Dataset Information

Differential Expression of Long Noncoding RNAs in Human Cumulus Cells Related to Embryo Developmental Potential: A Microarray Analysis.

ABSTRACT: Long noncoding RNAs (lncRNAs), which are prevalently transcribed in the genome, are involved in a variety of biological functions, yet little is known about their abundance in human cumulus cells (CCs) during oocyte development. Here, we describe the expression profile of lncRNAs in 3 pairs of cumulus cells from mature oocytes that result in high-quality embryo (H-CCs) and from oocytes that result in poor-quality embryo (P-CCs) using microarray analysis. In this study, a total of 20 563 lncRNAs were expressed in human CCs. One hundred and twenty four lncRNAs were consistently upregulated, and 509 lncRNAs were consistently downregulated in all samples analyzed (fold change ? 2.0, P < .05). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate 5 upregulated and 7 downregulated lncRNAs. The qRT-PCR results in the study were confirmed to be consistent with the microarray results. Network analysis was used for further research. The results displayed the differentially expressed lncRNAs in P-CCs between H-CCs, which suggested that lncRNAs may contribute to the processes of oocyte and early embryo development.

SUBMITTER: Xu XF

PROVIDER: S-EPMC4502809 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Differential Expression of Long Noncoding RNAs in Human Cumulus Cells Related to Embryo Developmental Potential: A Microarray Analysis.

Xu Xiao-Feng XF Li Juan J Cao Yun-Xia YX Chen Da-Wei DW Zhang Zhi-Guo ZG He Xiao-Jin XJ Ji Dong-Mei DM Chen Bei-Li BL

Reproductive sciences (Thousand Oaks, Calif.) 20141218 6

Long noncoding RNAs (lncRNAs), which are prevalently transcribed in the genome, are involved in a variety of biological functions, yet little is known about their abundance in human cumulus cells (CCs) during oocyte development. Here, we describe the expression profile of lncRNAs in 3 pairs of cumulus cells from mature oocytes that result in high-quality embryo (H-CCs) and from oocytes that result in poor-quality embryo (P-CCs) using microarray analysis. In this study, a total of 20 563 lncRNAs ...[more]

PMID: 25527423

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Project description:INTRODUCTION: In addition to the well-known short noncoding RNAs such as microRNAs (miRNAs), increasing evidence suggests that long noncoding RNAs (lncRNAs) act as key regulators in a wide aspect of biologic processes. Dysregulated expression of lncRNAs has been demonstrated being implicated in a variety of human diseases. However, little is known regarding the role of lncRNAs with regards to intervertebral disc degeneration (IDD). In the present study we aimed to determine whether lncRNAs are differentially expressed in IDD. METHODS: An lncRNA-mRNA microarray analysis of human nucleus pulposus (NP) was employed. Bioinformatics prediction was also applied to delineate the functional roles of the differentially expressed lncRNAs. Several lncRNAs and mRNAs were chosen for quantitative real-time PCR (qRT-PCR) validation. RESULTS: Microarray data profiling indicated that 116 lncRNAs (67 up and 49 down) and 260 mRNAs were highly differentially expressed with an absolute fold change greater than ten. Moreover, 1,052 lncRNAs and 1,314 mRNAs were differentially expressed in the same direction in at least four of the five degenerative samples with fold change greater than two. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for the differentially expressed mRNAs indicated a number of pathways, such as extracellular matrix (ECM)-receptor interaction. A coding-noncoding gene co-expression (CNC) network was constructed for the ten most significantly changed lncRNAs. Annotation terms of the coexpressed mRNAs were related to several known degenerative alterations, such as chondrocyte differentiation. Moreover, lncRNAs belonging to a particular subgroup were identified. Functional annotation for the corresponding nearby coding genes showed that these lncRNAs were mainly associated with cell migration and phosphorylation. Interestingly, we found that Fas-associated protein factor-1 (FAF1), which potentiates the Fas-mediated apoptosis and its nearby enhancer-like lncRNA RP11-296A18.3, were highly expressed in the degenerative discs. Subsequent qRT-PCR results confirmed the changes. CONCLUSIONS: This is the first study to demonstrate that aberrantly expressed lncRNAs play a role in the development of IDD. Our study noted that up-regulated RP11-296A18.3 highly likely induced the over-expression of FAF1, which eventually promoted the aberrant apoptosis of disc cells. Such findings further broaden the understanding of the etiology of IDD.

Project description:To describe the long noncoding RNA (lncRNA) profiles in cumulus cells isolated from polycystic ovary syndrome (PCOS) patients by employing a microarray and in-depth bioinformatics analysis. This information will help us understand the occurrence and development of PCOS.In this study, we used a microarray to describe lncRNA profiles in cumulus cells isolated from ten patients (five PCOS and five normal women). Several differentially expressed lncRNAs were chosen to validate the microarray results by quantitative RT-PCR (qRT-PCR). Then, the differentially expressed lncRNAs were classified into three subgroups (HOX loci lncRNA, enhancer-like lncRNA, and lincRNA) to deduce their potential features. Furthermore, a lncRNA/mRNA co-expression network was constructed by using the Cytoscape software (V2.8.3, http://www.cytoscape.org/ ).We observed that 623 lncRNAs and 260 messenger RNAs (mRNAs) were significantly up- or down-regulated (?2-fold change), and these differences could be used to discriminate cumulus cells of PCOS from those of normal patients. Five differentially expressed lncRNAs (XLOC_011402, ENST00000454271, ENST00000433673, ENST00000450294, and ENST00000432431) were selected to validate the microarray results using quantitative RT-PCR (qRT-PCR). The qRT-PCR results were consistent with the microarray data. Further analysis indicated that many differentially expressed lncRNAs were transcribed from chromosome 2 and may act as enhancers to regulate their neighboring protein-coding genes. Forty-three lncRNAs and 29 mRNAs were used to construct the coding-non-coding gene co-expression network. Most pairs positively correlated, and one mRNA correlated with one or more lncRNAs.Our study is the first to determine genome-wide lncRNA expression patterns in cumulus cells isolated from PCOS patients by microarray. The results show that clusters of lncRNAs were aberrantly expressed in cumulus cells of PCOS patients compared with those of normal women, which revealed that lncRNAs differentially expressed in PCOS and normal women may contribute to the occurrence of PCOS and affect oocyte development.

Project description:Background: Adrenocortical adenocarcinoma (ACC) is known to be a relatively uncommon malignant tumor of the adrenal gland with patients having a poor prognosis. At present, few reports are available concerning the m6A modifications of lncRNAs as well as their clinical and immunological significance in the occurrence and progression of ACC. Materials and Methods: In the present research, 21 m6A-related genes were analyzed. Both multivariate and univariate Cox regression analyses were conducted to examine the prognostic m6A-related lncRNAs. A sum of 165 m6A-related lncRNAs was obtained from The Cancer Genome Atlas (TCGA) dataset. Based on the expressions of m6A-related lncRNAs, all ACC patients were classified into distinct subgroups using the consistent clustering method. Finally, m6A-related lncRNAs that were shown to have prognostic value were utilized to develop an m6A-related lncRNA risk model, which may be employed in the prediction of prognosis and survival. Results: Using TCGA data set, 26 m6A-associated lncRNAs having putative prognostic values were identified according to their expression levels, TCGA-AAC patients were classified into two clusters with the aid of consistent clustering analysis. The correlation between the two clusters was low, in which cluster1 consisted of 42% of all ACC patients. The survival analysis showed that cluster1 was associated with an unfavorable prognosis relative to cluster2. A risk model was constructed incorporating 26 m6A-associated lncRNAs that were correlated with patient prognosis. The model was subsequently validated by univariate and multivariate Cox, receiver operating characteristic (ROC) curve, and survival analyses. We also observed that the m6A-related risk model performed well in anticipating prognoses and survival status of patients with AAC. The overall survival (OS) of the high-risk cohort, as predicted by the model, was lower as opposed to that of the low-risk cohort. Conclusion: In the present research, we developed a risk model consisting of 4 m6A-related long-noncoding RNAs (lncRNAs), which can exert independent predictive values in patients with ACC. Our findings demonstrated that these 4 m6A-related lncRNAs perform integral functions in the tumor immune microenvironment, and also revealed the possibility of using these lncRNAs to guide the development of prognostic classifications and therapy approaches for ACC patients.

Dataset Information

Differential Expression of Long Noncoding RNAs in Human Cumulus Cells Related to Embryo Developmental Potential: A Microarray Analysis.

Publications

Differential Expression of Long Noncoding RNAs in Human Cumulus Cells Related to Embryo Developmental Potential: A Microarray Analysis.

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