Expression profile of long non-coding RNAs in human earlobe keloids
ABSTRACT: Microarray analysis was used to determine the expression profiles of lncRNAs and mRNAs between 3 pairs of earlobe keloid and normal specimens. Results provide insight into involement of lncRNAs in the pathological process of earlobe keloid formation. 3 pairs of earlobe keloid and normal specimens.
Project description:Microarray analysis was used to determine the expression profiles of lncRNAs and mRNAs between 3 pairs of earlobe keloid and normal specimens. Results provide insight into involement of lncRNAs in the pathological process of earlobe keloid formation. 3 pairs of earlobe keloid and normal specimens.
Project description:Microarray analysis was used to determine the expression profiles of lncRNAs and mRNAs between 3 pairs of earlobe keloid and normal specimens. Results provide insight into involement of lncRNAs in the pathological process of earlobe keloid formation. Overall design: 3 pairs of earlobe keloid and normal specimens.
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.
Project description:Introduction:Long non-coding RNA (lncRNA) plays a key role in various disorders. However, its role in keloid is still unclear. Aim:We explored differentially expressed (DE) lncRNAs and mRNAs between keloid tissue (KT)s and normal tissue (NT)s, as well as keloid fibroblast (KFB)s and normal fibroblast (NFB)s, respectively. Material and methods:We use KTs and NTs from the chest of 5 patients, and 3 pairs of KFBs and NFBs, to perform microarray respectively. Gene ontology and pathway analyses were conducted by online software DAVID (Database for Annotation, Visualization and Integrated Discovery). The validation of targeted lncRNAs were conducted by qRT-PCR in enlarged samples (79 KTs and 21 NTs). Results:We identified 3680 DE-lncRNAs in tissue essay, and 1231 DE-lncRNAs in cell essay. Furthermore, we found that many lncRNAs and their relative mRNAs were regulated simultaneously in keloid. We identified that ENST00000439703 and uc003jox.1 were up-regulated in both of the above essays through comparing the results of lncRNA screening between tissue essay and cell essay; the results were confirmed through qRT-PCR in enlarged samples. Conclusions:Our study demonstrates that numerous lncRNAs are involved in the pathogenesis and development of the keloid.
Project description:BACKGROUND: Keloids are benign skin tumors that are the effect of a dysregulated wound-healing process in genetically predisposed patients. They are inherited with an autosomal dominant mode with incomplete clinical penetrance and variable expression. Keloids are characterized by formation of excess scar tissue beyond the boundaries of the wound. The exact etiology is still unknown and there is currently no appropriate treatment for keloid disease. METHODS: We analyzed sample tissues were obtained from 20 patients with keloid skin lesions and normal skin was obtained from 20 healthy donors. The telomeres were measured by Terminal Restriction Fragment (TRF) analysis and Real-Time PCR assay. Quantitative Real-Time RT-PCR analysis of hTERT gene expression was performed and intracellular ROS generation was measured. RESULTS: In this study, we determined whether telomeric shortening and the expression of human telomerase reverse transcriptase (hTERT) occurs in keloid patients. Using Terminal Restriction Fragment (TRF) analysis and Real-Time PCR assay, we detected a significant telomere shortening of 30% in keloid specimens compared to normal skin. Using quantitative Real-Time RT-PCR, telomerase activity was found absent in the keloid tissues. Moreover, an increase in ROS generation was detected in fibroblasts cell cultures from keloid specimens as more time elapsed compared to fibroblasts from normal skin. CONCLUSION: Telomere shortening has been reported in several metabolic and cardiovascular diseases. We found that telomere shortening can also be associated with human keloids. Chronic oxidative stress plays a major role in the pathophysiology of several chronic inflammatory diseases. Here we found increased ROS generation in fibroblasts from keloid fibroblasts cell cultures when compared to normal skin fibroblasts. Hence we conclude that oxidative stress might be an important modulator of telomere loss in keloid because of the absence of active telomerase that counteracts telomere shortening.
Project description:<h4>Background</h4>The role of epithelial-mesenchymal transition (EMT) in the pathogenesis of keloids is currently raising increasing attention. Long noncoding RNAs (lncRNAs) govern a variety of biological processes, such as EMT, and their dysregulation is involved in many diseases including keloid disease. The aim of this study was to identify differentially expressed EMT-related lncRNAs in keloid tissues versus normal tissues and to interpret their functions.<h4>Results</h4>Eleven lncRNAs and 16 mRNAs associated with EMT were identified to have differential expression between keloid and normal skin tissues (fold change > 1.5, P < 0.05). Gene Ontology (GO) analysis showed that these differentially expressed mRNAs functioned in the extracellular matrix, protein binding, the positive regulation of cellular processes, the Set1C/COMPASS complex and histone acetyltransferase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these mRNAs are involved in pathways in cancer. The lncRNA, XLOC_000587 may promote cell proliferation and migration by enhancing the expression of ENAH, while AF268386 may facilitate the invasive growth of keloids by upregulating DDR2.<h4>Conclusions</h4>We characterized the differential expression profiles of EMT-related lncRNAs and mRNAs in keloids, which may contribute to preventing the occurrence and development of keloids by targeting the corresponding signaling pathways. These lncRNAs and mRNAs may provide biomarkers for keloid diagnosis and serve as potential targets for the treatment of this disease.
Project description:The long non-coding RNAs (lncRNAs) regulating encoding transcripts/genes involved in Wnt signalling pathway in keloids is largely unclear. We used a pathway-focused lncRNA microarray to detect the differentiated expression profiles of both lncRNAs and genes involved in Wnt pathway, thus a total of 116 Wnt-targeted genes and 69 Wnt-related lncRNAs aberrantly expressed in keloids were initially identified. A stepwise bioinformatics was further performed to find skin-related lncRNA/gene pairs in Wnt pathway in keloids. Firstly, an lncRNA/gene co-expression network with clustered functional modules was constructed; simultaneously, 114 Wnt-genes regarding to dermis were online enriched using Phenotype Enrichment. Secondly, 17 skin-related keloid-aberrant Wnt-genes were acquired by overlapping the 114 skin-related Wnt-genes with the 116 keloid-aberrant Wnt-genes. Thirdly, after co-expression coefficient of each lncRNA/gene profile being ranked respectively, 11 top co-expressed lncRNAs characterized with the highest co-expression coefficients to the 17 genes were identified. Fourthly, seven of the 11 top co-expressed lncRNAs exhibiting array-detected aberrant expression in keloids, together with their 12 most interactive Wnt-genes, were selected to undergo in-pair intracellularly quantitative PCR validation in keloids. As a result, four lncRNAs including CACNA1G-AS1, HOXA11-AS, LINC00312 and RP11-91I11.1 with their six paired Wnt-genes undergoing both array-and-qPCR as well as lncRNA-and-gene double validation were finally identified as skin-related lncRNA/gene pairs that involved in Wnt signalling pathway in keloids. In conclusion, in-depth exploration on these easily-accessible lncRNAs in keloids might aid to find the novel target on how to maintain highly recurrent tumours benign via Wnt-involved network regulation.
Project description:Background:We hypothesized that crosstalk between noncoding RNAs, including microRNA (miRNA), lncRNA, and circRNA, might play a critical role in keloids development and physiology. To reveal the molecular mechanisms involved in the pathogenesis of keloids, we compared their gene expression profiles and differential expressions in keloid and normal skin tissues. Methods:Expression profiles of mRNAs and lncRNAs and circRNAs in 2 pairs (identification set) of keloid and matched normal skin tissues were analyzed through sequencing. Real-time quantitative PCR was performed to validate the sequencing results using 5 pairs (validation set) of keloid and matched normal skin tissues. Presumed targets of differentially expressed lncRNAs and circRNAs were functionally annotated by bioinformatics approaches. Results:The differential expression of mRNAs in keloid and normal skin by high-throughput sequencing was 2,528, of which 1,271 were downregulated, whereas 1,257 were upregulated. In the meantime, sequencing identified 2,227 differentially expressed lncRNAs, including 1,224 upregulated and 1,003 downregulated in keloid tissue compared with normal skin tissue. Additionally, 154 differentially expressed circRNAs were identified, including 81 upregulated and 73 downregulated in keloid tissue compared with normal skin tissue. Functional annotations of differentially expressed circRNA targets revealed their enrichment in several signaling pathways important for scar wound healing. Conclusions:Expression profiles of mRNAs, lncRNAs, and circRNAs were altered in keloid tissue, which may partly contribute to the etiology of keloids by affecting several signaling pathways relevant to scar wound healing. A better understanding of keloids pathogenesis may identify new therapeutic targets for keloids.
Project description:Genome wide DNA methylation profiling of normal skin and keloid samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in keloid and normal samples. Samples included 6 normal skin, 6 Keloid. Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.1