Microarray analysis of long noncoding RNAs in primary human keratinocytes in response to CaCl2 stimulation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE212548 | GEO | 2022/09/02
REPOSITORIES: GEO
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Project description:Microarray analysis of long noncoding RNAs in primary human keratinocytes in response to CaCl2 stimulation
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Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal.
2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging.
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4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.
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Project description:Tumour DNA contains thousands of somatic single nucleotide variants (SNVs) in non-protein-coding elements, yet their functional significance remains poorly understood. Amongst the most highly mutated elements are long noncoding RNAs (lncRNAs), functional transcripts with known roles in carcinogenesis. To search for driver mutations in lncRNAs, we apply an integrative driver discovery algorithm to SNVs from 2583 primary tumours and 3527 metastases to reveal 54 potential “driver lncRNAs”. Our algorithm confirms a particularly high mutation rate in the iconic cancer lncRNA, NEAT1, which has been ascribed by recent studies to passenger effects. We directly test the functionality of NEAT1 SNVs using in cellulo mutagenesis, identifying discrete regions where mutations reproducibly increase cell proliferation in diverse cell backgrounds, both cancerous and normal. In particular, mutations in the 5’ region alter ribonucleoprotein assembly and boost the population of subnuclear paraspeckles, thus mechanistically linking mutations to cellular proliferation. We then used RNA-pull down followed by mass spectrometry to identify the protein interactor changing between the wild type and mutant form of NEAT1.
2023-07-20 | PXD034007 | Pride
Project description:DNA damage repair and G2/M arrest are the key factors regulating the survival of cancer cells exposed to radiation. Recent studies have shown that long noncoding RNAs (lncRNAs) play important roles in a variety of biological processes, including DNA repair, cell cycle regulation, differentiation, and epigenetic regulation. However, the knowledge about the genome scale of lncRNAs and their potential biological functions in tumor cells exposed to radiation are still unclear. In this study, we used LncRNA + mRNA Human Gene Expression Microarray V4.0 to profile lncRNA and messenger RNA (mRNA) from HeLa, MCF-7, and A549 cells after irradiation with 4 Gy of ?-radiation. We identified 230, 227, and 274 differentially expressed lncRNAs and 150, 214, and 274 differentially expressed mRNAs in HeLa, MCF-7, and A549 cells, respectively, among which there are 14 common differentially expressed lncRNAs and 22 common differentially expressed mRNAs in all of the 3 cell lines. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that these differentially expressed mRNAs were mainly associated with cell cycle. Further, we also predicted the target genes and functions of these differentially expressed lncRNAs. Our study on lncRNAs has greatly expanded the field of gene research in the relationship of radiation, cell cycle, and DNA damage.
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Project description:GM0637 cell were treated with or without DNA damaging agent neocarzinostatin (NCS), and cells were harvested after 4 hours and 8 hours for the microarray analyses of whole-genome long noncoding RNAs. To examine how long noncoding RNAs are regulated in the DNA damage response, we assessed the genome-wide long noncoding RNA expression in GM0637 cells treated with or without DNA damage
2013-01-17 | E-GEOD-43509 | biostudies-arrayexpress
Project description:Primary keratinocytes from Pla2g2f-/- mice were defective in proper differentiation and activation. Pla2g2f+/+ and Pla2g2f-/- keratinocytes after culture for 48 h with (differentiated) or without (control) 1 mM CaCl2. Equal amounts of total RNA were pooled from keratinocytes from 6 mice for each genotype.
2015-08-08 | E-GEOD-71826 | biostudies-arrayexpress
Project description:Regulation of neuroregeneration by long noncoding RNAs
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Project description:Analysis of long noncoding RNAs in macrophages
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Project description:Noncoding RNAs include small transcripts, such as microRNAs and piwi-interacting RNAs, and a wide range of long noncoding RNAs (lncRNAs). Although many lncRNAs have been identified, only a small number of lncRNAs have been characterized functionally. Here, we sought to identify lncRNAs differentially expressed during replicative senescence. We compared lncRNAs expressed in proliferating, early-passage, 'young' human diploid WI-38 fibroblasts [population doubling (PDL) 20] with those expressed in senescent, late-passage, 'old' fibroblasts (PDL 52) by RNA sequencing (RNA-Seq). Numerous transcripts in all lncRNA groups (antisense lncRNAs, pseudogene-encoded lncRNAs, previously described lncRNAs and novel lncRNAs) were validated using reverse transcription (RT) and real-time, quantitative (q)PCR. Among the novel senescence-associated lncRNAs (SAL-RNAs) showing lower abundance in senescent cells, SAL-RNA1 (XLOC_023166) was found to delay senescence, because reducing SAL-RNA1 levels enhanced the appearance of phenotypic traits of senescence, including an enlarged morphology, positive β-galactosidase activity, and heightened p53 levels. Our results reveal that the expression of known and novel lncRNAs changes with senescence and suggests that SAL-RNAs play direct regulatory roles in this important cellular process. RNA was extracted from both young and senescent WI-38 cells and used for total RNA-Seq.
2016-02-08 | E-GEOD-77675 | biostudies-arrayexpress
Project description:Background. Long noncoding RNAs (lncRNAs) play key roles in a wide range of biological processes and their deregulation results in human disease, including keloids. Earlobe keloid is a type of pathological skin scar, and the molecular pathogenesis of this disease remains largely unknown. Methods. In this study, microarray analysis was used to determine the expression profiles of lncRNAs and mRNAs between 3 pairs of earlobe keloid and normal specimens. Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to identify the main functions of the differentially expressed genes and earlobe keloid-related pathways. Results. A total of 2068 lncRNAs and 1511 mRNAs were differentially expressed between earlobe keloid and normal tissues. Among them, 1290 lncRNAs and 1092 mRNAs were upregulated, and 778 lncRNAs and 419 mRNAs were downregulated. Pathway analysis revealed that 24 pathways were correlated to the upregulated transcripts, while 11 pathways were associated with the downregulated transcripts. Conclusion. We characterized the expression profiles of lncRNA and mRNA in earlobe keloids and suggest that lncRNAs may serve as diagnostic biomarkers for the therapy of earlobe keloid.
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