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

ABSTRACTRNA-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.IMPORTANCEHigh-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.

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Expression Profile of RNA Binding Protein in Cervical Cancer

10.21203/rs.3.rs-655697/v1 ◽

2021 ◽

Author(s):

Zhiyuan Huang ◽

Fang Li ◽

Qinchuan Li

Keyword(s):

Risk Factors ◽

Cervical Cancer ◽

Risk Score ◽

Normal Tissue ◽

Binding Proteins ◽

Rna Binding ◽

Cox Regression ◽

Rna Binding Proteins ◽

Risk Group ◽

Tissue Samples

Abstract Background: It has been demonstrated by studies globally that RNA binding proteins (RBPs) took part in the development of cervical cancer (CC). Few studies concentrated on the correlation between RBPs and overall survival of CC patients. We retrieved significant DEGs (differently expressed genes, RNA binding proteins) correlated to the process of cervical cancer development. Methods: Expressions level of genes in cervical cancer and normal tissue samples were obtained from GTEx and TCGA database. Differently expressed RNA binding proteins (DEGs) were retrieved by Wilcoxon sum-rank test. ClusterProfiler package worked in R software was used to perform GO and KEGG enrichment analyses. Univariate propotional hazard cox regression and multivariate propotional hazard cox regressions were applied to identify DEGs equipped with prognostic value and other clinical independent risk factors. ROC curve was drawn for comparing the survival predict feasibility of risk score with other risk factors in CC patients. Nomogram was drawn to exhibit the prediction model and validated by C-index and calibration curve. Correlations between Differentially expressed RNA binding proteins (DEGs) and other clinical features were investigated by t test or Cruskal wallis analysis. Correlation between Immune and DEGs in cervical cancer was investigated by ssGSEA. Results: 347 differentially expressed RBPs (DEGs) were retrieved from cervical cancer tissue and normal tissue samples. GO enrichment analysis showed that these DEGs involved in RNA splicing, catabolic process and metabolism. Cox regression medel showed that there were ten DEGs significantly associated with overall survival of cervical caner patients. WDR43 (HR = 0.423, P=0.008), RBM38 (HR = 0.533, P<0.001), RNASEH2A (HR=0.474, P=0.002) and HENMT1 (HR=0.720, P=0.071) played protective roles in survival among these ten genes. Stage (Stage IV vs Stage I HR = 3.434, P<0.001) and risk score (HR = 1.214, P< 0.001) were sorted as independent prognostic risk factors based on multivariate cox regression. ROC curve validated that risk score was preferable to predict survival of CC patients than other risk factors. Additionally, we found some of these ten predictor DEGs were correlated significantly in statistic with tumor grade or stage, clinical T stage, clinical N stage, pathology or risk score (all P< 0.05). Part of immune cells and immune functions showed a lower activity in high risk group than low risk group which is distincted by median risk score. Conclusion: Our discovery showed that many RNA binding proteins involved in the progress of cervical cancer, which could probably serve as prognostic biomarkers and accelerate the discovery of treatment targets for CC patients.

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Expression profile of RNA binding protein in cervical cancer using bioinformatics approach

Cancer Cell International ◽

10.1186/s12935-021-02319-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhiyuan Huang ◽

Fang Li ◽

Qinchuan Li

Keyword(s):

Risk Factors ◽

Cervical Cancer ◽

Risk Score ◽

Binding Proteins ◽

Rna Binding ◽

Cox Regression ◽

Rna Binding Proteins ◽

Risk Group ◽

Proportional Hazard ◽

Tissue Samples

Abstract Background It has been demonstrated by studies globally that RNA binding proteins (RBPs) took part in the development of cervical cancer (CC). Few studies concentrated on the correlation between RBPs and overall survival of CC patients. We retrieved significant DEGs (differently expressed genes, RNA binding proteins) correlated to the process of cervical cancer development. Methods Expressions level of genes in cervical cancer and normal tissue samples were obtained from GTEx and TCGA database. Differently expressed RNA binding proteins (DEGs) were retrieved by Wilcoxon sum-rank test. ClusterProfiler package worked in R software was used to perform GO and KEGG enrichment analyses. Univariate proportional hazard cox regression and multivariate proportional hazard cox regressions were applied to identify DEGs equipped with prognostic value and other clinical independent risk factors. ROC curve was drawn for comparing the survival predict feasibility of risk score with other risk factors in CC patients. Nomogram was drawn to exhibit the prediction model and validated by C-index and calibration curve. Correlations between differentially expressed RNA binding proteins (DEGs) and other clinical features were investigated by t test or Cruskal Wallis analysis. Correlation between Immune and DEGs in cervical cancer was investigated by ssGSEA. Results 347 differentially expressed RBPs (DEGs) were retrieved from cervical cancer tissue and normal tissue samples. GO enrichment analysis showed that these DEGs involved in RNA splicing, catabolic process and metabolism. Cox regression model showed that there were ten DEGs significantly associated with overall survival of cervical cancer patients. WDR43 (HR = 0.423, P = 0.008), RBM38 (HR = 0.533, P < 0.001), RNASEH2A (HR = 0.474, P = 0.002) and HENMT1 (HR = 0.720, P = 0.071) played protective roles in survival among these ten genes. Stage (Stage IV vs Stage I HR = 3.434, P < 0.001) and risk score (HR = 1.214, P < 0.001) were sorted as independent prognostic risk factors based on multivariate cox regression. ROC curve validated that risk score was preferable to predict survival of CC patients than other risk factors. Additionally, we found some of these ten predictor DEGs were correlated significantly in statistic with tumor grade or stage, clinical T stage, clinical N stage, pathology or risk score (all P < 0.05). Part of immune cells and immune functions showed a lower activity in high risk group than low risk group which is stratified by median risk score. Conclusion Our discovery showed that many RNA binding proteins involved in the progress of cervical cancer, which could probably serve as prognostic biomarkers and accelerate the discovery of treatment targets for CC patients.

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The Role of RNA-Binding Proteins in Vertebrate Neural Crest and Craniofacial Development

Journal of Developmental Biology ◽

10.3390/jdb9030034 ◽

2021 ◽

Vol 9 (3) ◽

pp. 34

Author(s):

Thomas E. Forman ◽

Brenna J. C. Dennison ◽

Katherine A. Fantauzzo

Keyword(s):

Gene Expression ◽

Neural Crest ◽

Binding Proteins ◽

Rna Binding ◽

Gene Expression Regulation ◽

Rna Binding Proteins ◽

Craniofacial Development ◽

Specific Sequence ◽

Altered Expression ◽

Binding Domains

Cranial neural crest (NC) cells delaminate from the neural folds in the forebrain to the hindbrain during mammalian embryogenesis and migrate into the frontonasal prominence and pharyngeal arches. These cells generate the bone and cartilage of the frontonasal skeleton, among other diverse derivatives. RNA-binding proteins (RBPs) have emerged as critical regulators of NC and craniofacial development in mammals. Conventional RBPs bind to specific sequence and/or structural motifs in a target RNA via one or more RNA-binding domains to regulate multiple aspects of RNA metabolism and ultimately affect gene expression. In this review, we discuss the roles of RBPs other than core spliceosome components during human and mouse NC and craniofacial development. Where applicable, we review data on these same RBPs from additional vertebrate species, including chicken, Xenopus and zebrafish models. Knockdown or ablation of several RBPs discussed here results in altered expression of transcripts encoding components of developmental signaling pathways, as well as reduced cell proliferation and/or increased cell death, indicating that these are common mechanisms contributing to the observed phenotypes. The study of these proteins offers a relatively untapped opportunity to provide significant insight into the mechanisms underlying gene expression regulation during craniofacial morphogenesis.

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The E545 Mutation of PIK3CA in Cervical Cancer Promotes the Survival by Several Different Pathways

10.21203/rs.3.rs-644504/v1 ◽

2021 ◽

Author(s):

Yan Chen ◽

Ma-Chi Yuan ◽

Jia-Zhen Shi ◽

Xia Zhao ◽

Nan He ◽

...

Keyword(s):

Cervical Cancer ◽

Differential Expression ◽

Bioinformatics Analysis ◽

Cancer Tissue ◽

Ppi Network ◽

Tissue Samples ◽

Cervical Cancer Tissue ◽

Differential Expression Genes ◽

High Degree

Abstract Backgroud: The E545 mutation of PIK3CA in Cervical cancer is frequently happened. But the role of E545 mutation of PIK3CA in Cervical cancer is not clear.Methods: In this study, we analysised the molecular signatures of E545 mutation Cervical cancer by bioinformatics methods.Results: We collected transcriptome sequencing results of 227 no mutation cervical cancer tissue samples and 36 mutation cervical cancer tissue samples, then analyzed the data combining bioinformatics methods. A total of 5 differential expression miRNAs were obtained, including 3 up-regulated miRNAs, 1 down-rugulated miRNA. A total of 174 differential expression genes were obtained, including 132 up-regulated genes, 40 down-rugulated genes. GO analysis suggested that the up-regulated DEGs were mainly enriched in transcription factor activity, leukotriene signaling pathway and so on. Besides, we constructed a PPI network with DEGs to screen the top hub genes with a relatively high degree of connectivity. Among them CAV1, KRT20, FOS, had a degree of connectivity larger than 5 and functioned as hub module genes to promote the survival of E545 mutation cervical cancer. We also identified different miRNA-DEG axis, including hsa-mir-449a-AXL, hsa-mir-508-CGA, COL15A1, NNMT, hsa-mir-552-CHST6, NWD1. These axis regulated the survival of E545 mutation cervical cancer togetherly. Conclusions: In conclusion, this study identified DEGs and screened the key genes and pathways closely related to E545 mutation in Cervical cancer by bioinformatics analysis, These results might hold promise for finding potential therapeutic targets of cervical cancer harboring E545 mutation of PI3KCA.

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A high yield gold nanoparticle-based DNA isolation method for human papillomaviruses genotypes from cervical cancer tissue samples

10.3762/bxiv.2019.106.v1 ◽

2019 ◽

Author(s):

Noorossadat Seyyedi ◽

Fatemeh Farjadian ◽

Ali Farhadi ◽

Gholamreza Rafiei Dehbidi ◽

Reza Ranjbaran ◽

...

Keyword(s):

Cervical Cancer ◽

Dna Sequences ◽

Hpv Infection ◽

Human Papillomaviruses ◽

High Yield ◽

Cancer Tissue ◽

Purification Method ◽

Tissue Samples ◽

Hpv Dna ◽

Cervical Cancer Tissue

Gold nanoparticles (AuNPs) are commonly used in biosensors of various kinds. The purification of DNA from cancer tissues is an important step in diagnostic and therapeutic development, but current methods are not optimal. Many cervical cancer patients are also susceptible to high-risk human papillomavirus (HR-HPV) infection. Accurate viral diagnosis has so far relied on the extraction of adequate amounts of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. Since the sensitivity and specificity of commercially available purification kits are not optimal, we designed a DNA purification method based on AuNPs to purify sufficient amounts of HR-HPV DNA from cervical cancer tissue samples. AuNPs were coated with a series of oligonucleotide probes to hybridize to specific DNA sequences of HR-HPV genotypes. With this method, we recovered 733 out of 800 copies of type-specific HPV DNA with complete specificity, compared to 36 copies with a standard commercial kit (Qiagen FFPE).

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Quantitative Analysis of Heparanase Gene Expression in Normal Cervical, Cervical Intraepithelial Neoplastic, and Cervical Carcinoma Tissues

International Journal of Gynecological Cancer ◽

10.1111/igc.0b013e3181ae3f40 ◽

2009 ◽

Vol 19 (9) ◽

pp. 1614-1619 ◽

Cited By ~ 4

Author(s):

Eugene Varchalama ◽

Alexander Rodolakis ◽

Areti Strati ◽

Theocharis Papageorgiou ◽

Christos Valavanis ◽

...

Keyword(s):

Gene Expression ◽

Cervical Cancer ◽

Heparan Sulfate ◽

Mrna Expression ◽

Tumor Size ◽

Invasive Cervical Cancer ◽

Cancer Tissue ◽

Low Grade ◽

Tissue Samples ◽

Cervical Cancer Tissue

Heparanase is an endoglycosidase that specifically cleaves heparan sulfate side chains of heparan sulfate proteoglycans, the major proteoglycans in the extracellular matrix and cell surfaces. Traditionally, heparanase activity was implicated in cellular invasion associated with angiogenesis, inflammation, and cancer metastasis. More recently, heparanase up-regulation was documented in an increasing number of primary human tumors. Ιn this study, we sought to investigate the expression of heparanase messenger RNA (mRNA) in normal cervical tissue and intraepithelial cervical lesion and its clinicopathologic importance in invasive cervical cancer. Gene expression of heparanase was assessed by quantitative real-time reverse transcriptase polymerase chain reaction in 28 normal cervical, 26 intraepithelial neoplastic, and 48 cervical cancer tissue samples. Heparanase mRNA expression was different between the 3 groups and lower in normal cervical specimens in relationship with intraepithelial cervical lesions and invasive cervical cancer tissue samples (P = 0.048). Gradually increasing expression of heparanase was evident as the cells progressed from low-grade to high-grade squamous intraepithelial lesions (P = 0.002). In invasive cervical cancer cases, there was a direct correlation between heparanase expression and tumor size (P = 0.002). In cases treated with radical hysterectomy and pelvic lymphadenectomy, the heparanase mRNA expression was significantly higher in tumors exhibiting lymph vascular space invasion (P = 0.044) and in cases with big tumor size (P = 0.005). In our study, we did not find any significant correlation between disease-free and overall survival rates and expression of heparanase (P = 0.396 and P = 0.712, respectively). The results of this study suggest that the gene expression of heparanase in cervical cancer enhances growth, invasion, and angiogenesis of the tumor and may have therapeutic applications.

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