Both HPV-positive and negative cervical cancers are associated with cell cycle deregulation, but the actual molecular events, remain elusive. To this end, we employed in vitro and in vivo models of cervical cancer by i) investigating the genomic and transcriptomic effects of the presence or absence of HPV in four nformative cervical cell lines, and ii) validating these transccriptomic patterns in tissues from patients with normal, CIN3 and cervical cancer stages.
Whole exome sequencing and RNA sequencing were performed in a normal cervical cell line (HCK1T), in one HPV (–) C33A, and in two HPV (+) cell lines, HeLa [HPV18+] and SiHa [HPV16+], and in 12 samples of normal, CIN3 and cancer stages.
RNA-sequencing revealed the main integration sites of HPV18 and HPV16 in chromosomes 8 and 13, respectively. Furthermore, a total of 212 genes (85 upregulated and 127 downregulated) were differentially expressed in HeLa and SiHa only. The majority of the downregulated genes are involved in processes of cell adhesion, cell-cell signaling and differentiation. The upregulated genes are involved in embryonic morphogenesis, apoptosis, cell cycle and in positive regulation of transcription. Whole exome sequencing revealed that 1,257 genes were mutated in HeLa and SiHa cells only, consistent with their expression profiles affecting processes of cell adhesion and development. Sixteen of these mutated genes were also differentially expressed between HPV [+] and HPV [-] cells. We validated these data in clinical samples from normal, CIN3 and cervical cancer tissues. The CIN3 and cervical cancer transcriptomes exhibited minimal similarities. With more than 2,000 transcripts differentially expressed among CIN3, cervical cancer and normal tissues, <400 genes showed similar expression patterns. Chemotaxis and immune-related processes were downregulated in CIN3 patients, while cell cycle and mitosis were upregulated only in cervical cancer patients. Consistent with this, most of the transcriptional regulators controlling the immune and defense response, several cytokines and interferon regulatory factors, were downregulated, while in cervical cancer, regulators controlling cell cycle progression, were upregulated. Interestingly, many pluripotency-related genes displayed elevated gene expression only in CIN3, suggesting the establishment of a transient pluripotency-like phenotype.
These combined data imply that the presence of HPV in cervical cells initially leads to aberrant expression of genes controlling cell-cell signaling and cell adhesion, while at the precancerous stages, distinct genes and pathways are deregulated during the transition from CIN3 to cervical cancer.