Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE172140 | GEO | 2024/04/25
REPOSITORIES: GEO
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Project description:This study aimed to explore the differential lncRNAs in CA and their probable function on CA development.We used RNA-sequencing to assess the genome-wide expression levels of lncRNAs in CA and paired adjacent normal tissues. We further validated the candidate lncRNAs in larger-size of CA specimen using RT-qPCR. Furthermore, the functional enrichment analysis for these candidate lncRNAs and differential mRNAs were analyzed using GO terms, KEGG and STRING database. The coexpressed mRNAs for the candidate lncRNAs, calculated by Pearson?s correlation coefficient, were also analyzed using GO analysis.A total of 657 lncRNAs and 1486 mRNAs were found to dysregulated in CA compared to adjacent mucosal tissues. The microarray data of candidate lncRNAs, including HOXC13-AS, HOTAIR, PICSAR, FGF14-AS1, ADGRD1-AS1, TMEM108-AS1, TUSC7 and FGF10-AS1, were validated with a larger-size of specimen using RT-qPCR. The functional GO term and pathways analysis of DEGs are associated with the pathogenesis and development of CA, including cell proliferation and development, cellular adhesion, immune defense, cell migration and chemotaxis, angiogenesis, and maintaining skin hemostasis.LncRNAs that were differentially expressed between CA and normal tissues may be helpful to explore effective recurrence risk markers and potential intervention targets for CA.
2024-04-25 | GSE172139 | GEO
Project description:This study aimed to explore the differential lncRNAs in CA and their probable function on CA development.We used RNA-sequencing to assess the genome-wide expression levels of lncRNAs in CA and paired adjacent normal tissues. We further validated the candidate lncRNAs in larger-size of CA specimen using RT-qPCR. Furthermore, the functional enrichment analysis for these candidate lncRNAs and differential mRNAs were analyzed using GO terms, KEGG and STRING database. The coexpressed mRNAs for the candidate lncRNAs, calculated by Pearson?s correlation coefficient, were also analyzed using GO analysis.A total of 657 lncRNAs and 1486 mRNAs were found to dysregulated in CA compared to adjacent mucosal tissues. The microarray data of candidate lncRNAs, including HOXC13-AS, HOTAIR, PICSAR, FGF14-AS1, ADGRD1-AS1, TMEM108-AS1, TUSC7 and FGF10-AS1, were validated with a larger-size of specimen using RT-qPCR. The functional GO term and pathways analysis of DEGs are associated with the pathogenesis and development of CA, including cell proliferation and development, cellular adhesion, immune defense, cell migration and chemotaxis, angiogenesis, and maintaining skin hemostasis.LncRNAs that were differentially expressed between CA and normal tissues may be helpful to explore effective recurrence risk markers and potential intervention targets for CA.
2024-04-25 | GSE172137 | GEO
Project description:Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics
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Project description:Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics [clip-seq]
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Project description:Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics [RNA-seq]
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Project description:Long non-coding RNAs (LncRNAs) have been reported to be involved in tumorigenesis and tumor progression. Single nucleotide polymorphisms (SNPs) in the lncRNAs also play a vital role in carcinogenesis. The aim of this study was to assess the relationships between the four selected tagSNPs (rs944289, rs3787016, rs1456315, rs7463708) in the lncRNAs and the risk of female breast cancer in a Chinese population. A case-control study was carried out involving in a total of 439 breast cancer patients and 439 age-matched healthy controls. The genotyping was performed with Sequenom MassARRAY and the expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER-2) in tumor tissues was measured by the immunohistochemistry (IHC) assay. We found that rs3787016 TT genotype (adjusted odds ratio (OR) = 1.62, 95% confidence interval (CI) = 1.09-2.41, P = 0.018) was associated with an increased risk of female breast cancer, especially among the patients with premenopausal status (adjusted OR = 2.55, 95% CI = 1.30-4.97, P = 0.006). Moreover, a statistically significant increased risk of the rs3787016 TT genotype was observed among the patients with advanced tumor stage (Ⅲ and Ⅳ), poor histological grade (G3-G4), positive lymph node involvement, positive expression of ER and PR and negative expression of HER-2; rs7463708 GT and GT/GG genotype were associated with decreased risk of breast cancer in the subgroup of patients with postmenopausal status (GT versus (vs.) TT: adjusted OR = 0.67, 95% CI = 0.46-0.99, P = 0.043; GT/GG vs. TT: adjusted OR = 0.68, 95% CI = 0.47-0.98, P = 0.041) and tumor late-stage (GT vs. TT: adjusted OR = 0.65, 95% CI = 0.43-0.97, P = 0.037; GT/GG vs. TT: adjusted OR = 0.65, 95% CI = 0.44-0.96, P = 0.029). In short, rs3787016 TT genotype was associated with increased breast cancer risk and clinicopathologic features of the tumor, especially among premenopausal women.
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