacterium, and Limosilactobacillus, while reducing Lactobacillus, Gardnerella, Bacillus, and Streptococcus. There were also genotype-specific patterns in Bifidobacterium, Actinomyces, and Atopobium. Although no significant correlations were found between the microbiome composition and CCNE1/CDK2 transcription, descriptive analysis suggested a potential correlation. Conclusion This study shows that HPV infection, especially high-risk genotypes, is linked to an increase in transcription of CCNE1 and CDK2, indicating cell cycle dysregulation in cervical intraepithelial neoplasia. Although no significant difference in overall microbial diversity was detected between infected and non-infected individuals, a change in specific bacterial genera was observed that was correlated with alterations in the transcription of G1/S cell cycle mediators.