Microarray Expression Profiles and bioinformatics analysis of mRNAs, lncRNAs and circRNAs in the secondary temozolomide-resistant glioblastoma
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PROVIDER: PRJNA587112 | ENA |
REPOSITORIES: ENA
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Project description:Glioblastoma multiforme (GBM) is the most common and aggressive primary human brain tumor. Although comprehensive therapies combining radiotherapy and chemotherapy after surgery can prolong survival, the prognosis is still poor with a median survival of only 14.6 months. Chemoresistance is one of the major causes of relapse as well as poor survival in glioma patients. Therefore, novel strategies to overcome chemoresistance are desperately needed for improved treatment of human GBM. Recent studies have demonstrated that long non‑coding RNAs are closely related to resistance to cancer chemotherapy. Here, we simultaneously detected, for the first time, the expression profiles of mRNAs, lncRNAs, and circRNAs in three pairs of secondary temozolomide-resistant glioblastoma (STRG) and matched primary glioblastoma tissues by microarrays. A total of 92 mRNA, 299lncRNAs, and 53 circRNAs were altered during the Chemoresistance. The functions of these differentially expressed RNAs were predicted by Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Co-expression networks of lncRNA-mRNA and circRNA-miRNA were conducted to uncovered the hidden ceRNA mechanisms. Our findings revealed the alteration of expression patterns of mRNAs, lncRNAs, and circRNAs in the secondary temozolomide-resistant glioblastoma. These mRNAs, lncRNAs, and circRNAs might be potential therapeutic targets for the treatment of glioblastoma.
2020-12-17 | GSE139826 | GEO
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2023-12-01 | GSE218847 | GEO
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. The expressions of miRs were examined in HEK-293, HUVEC and Hs68 cells.
2016-07-06 | E-GEOD-73690 | biostudies-arrayexpress
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. The expressions of miRs were examined in HEK-293 cells that were LINC00324- or LOC400043-silenced using siRNA.
2016-07-06 | E-GEOD-73689 | biostudies-arrayexpress
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. Using HEK-293 cells, we performed microarray experiments (n=2) for siRNA-mediated silencing of LINC00324 and LOC40043.
2016-07-06 | E-GEOD-73683 | biostudies-arrayexpress
Project description:Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs circRNAs and miRNAs. We identified that the expression of 501 lncRNAs, 1789 mRNAs, 2038 circRNAs and 143 miRNAs were often altered between glioblastoma and matched normal brain tissue. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on these differentially expressed mRNAs and miRNA-mediated target genes of lncRNAs and circRNAs. Furthermore, we used a multi-step computational framework and several bioinformatics methods to construct a ceRNA network combining mRNAs, miRNAs, lncRNAs and circRNA, based on co-expression analysis between the differentially expressed RNAs. We identified that plenty of lncRNAs, CircRNAs and their downstream target genes in the ceRNA network are related to glutamatergic synapse, suggesting that glutamate metabolism is involved in glioma biological functions. Our results will accelerate the understanding of tumorigenesis, cancer progression and even therapeutic targeting in glioblastoma. We hope to inspire researchers to study the role of non-coding RNAs in glioblastoma.
2016-08-30 | GSE86202 | GEO
Project description:Subcutaneous preadipocyte differentiation play a critical role in fat deposition of pigs. However, the action of different RNAs in subcutaneous preadipocyte differentiation, such as messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are still largely unclear. In the present study, a transcriptome analysis including mRNAs, lncRNAs, and circRNAs was performed in different stages of D0, D2, D4, and D8 using RNA-seq technology. Our results identified 1,554, 470, 1,344, 1,777, and 676 differentially expressed (DE) mRNAs, 112, 58, 95, 136, and 93 DE lncRNAs, and 902, 787, 710, 932, and 850 DE circRNAs between D2 and D0, between D4 and D2, between D8 and D4, between D4 and D0, and between D8 and D0, respectively. Moreover, functional enrichment analysis showed that the common DE mRNAs during entire differentiation were mainly involved in lipid metabolic and cell differentiation processes. Additionally, co-expression network analysis identified the potential lncRNAs related to adipogenesis, e.g., MSTRG.42239 and MSTRG.146410. Taken together, this study provides a genome-wide landscape of RNA expression profiles during subcutaneous preadipocyte differentiation, thus improving our understanding of molecular mechanism in regulating subcutaneous adipogenesis of pigs.
2018-11-14 | GSE114583 | GEO
Project description:Periodontitis is an independent risk factor for atherosclerosis, and F. nucleatum is one of the periodontal pathogens. Several studies have confirmed that non-coding RNAs could affect all aspects of AS disease progression, including lipid metabolism, foam cell formation, cell necrosis, etc. However, no studies have explored whether F. nucleatum could affect AS disease progression by regulating non-coding RNAs. In this study, we intend to acquire mRNAs, lncRNAs and circRNAs expression profiles of aorta samples of AS mice from the F. nucleatum group and the Control group by next-generation sequencing(NGS) and perform bioinformatics analysis. Results revealed that 465 mRNA expression were up-regulated and 382 mRNA expression were down-regulated significantly. Some lncRNAs and circRNAs could suppress the binding of miRNA with target genes in post-transcriptional regulation. By integrating with DE-miRNAs-DEGs pairs and screening the common miRNAs, and mRNAs, lncRNAs, circRNAs that have targeted and negatively correlated relationship with the common miRNAs, lncRNA-miRNA-mRNA (including 34 DE-miRNAs, 42 DE-lncRNAs, and 111 DE-mRNAs) and circRNA-miRNA-mRNA (including 19 DE-miRNAs, 49 DE-circRNAs, and 87 DE-mRNAs) regulatory co-expression networks were constructed. GO enrichment analysis was performed on the differentially expressed mRNAs, which were found to be related to molecular functions, biological processes and cellular components such as protein binding, nucleus, postsynaptic dense zone, protein phosphorylation. KEGG analysis showed that they were related to ErbB signaling pathway, neurotrophic factor signaling pathway, glucagon signaling pathway and apoptosis signaling pathway. This suggested that F. nucleatum could promote the development of atherosclerosis through non-coding RNAs network regulation.
2023-02-22 | GSE225589 | GEO
Project description:Colorectal cancer (CRC) is recognized as the third most common cancer worldwide, and it is one of the leading causes of cancer-related death. However, the current therapeutic regimens were not always effective. Here, the expression profiles of mRNAs, lncRNAs and circRNAs in four pairs of HCT116 and FHC cells were detected by microarray technology
2022-08-18 | GSE211496 | GEO
Project description:Background: Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were less understood. Long non-coding RNA (lncRNA) and circular RNA (circRNA) were discovered to play an important role in regulating occurrence and progression of many diseases and identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of mRNA, lncRNA and circRNA associated with C. baileyi infection were investigated for the first time. Results: The tracheal tissues of experimental (C. baileyi infection) and control chickens were collected for deep RNA sequencing, and 545,479,934 clean reads were obtained. Of them, 1376 novel lncRNAs were identified, including 1161 long intergenic non-coding RNAs (lincRNAs) and 215 anti-sense lncRNAs. 124 lncRNAs were found to be significantly differentially expressed between experimental and control groups. Additionally, 14,698 mRNAs and 9085 circRNAs were identified, and significantly different expressions were observed for 1317 mRNAs and 104 circRNAs between two groups. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of their targets and background genes suggested that these dysregulated genes would be involved in the interaction between host and C. baileyi. Conclusions: The present study firstly provides the expression profiles of mRNAs, lncRNAs and circRNAs during C. baileyi infection, and describes a novel perspective on the potential roles of lncRNAs and circRNAs underlying the pathogenesis mechanism of Cryptosporidium infection.
2018-04-28 | GSE108147 | GEO