Human transcriptome expression analysis of cervical cancer
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE55940 | GEO | 2014/10/27
SECONDARY ACCESSION(S): PRJNA241383
REPOSITORIES: GEO
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Project description:Although many protein-coding genes have been identified to be aberrantly expressed in cervical cancer, the mechanisms of development and progression of cervical cancer remain unclear. In recent years, non-coding RNAs, especially including microRNAs and long non-coding RNAs, have been shown to play important regulatory roles in mammalian cell biology. In our study, we investigated the whole genome gene expression level changes by human transcriptome array in tumor tissues and paired adjacent non-tumor tissue of patients with cervical cancer. The functions of different expression microRNAs, long non-coding RNAs and mRNAs were further analyzed in vitro and in vivo using loss-of-function and gain-of-function approaches. A ten chip study using total RNA recovered from five separate cervical cancer tissues and five paired adjacent non-tumor samples.
2014-10-27 | E-GEOD-55940 | biostudies-arrayexpress
Project description:In this study, we have identified a microRNA-based signature for the prediction of cervical cancer survival. MicroRNAs (miRNAs) are a newly identified family of small non-coding RNAs that are extensively involved in human cancers. Using our recently established PCR-based miRNA assays, we have analyzed 102 cervical cancers and identified two miRNAs (miR-200a and miR-9) that are likely to predict patient survival. A logistic regression model was developed based on these two miRNAs and the prognostic value of the model was subsequently validated with 42 independent cervical cancers. Furthermore, functional studies were performed to characterize the effect of miRNAs in cervical cancer cells. Our results suggest that both miR-200a and miR-9 could play important regulatory roles in cervical cancer control. In particular, miR-200a is likely to affect the metastatic potential of cervical cancer cells by simultaneously suppressing the expression of multiple genes that are important to cell motility.
2010-02-15 | GSE18545 | GEO
Project description:Approximately half of all microRNAs reside within intronic regions and are often co-transcribed with their host genes. However, most studies on intronic microRNAs focus on individual microRNAs, and conversely most studies on protein-coding and non-coding genes frequently ignore any intron-derived microRNAs. We hypothesize that the individual components of such multi-genic loci may play cooperative or competing roles in driving disease progression, and that examining the combinatorial effect of these components would uncover deeper insights into their functional importance. To address this, we perform systematic analyses of intronic microRNA:host loci in colon cancer. We observe that the FTX locus, comprising of a long non-coding RNA FTX and multiple intronic microRNAs, is highly upregulated in cancer and demonstrate that cooperativity within this multi-component locus promotes cancer growth. In addition, we show that FTX interacts with DHX9 and DICER and delineate its novel roles in regulating A-to-I RNA editing and microRNA expression. These results show for the first time that a long non-coding RNA can regulate A-to-I RNA editing, further expanding the functional repertoire of long non-coding RNAs. We further demonstrate the inhibitory effects of intronic miR-374b and -545 on the tumor suppressors PTEN and RIG-I to enhance the proto-oncogenic PI3K-AKT signaling. Finally, we show that intronic miR-421 may exert an autoregulatory effect on miR-374b and -545. Taken together, our data unveil the intricate interplay between intronic microRNAs and their host transcripts in the modulation of key signaling pathways and disease progression, adding new perspectives to the functional landscape of multi-genic loci.
2021-01-05 | PXD021823 | Pride
Project description:Background. MicroRNAs (miRNAs) are short (~22 nt) non-coding regulatory RNAs that control gene expression at the translational level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. This prompted the development of miRNA-chips for cancer diagnosis or prognosis, opening a new door to understand carcinogenesis. Cervical cancer is one of the most common cancers in women worldwide. Therefore, there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform developed in house containing probes for mature miRNAs. Results. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL) and 9 low-grade squamous intraepithelial lesion (LSIL) samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, miRNAs deregulation in malignant and pre-malignant cervical tissues was detected after tackling the high variability observed. We were also able to identify putative targets of relevant candidate miRNAs. Conclusions. Our results show that miRNA deregulation may play an important role in the malignant transformation of cervical squamous cells. In addition, deregulated miRNAs highlight new candidate targets allowing a better understanding of the molecular mechanism of this tumour type.
2010-08-01 | GSE19611 | GEO
Project description:Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs, which drew little attention in the past. Recently, limited data showed their promising future to act as biomarkers in human cancer, but the characteristics and functions remain largely unknown in human cervical cancer. In this study, we demonstrated the expression profile of circRNAs in cervical squamous cell carcinoma(SCC) patients with circRNA microarray, and identified a large number of circRNAs possibly expressed in SCC.
2017-08-16 | GSE102686 | GEO
Project description:Background. MicroRNAs (miRNAs) are short (~22 nt) non-coding regulatory RNAs that control gene expression at the translational level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. This prompted the development of miRNA-chips for cancer diagnosis or prognosis, opening a new door to understand carcinogenesis. Cervical cancer is one of the most common cancers in women worldwide. Therefore, there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform developed in house containing probes for mature miRNAs. Results. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL) and 9 low-grade squamous intraepithelial lesion (LSIL) samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, miRNAs deregulation in malignant and pre-malignant cervical tissues was detected after tackling the high variability observed. We were also able to identify putative targets of relevant candidate miRNAs. Conclusions. Our results show that miRNA deregulation may play an important role in the malignant transformation of cervical squamous cells. In addition, deregulated miRNAs highlight new candidate targets allowing a better understanding of the molecular mechanism of this tumour type. In this study we used a common reference design experiment where the common reference used was a commercial RNA from normal cervix (Ambion) and the test samples were 4 pre-treatment squamous cell cervical carcinoma, 7 high-grade Squamous Intraepithelial Lesion (CINII, n=2 and CIN III, n=5) sample, 9 low-grade Squamous Intraepithelial Lesion (CIN I) samples, 19 normal cervix samples and 4 pools of normal cervix samples.
2010-08-01 | E-GEOD-19611 | biostudies-arrayexpress
Project description:Background: Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and microRNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interaction has not been investigated in cervical cancer of Uygur woman. High throughput sequencing were used to identify differentially expressed lncRNA, miRNA, and mRNA profiles between normal, cervical intraepithelial neoplasia and cervix carcinoma tissues. Gene Oncology (GO), KEGG enrichment analysis were performed. Gene co-expression network were constructed and pivotal genes were screened out. A total of 1464 lncRNAs were differentially expressed between normal, cervical intraepithelial neoplasia and cervical cancer tissues. GO and KEGG analysis show that related molecular mechanisms and biological processes play a role in cervical cancer. The gene-gene interaction network was constructed and visualized based on Pearson correlation coefficients and TargetScan prediction. These results have shown the potential of lncRNA, miRNA, and mRNA as clinical biomarkers and in elucidating pathological mechanisms of cervical cancer from a transcriptomic perspective.
2021-03-10 | GSE149763 | GEO
Project description:We sequenced plasma exosomal RNA obtained from 58 blood samples from 29 cervical cancer patients treated with concurrent chemoradiotherapy (CCRT) followed by intracavitary brachytherapy. The patients with 2018 International Federation of Gynecology and Obstetrics [FIGO] stage IB-IVB at diagnosis were included. The 29 cervical cancer patients had two blood samples for each patient drawn before and after CCRT. Next generation sequencing data from plasma exosome included small RNAs, long non-coding RNAs, and mRNAs, of which miRNAs and mRNAs were used for analysis. The log2 fold change values were calculated between the two samples from each patient to detect miRNAs as predictors of early progression and metastasis. We analysed their biological functions through miRNA-mRNA network analysis after selecting several potential exosomal miRNAs associated with clinical results.
2021-05-23 | E-MTAB-10215 | biostudies-arrayexpress
Project description:We sequenced plasma exosomal RNA obtained from 24 blood samples from 12 cervical cancer patients treated with concurrent chemoradiotherapy (CCRT) followed by intracavitary brachytherapy. The patients with 2018 International Federation of Gynecology and Obstetrics [FIGO] stage IB-3C2 at diagnosis were included. The 12 cervical cancer patients had two blood samples for each patient drawn before and after CCRT. Next generation sequencing data from plasma exosome included small RNAs, long non-coding RNAs, and mRNAs, of which miRNAs and mRNAs were used for analysis. The log2 fold change values were calculated between the two samples from each patient to detect mRNAs as predictors of slope of function estimated from ALCs and survival. We selected several potential exosomal mRNAs associated with clinical results.
2023-08-13 | E-MTAB-12187 | biostudies-arrayexpress
Project description:Cervical cancer is the second most common cancer in women worldwide. In addition to the important role played by HPV, the underlying mechanism promoting cervical tumorigenesis is complex and involves deregulation of key signaling pathways. Recently, role of miRNA mediated abnormal regulatory mechanisms is implicated in the pathogenesis of cervical cancer. Micro RNAs are regulatory, non‐coding RNAs about 21–23 nucleotides in length and effects the expression of a number of genes at the post‐transcriptional level. For the past few decades, role of curcumin in inhibiting the growth of cervical cancer and increasing the chemo and radio- sensistivity has been studied extensively. Interestingly, curcumin was shown to downregulate NF-κB, Wnt/β-catenin, TGF‐β and various other signaling pathways in cervical cancer cells. Although, a number of microarray studies have examined the use of miRNAs as cancer diagnostic markers, the regulation of miRNAs upon treatment with curcumin in cervical cancer cells has not been studied. The current study is aimed to perform miRNA profiling in cervical cancer cells following curcumin treatment and to study the role of miRNAs in regulating the different signaling pathways.
2022-06-30 | GSE134723 | GEO