Transcriptome profiling of cancer and normal tissues from cervical squamous cancer patients by deep sequencing

Multidimensional outlook on the pathophysiology of cervical cancer invasion and metastasis

Cervical cancer being one of the primary causes of high mortality rates among women is an area of concern, especially with ineffective treatment strategies. Extensive studies are carried out to understand various aspects of cervical cancer initiation, development and progression; however, invasive cervical squamous cell carcinoma has poor outcomes. Moreover, the advanced stages of cervical cancer may involve lymphatic circulation with a high risk of tumor recurrence at distant metastatic sites. Dysregulation of the cervical microbiome by human papillomavirus (HPV) together with immune response modulation and the occurrence of novel mutations that trigger genomic instability causes malignant transformation at the cervix. In this review, we focus on the major risk factors as well as the functionally altered signaling pathways promoting the transformation of cervical intraepithelial neoplasia into invasive squamous cell carcinoma. We further elucidate genetic and epigenetic variations to highlight the complexity of causal factors of cervical cancer as well as the metastatic potential due to the changes in immune response, epigenetic regulation, DNA repair capacity, and cell cycle progression. Our bioinformatics analysis on metastatic and non-metastatic cervical cancer datasets identified various significantly and differentially expressed genes as well as the downregulation of potential tumor suppressor microRNA miR-28-5p. Thus, a comprehensive understanding of the genomic landscape in invasive and metastatic cervical cancer will help in stratifying the patient groups and designing potential therapeutic strategies.

Tumor Necrosis Factor-α Promotes the Tumorigenesis, Lymphangiogenesis, and Lymphatic Metastasis in Cervical Cancer via Activating VEGFC-Mediated AKT and ERK Pathways

Background

Lymphatic metastasis is a common phenomenon of cervical cancer. Tumor necrosis factor-α (TNF-α) was found to be closely associated with lymphatic cancer metastasis. However, the mechanism through which TNF-α regulates lymphatic metastasis in cervical cancer remains unclear.

Methods

In this study, cervical cancer cells were cultured in Dulbecco's modified Eagle's medium (DMEM) with or without TNF-α for 48 h, and then the corresponding conditional medium (CM-TNF-α or CM) was collected. The level of vascular endothelial growth factor (VEGFC) in the corresponding CM was then detected using an enzyme-linked immunosorbent assay (ELISA). Next, human lymphatic endothelial cells (HLECs) were cultured in CM-TNF-α or CM for 48 h. Cell viability was measured using the cell counting kit-8 (CCK-8) assay, and angiogenesis was detected using a tube formation assay. Subsequently, the expressions of AKT, p-AKT, ERK, and p-ERK in HLECs were detected using western blotting. In addition, to further investigate the effect of TNF-α on the progression of cervical cancer, a C33A subcutaneous xenograft model was established in vivo.

Results

We found that TNF-α significantly stimulated cervical cancer cells to secrete VEGFC. Additionally, the CM collected from the TNF-α-treated cervical cancer cells notably promoted the proliferation, migration, and angiogenesis of HLECs; however, these changes were reversed by MAZ51, a VEGFR3 inhibitor. Moreover, TNF-α obviously elevated D2-40 and VEGFC protein expressions in tumor tissues, promoting lymphangiogenesis and lymphatic metastasis in vivo. Meanwhile, TNF-α markedly upregulated p-AKT and p-ERK expressions in tumor tissues, whereas these changes were reversed by MAZ51.

Conclusion

Collectively, TNF-α could promote tumorigenesis, lymphangiogenesis, and lymphatic metastasis in vitro and in vivo in cervical cancer via activating VEGFC-mediated AKT and ERK pathways. These results may provide new directions for the treatment of cervical cancer.

Transcriptomic Network Analysis Using Exfoliative Cervical Cells Could Discriminate a Potential Risk of Progression to Cancer in HPV-related Cervical Lesions: A Pilot Study

BACKGROUND/AIM

Cervical cancer is the fourth most common type of cancer in women worldwide and it is a major cause of cancer-related deaths in developing countries. Despite the marked reduction observed in the rates of the disease as a result of screening programs, it is necessary to develop robust biomarkers that can detect the neoplastic progression early in HPV-related cervical lesions.

MATERIALS AND METHODS

We performed comparative mRNA sequencing from exfoliative cervical cytology samples from nine Korean women using the Illumina NovaSeq6000 platform. Each pathological tissue was matched to the corresponding cytological sample. The pathologic diagnosis was scrutinized with ancillary immunohistochemistry and was considered a confirmative (endpoint) diagnosis. The pathological diagnoses consisted of three cases of chronic cervicitis, 2 high-grade squamous intraepithelial lesions (HSILs), 2 squamous cell carcinomas in situ (CIS), and 2 invasive squamous cell carcinomas (SQCCs), respectively. Using bioinformatic analyses, differentially expressed genes (DEGs; fold change ≥1.5; p<0.05) were applied for Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA), and protein-protein interaction (PPI) networks.

RESULTS

From a total of 55,882 genes, 438 DEGs were pinpointed; 282 genes were up-regulated and 156 genes down-regulated. These transcriptomic profiles were clearly divided into neoplastic (HSIL, CIS, and SQCC; ≥HSILs) and non-neoplastic lesions. The up-regulated DEGs were HIF-1a, EDN1, PIK3R3, PPP1CA and AKR1C1. GO, GSEA, and PPI network analyses showed marked associations with metabolism, proteolysis, or proteoglycan process pathways in cervical carcinogenesis.

CONCLUSION

The transcriptomic analysis using exfoliative cervical cells was more likely representative of its corresponding histopathological diagnosis, thus emphasizing its potential utility in clinical practice. This study provides comprehensive transcriptomic network analyses for robust biomarkers that might present a high potential risk of progression to cancer in the exfoliative cervical cytology; our findings support their clinical utility for improved cervical cancer screening.

Endothelin-3 is epigenetically silenced in endometrioid endometrial cancer

Purpose

Changes in the activity of endothelins and their receptors may promote neoplastic processes. They can be caused by epigenetic modifications and modulators, but little is known about endothelin-3 (EDN3), particularly in endometrial cancer. The aim of the study was to determine the expression profile of endothelin family and their interactions with miRNAs, and to assess the degree of EDN3 methylation.

Methods

The study enrolled 45 patients with endometrioid endometrial cancer and 30 patients without neoplastic changes. The expression profile of endothelins and their receptors was determined with mRNA microarrays and RT-qPCR. The miRNA prediction was based on the miRNA microarray experiment and the mirDB tool. The degree of EDN3 methylation was assessed by MSP.

Results

EDN1 and EDNRA were overexpressed regardless of endometrial cancer grade, which may be due to the lack of regulatory effect of miR-130a-3p and miR-485-3p, respectively. In addition, EDN3 and EDNRB were significantly downregulated.

Conclusion

The endothelial axis is disturbed in endometrioid endometrial cancer. The observed silencing of EDN3 activity may be mainly due to DNA methylation.

Transcriptomic Profiling Reveals AKR1C1 and AKR1C3 Mediate Cisplatin Resistance in Signet Ring Cell Gastric Carcinoma via Autophagic Cell Death

Signet ring cell gastric carcinoma (SRCGC) is a lethal malignancy that has developed drug resistance to cisplatin therapies. The aim of this study was to characterize the acquisition of the cisplatin-resistance SRCGC cell line (KATO/DDP cells) and to understand the molecular mechanisms underlying cisplatin resistance. Transcriptomic and bioinformatic analyses were used to identify the candidate gene. This was confirmed by qPCR and Western blot. Aldoketoreductase1C1 and 1C3 (AKR1C1 and AKR1C3) were the most promising molecules in KATO/DDP cells. A specific inhibitor of AKR1C1 (5PBSA) and AKR1C3 (ASP9521) was used to enhance cisplatin-induced KATO/DPP cell death. Although cisplatin alone induced KATO/DDP apoptosis, a combination treatment of cisplatin and the AKR1C inhibitors had no influence on percent cell apoptosis. In conjunction with the autophagy inhibitor, 3MA, attenuated the effects of 5PBSA or ASP9521 to enhance cisplatin-induced cell death. These results indicated that AKR1C1 and 1C3 regulated cisplatin-induced KATO/DDP cell death via autophagy. Moreover, cisplatin in combination with AKR1C inhibitors and N-acetyl cysteine increased KATO/DDP cells' viability when compared with a combination treatment of cisplatin and the inhibitors. Taken together, our results suggested that AKR1C1 and 1C3 play a crucial role in cisplatin resistance of SRCGC by regulating redox-dependent autophagy.

Genomic landscape analyses in cervical carcinoma and consequences for treatment

Where we are on the road to 'tailor-made' precision medicine for drug-resistant cervical carcinoma? We explored studies about analyses of viral and human genomes, epigenomes and transcriptomes, DNA mutation analyses, their importance in detecting HPV sequences, mechanisms of drug resistance to established and targeted therapies with small molecule or therapeutic antibodies, to radiosensitivity and to chemoradiotherapy. The value of repurposing of old drugs initially approved for other disease indications and now considered for cervix cancer therapy is also discussed. The microbiome influences drug response and survival too. HPV genomic integration sites were less significant. Nomograms (Lee et al., 2013) even outperformed FIGO staging regarding prediction of five-year overall survival times. We conclude that there are still many loose threads to be followed up, before coherent conclusions for individualized therapy of drug-resistant cervical carcinoma can be drawn.

Transcriptomic analysis of peripheral blood mononuclear cells in head and neck squamous cell carcinoma patients

OBJECTIVES

To investigate the gene expression profile of peripheral blood mononuclear cells (PBMCs) from head and neck squamous cell carcinoma (HNSCC), including oral cancer (OC) and oropharyngeal cancer (OPC) patients, and compare them with healthy controls (HC).

MATERIALS AND METHODS

Transcriptomic analysis of PBMCs was performed by RNA-sequencing. The upregulated candidate genes were selected for validation by quantitative real-time polymerase chain reaction (qPCR). In addition, related plasma protein levels were determined by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Three significantly upregulated genes, including high mobility group nucleosomal binding domain 2 (HMGN2), folate receptor gamma (FOLR3), and amphiregulin (AREG), were selected. In the first cohort, the results showed that only HMGN2 expression was significantly increased in OC patients. In the larger sample size, the overall results demonstrated that HMGN2 expression had a tendency to increase in both OC and OPC patients compared with HC. Interestingly, the plasma HMGN2 (HMG-17) protein level exhibited the same trend as that observed at the transcriptional level.

CONCLUSION

HMGN2 expression and plasma HMG-17 (HMGN2 protein) were increased in both cancer patients compared with HC. This gene may be important for further functional studies in the PBMCs of HNSCC patients.

Markers of Angiogenesis, Lymphangiogenesis, and Epithelial-Mesenchymal Transition (Plasticity) in CIN and Early Invasive Carcinoma of the Cervix: Exploring Putative Molecular Mechanisms Involved in Early Tumor Invasion

The establishment of a proangiogenic phenotype and epithelial-to-mesenchymal transition (EMT) are considered as critical events that promote the induction of invasive growth in epithelial tumors, and stimulation of lymphangiogenesis is believed to confer the capacity for early dissemination to cancer cells. Recent research has revealed substantial interdependence between these processes at the molecular level as they rely on common signaling networks. Of great interest are the molecular mechanisms of (lymph-)angiogenesis and EMT associated with the earliest stages of transition from intraepithelial development to invasive growth, as they could provide the source of potentially valuable tools for targeting tumor metastasis. However, in the case of early-stage cervical cancer, the players of (lymph-)angiogenesis and EMT processes still remain substantially uncharacterized. In this study, we used RNA sequencing to compare transcriptomes of HPV(+) preinvasive neoplastic lesions and early-stage invasive carcinoma of the cervix and to identify (lymph-)angiogenesis- and EMT-related genes and pathways that may underlie early acquisition of invasive phenotype and metastatic properties by cervical cancer cells. Second, we applied flow cytometric analysis to evaluate the expression of three key lymphangiogenesis/EMT markers (VEGFR3, MET, and SLUG) in epithelial cells derived from enzymatically treated tissue specimens. Overall, among 201 differentially expressed genes, a considerable number of (lymph-)angiogenesis and EMT regulatory factors were identified, including genes encoding cytokines, growth factor receptors, transcription factors, and adhesion molecules. Pathway analysis confirmed enrichment for angiogenesis, epithelial differentiation, and cell guidance pathways at transition from intraepithelial neoplasia to invasive carcinoma and suggested immune-regulatory/inflammatory pathways to be implicated in initiation of invasive growth of cervical cancer. Flow cytometry showed cell phenotype-specific expression pattern for VEGFR3, MET, and SLUG and revealed correlation with the amount of tumor-infiltrating lymphocytes at the early stages of cervical cancer progression. Taken together, these results extend our understanding of driving forces of angiogenesis and metastasis in HPV-associated cervical cancer and may be useful for developing new treatments.

Genes Regulated by HPV 16 E6 and High Expression of NFX1-123 in Cervical Cancers

Purpose

High-risk human papillomaviruses (HR HPV) cause cervical cancer, and in these cancers, HPV type 16 is the most common HR type. The HR viral oncogenes E6 and E7 partner with cellular proteins to drive cancer and modulate immune pathways; previously, we demonstrated in keratinocytes that HPV 16 E6 and high expression of the endogenous host protein partner NFX1-123 led to the increased expression of multiple genes, including Notch1, secretory leukocyte peptidase inhibitor (SLPI), and retinoic acid early transcript 1G (RAET1G). The present study was conducted to determine if NFX1-123 was highly expressed in cervical cancer and if genes increased by NFX1-123 and 16E6 in keratinocytes were also increased in cervical cancers.

Materials and Methods

The Cancer Genome Atlas (TCGA) database and The Human Protein Atlas database were used to compare relative mRNA and protein gene expression, respectively, in the normal cervix and cervical cancers. Formalin-fixed paraffin-embedded (FFPE) normal cervix and HPV 16 positive cervical cancer samples were analyzed for relative protein expression by immunohistochemical staining. Protein expression of a subset of regulated genes was quantified by Western blot of HPV positive and negative cell lines.

Results

Immunohistochemical staining of HPV 16 positive cervical dysplasias and cancers revealed high NFX1-123, Ki67, and Notch1 expression. NFX1 and NFX1L1 mRNA levels were increased in cervical cancers compared to normal cervix in the TCGA database. Fourteen genes previously identified as upregulated in keratinocytes with 16E6 and overexpressed NFX1-123 also had high mRNA expression and selected genes had high protein expression in cervical cancers and cell lines.

Conclusion

In cervical cancer, NFX1-123 is highly expressed, and 16E6 and NFX1-123 together alter the expression of a wide set of genes. The involvement of these genes in cell proliferation, differentiation, invasion, and metastasis provides further insight into potential ways that HR HPVs promote cancer initiation and maintenance.

Differentially Expressed Genes in Matched Normal, Cancer, and Lymph Node Metastases Predict Clinical Outcomes in Patients With Breast Cancer

Genome-wide screening of transcriptional changes among normal, cancer, and nodal metastases provides insights into the molecular basis of breast cancer (BC) progression and metastasis. To identify transcriptional changes and differentially expressed genes (DEGs) in the metastatic progression of BC and to determine the prognostic role of these DEGs in clinical outcome, we compared transcriptome profiling in matched normal, cancer, and lymph node metastatic tissues of 7 patients with estrogen receptor-positive, HER2-negative BC by using massive parallel RNA sequencing. The global profiles of gene expression in cancer and nodal metastases were highly correlated (r=0.962, P<0.001). In 6 (85.8%) patients, cancer and corresponding nodal metastases from the same patient clustered together. We identified 1522 and 664 DEGs between normal and cancer and between cancer and nodal metastases, respectively. The DEGs in normal versus cancer and cancer versus nodal metastases were significantly clustered in 1 and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. The chemokine signaling pathway was the most significant pathway in the cancer-to-nodal metastasis transition (false discovery rate=2.15E-13). The expression of 2 dysregulated RAC2 and PTGDS genes was confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry. Interestingly, the lower RAC2 and PTGDS expression were associated with significantly worse disease-free survival in patients with BC. Our results show a high concordance of gene expression in BC and their nodal metastases, and identify DEGs associated with the metastatic progression of BC. The DEGs identified in this study represent novel biomarkers for predicting the prognosis of patients with BC.

Transcriptome profiling of cervical cancer cells acquired resistance to cisplatin by deep sequencing

Cervical cancer is one of the most fatal malignancies in females. Acquired resistance to chemotherapeutic agent is one reason behind this lethality. In this study, we developed cisplatin resistance cell line, subsequently examined the molecular mechanisms linked. Transcriptome sequencing technology was utilized to compare the various expression models between the cisplatin-resistant cell line (Hela/DDP) and its parental cell line human cervical adenocarcinoma Hela. The present study has identified 2,312 differentially expressed genes (DEGs). Results showed there were 1,437 up-regulated genes and 875 down-regulated ones. Databases analysis including Gene ontology (GO), Cluster of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed to reveal potential molecular mechanisms. We studied AKT3, a crucial gene in the PI3K/AKT pathway which clustered the most DEGs. Silencing AKT3 in Hela/DDP could enhance its sensibility to cisplatin. Quantitative real-time reverse transcription PCR (qRT-PCR) and western blot experiments were showed that expression of AKT3 was decreased after siRNA interference and inhibitor treatment. CCK-8 experiments showed that low expression of Akt3/pAkt enhanced the sensitivity of drug-resistant cells to cisplatin. Apoptotic analysis demonstrated that inhibition of AKT3 increased the rate of Hela/DDP apoptosis. Our results suggest a novel mechanism by which upregulated expression of AKT3 in cervical cancer may lead to resistance to cisplatin.

Transcriptome profiling in Rift Valley fever virus infected cells reveals modified transcriptional and alternative splicing programs

Rift Valley fever virus (RVFV) is a negative-sense RNA virus belonging to the Phenuiviridae family that infects both domestic livestock and humans. The NIAID has designated RVFV as a Category A priority emerging pathogen due to the devastating public health outcomes associated with epidemic outbreaks. However, there is no licensed treatment or vaccine approved for human use. Therefore it is of great interest to understand RVFV pathogenesis in infected hosts in order to facilitate creation of targeted therapies and treatment options. Here we provide insight into the host-pathogen interface in human HEK293 cells during RVFV MP-12 strain infection using high-throughput mRNA sequencing technology. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes showed robust innate immune and cytokine-mediated inflammatory pathway activation as well as alterations in pathways associated with fatty acid metabolism and extracellular matrix receptor signaling. We also analyzed the promoter regions of DEGs for patterns in transcription factor binding sites, and found several that are known to act synergistically to impact apoptosis, immunity, metabolism, and cell growth and differentiation. Lastly, we noted dramatic changes in host alternative splicing patterns in genes associated with mRNA decay and surveillance, RNA transport, and DNA repair. This study has improved our understanding of RVFV pathogenesis and has provided novel insight into pathways and signaling modules important for RVFV diagnostics and therapeutic development.

Novel Genomic Biomarker Candidates for Cervical Cancer As Identified by Differential Co-Expression Network Analysis

Cervical cancer is the second most common malignancy and the third reason for mortality among women in developing countries. Although infection by the oncogenic human papilloma viruses is a major cause, genomic contributors are still largely unknown. Network analyses, compared with candidate gene studies, offer greater promise to map the interactions among genomic loci contributing to cervical cancer risk. We report here a differential co-expression network analysis in five gene expression datasets (GSE7803, GSE9750, GSE39001, GSE52903, and GSE63514, from the Gene Expression Omnibus) in patients with cervical cancer and healthy controls. Kaplan-Meier Survival and principle component analyses were employed to evaluate prognostic and diagnostic performances of biomarker candidates, respectively. As a result, seven distinct co-expressed gene modules were identified. Among these, five modules (with sizes of 9-45 genes) presented high prognostic and diagnostic capabilities with hazard ratios of 2.28-11.3, and diagnostic odds ratios of 85.2-548.8. Moreover, these modules were associated with several key biological processes such as cell cycle regulation, keratinization, neutrophil degranulation, and the phospholipase D signaling pathway. In addition, transcription factors ETS1 and GATA2 were noted as common regulatory elements. These genomic biomarker candidates identified by differential co-expression network analysis offer new prospects for translational cancer research, not to mention personalized medicine to forecast cervical cancer susceptibility and prognosis. Looking into the future, we also suggest that the search for a molecular basis of common complex diseases should be complemented by differential co-expression analyses to obtain a systems-level understanding of disease phenotype variability.

Downregulated GBX2 gene suppresses proliferation, invasion and angiogenesis of breast cancer cells through inhibiting the Wnt/β-catenin signaling pathway

OBJECTIVE

Gastrulation brain homeobox 2 (GBX2), a gene involved in mid/hindbrain region, has been revealed as one of the oncogene associated with certain cancers, as an example being prostate cancer. However, despite years of worldwide research, the underlying mechanism of GBX2 as well as its significance in breast cancer still remains unclear. Therefore, the present study evaluates the abilities of GBX gene silencing providing for the proliferation, invasion and angiogenesis of breast cancer cells by way of the Wnt/β-catenin signaling pathway.

METHODS

We employed a microarray analysis to screen out differentially expressed genes relative to breast cancer. Moreover, we retrieved GBX2 expression in breast cancer to find out the relationship between GBX2 expression and prognosis in breast cancer. We performed RT-qPCR to screen out cell lines with high GBX2 expression. Subsequently, both RT-qPCR and western blot analysis were employed so as to measure the combination of the mRNA and protein expressions of GBX2, β-catenin, vascular endothelial growth factor (VEGF), matrix metalloproteinase (MMP)-2, and MMP-9. The effect that GBX2 gene silencing and the Wnt/β-catenin signaling pathway had on cell proliferation, invasion, angiogenesis, and tumorigenic ability were evaluated.

RESULTS

GBX2 gene was also identified having played a role in breast cancer development due to its association with the Wnt/β-catenin signaling pathway. GBX2 gene silencing was found to be an inhibitor for the mRNA and protein expressions regulating β-catenin, VEGF, MMP-2, and MMP-9. Cell proliferation, invasion, angiogenesis, as well as tumorigenic ability in breast cancer were investigated and found to have been suppressed by the GBX2 gene silencing or inactivation of the Wnt/β-catenin signaling pathway.

CONCLUSION

The study has made an attempt to provide evidence to the idea that GBX2 gene silencing has an inhibition effect on the proliferation, invasion and angiogenesis of the breast cancer cells by inhibiting the activation of the Wnt/β-catenin signaling pathway.

Genome-Wide Profiling of Cervical RNA-Binding Proteins Identifies Human Papillomavirus Regulation of RNASEH2A Expression by Viral E7 and E2F1

High-risk HPV infections lead to development of cervical cancer. This study identified the differential expression of 16 novel genes (LY6K, FAM83A, CELSR3, ASF1B, IQGAP3, SEMA3F, CLDN10, MSX1, CXCL5, ASRGL1, ELAVL2, GRB7, KHSRP, NOVA1, PTBP1, and RNASEH2A) in HPV-infected cervical tissue samples and keratinocytes. Eight of these genes (CDKN2A, ELAVL2, GRB7, HSPB1, KHSRP, NOVA1, PTBP1, and RNASEH2A) encode RNA-binding proteins. Further studies indicated that both HPV16 and HPV18 infections lead to the aberrant expression of selected RBP-encoding genes. We found that viral E6 and E7 decrease NOVA1 expression but that E7 increases RNASEH2A expression via E2F1. The altered expression of these genes may be utilized as biomarkers for high-risk (HR)-HPV carcinogenesis and progression.

RNA-binding proteins (RBPs) control mRNA processing, stability, transport, editing, and translation. We recently conducted transcriptome analyses comparing normal (i.e., healthy) cervical tissue samples with human papillomavirus (HPV)-positive cervical cancer tissue samples and identified 614 differentially expressed protein-coding transcripts which are enriched in cancer-related pathways and consist of 95 known RBPs. We verified the altered expression of 26 genes with a cohort of 72 cervical samples, including 24 normal cervical samples, 25 cervical intraepithelial neoplasia grade 2 (CIN2) and CIN3 samples, and 23 cervical cancer tissue samples. LY6K (lymphocyte antigen 6 complex locus K), FAM83A (family member with sequence similarity 83), CELSR3, ASF1B, IQGAP3, SEMA3F, CLDN10, MSX1, CXCL5, ASRGL1, ELAVL2, GRB7, KHSRP, NOVA1, PTBP1, and RNASEH2A were identified as novel candidate genes associated with cervical lesion progression and carcinogenesis. HPV16 or HPV18 infection was found to alter the expression of 8 RBP genes (CDKN2A, ELAVL2, GRB7, HSPB1, KHSRP, NOVA1, PTBP1, and RNASEH2A) in human vaginal and foreskin keratinocytes. Both viral E6 and E7 decreased NOVA1 expression, but only E7 increased the expression of RNASEH2A in an E2F1-dependent manner. Proliferating cell nuclear antigen (PCNA) directs RNASEH2 activity with respect to DNA replication by removing the RNA primers to promote Okazaki fragment maturation, and two factors are closely associated with neoplasia progression. Therefore, we predict that the induction of expression of RNASEH2A via viral E7 and E2F1 may promote DNA replication and cancer cell proliferation.