mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer
Cervical cancer is one of the most frequent cancers in women and is associated with human papillomavirus (HPV) in 70 % of cases. Cervical cancer occurs because of progression of low-differentiated cervical intraepithelial neoplasia through grade 2 and 3 lesions. Along with the protein-coding genes,...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2024-05-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/4148 |
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| author | E. D. Kulaeva E. S. Muzlaeva E. V. Mashkina |
| author_facet | E. D. Kulaeva E. S. Muzlaeva E. V. Mashkina |
| author_sort | E. D. Kulaeva |
| collection | DOAJ |
| description | Cervical cancer is one of the most frequent cancers in women and is associated with human papillomavirus (HPV) in 70 % of cases. Cervical cancer occurs because of progression of low-differentiated cervical intraepithelial neoplasia through grade 2 and 3 lesions. Along with the protein-coding genes, long noncoding RNAs (lncRNAs) play an important role in the development of malignant cell transformation. Although human papillomavirus is widespread, there is currently no well-characterized transcriptomic signature to predict whether this tumor will develop in the presence of HPV-associated neoplastic changes in the cervical epithelium. Changes in gene activity in tumors reflect the biological diversity of cellular phenotype and physiological functions and can be an important diagnostic marker. We performed comparative transcriptome analysis using open RNA sequencing data to assess differentially expressed genes between normal tissue, neoplastic epithelium, and cervical cancer. Raw data were preprocessed using the Galaxy platform. Batch effect correction, identification of differentially expressed genes, and gene set enrichment analysis (GSEA) were performed using R programming language packages. Subcellular localization of lncRNA was analyzed using Locate-R and iLoc-LncRNA 2.0 web services. 1,572 differentially expressed genes (DEGs) were recorded in the “cancer vs. control” comparison, and 1,260 DEGs were recorded in the “cancer vs. neoplasia” comparison. Only two genes were observed to be differentially expressed in the “neoplasia vs. control” comparison. The search for common genes among the most strongly differentially expressed genes among all comparison groups resulted in the identification of an expression signature consisting of the CCL20, CDKN2A, CTCFL, piR-55219, TRH, SLC27A6 and EPHA5 genes. The transcription level of the CCL20 and CDKN2A genes becomes increased at the stage of neoplastic epithelial changes and stays so in cervical cancer. Validation on an independent microarray dataset showed that the differential expression patterns of the CDKN2A and SLC27A6 genes were conserved in the respective gene expression comparisons between groups. |
| format | Article |
| id | doaj-art-c763718a198241898b2299c7853be72b |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2024-05-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-c763718a198241898b2299c7853be72b2025-02-01T09:58:13ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592024-05-0128334235010.18699/vjgb-24-391469mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancerE. D. Kulaeva0E. S. Muzlaeva1E. V. Mashkina2Southern Federal UniversitySouthern Federal UniversitySouthern Federal UniversityCervical cancer is one of the most frequent cancers in women and is associated with human papillomavirus (HPV) in 70 % of cases. Cervical cancer occurs because of progression of low-differentiated cervical intraepithelial neoplasia through grade 2 and 3 lesions. Along with the protein-coding genes, long noncoding RNAs (lncRNAs) play an important role in the development of malignant cell transformation. Although human papillomavirus is widespread, there is currently no well-characterized transcriptomic signature to predict whether this tumor will develop in the presence of HPV-associated neoplastic changes in the cervical epithelium. Changes in gene activity in tumors reflect the biological diversity of cellular phenotype and physiological functions and can be an important diagnostic marker. We performed comparative transcriptome analysis using open RNA sequencing data to assess differentially expressed genes between normal tissue, neoplastic epithelium, and cervical cancer. Raw data were preprocessed using the Galaxy platform. Batch effect correction, identification of differentially expressed genes, and gene set enrichment analysis (GSEA) were performed using R programming language packages. Subcellular localization of lncRNA was analyzed using Locate-R and iLoc-LncRNA 2.0 web services. 1,572 differentially expressed genes (DEGs) were recorded in the “cancer vs. control” comparison, and 1,260 DEGs were recorded in the “cancer vs. neoplasia” comparison. Only two genes were observed to be differentially expressed in the “neoplasia vs. control” comparison. The search for common genes among the most strongly differentially expressed genes among all comparison groups resulted in the identification of an expression signature consisting of the CCL20, CDKN2A, CTCFL, piR-55219, TRH, SLC27A6 and EPHA5 genes. The transcription level of the CCL20 and CDKN2A genes becomes increased at the stage of neoplastic epithelial changes and stays so in cervical cancer. Validation on an independent microarray dataset showed that the differential expression patterns of the CDKN2A and SLC27A6 genes were conserved in the respective gene expression comparisons between groups.https://vavilov.elpub.ru/jour/article/view/4148human papillomavirusneoplasiacervical cancertranscriptome analysislncrnacdkn2accl20 |
| spellingShingle | E. D. Kulaeva E. S. Muzlaeva E. V. Mashkina mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer Вавиловский журнал генетики и селекции human papillomavirus neoplasia cervical cancer transcriptome analysis lncrna cdkn2a ccl20 |
| title | mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer |
| title_full | mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer |
| title_fullStr | mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer |
| title_full_unstemmed | mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer |
| title_short | mRNA-lncRNA gene expression signature in HPV-associated neoplasia and cervical cancer |
| title_sort | mrna lncrna gene expression signature in hpv associated neoplasia and cervical cancer |
| topic | human papillomavirus neoplasia cervical cancer transcriptome analysis lncrna cdkn2a ccl20 |
| url | https://vavilov.elpub.ru/jour/article/view/4148 |
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