Dataset Information

Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma.

ABSTRACT: Long non-coding RNAs (lncRNAs) are non-protein-coding RNAs longer than 200 nucleotides. Accumulating evidence demonstrates that lncRNA is a potential biomarker for cancer diagnosis and prognosis. However, there are no prognostic biomarkers and lncRNA models for multiple myeloma (MM). Hence, it is necessary to screen novel lncRNA that can potentially participate in the initiation and progression of MM and consequently construct a risk score system for the disease. Raw microarray datasets were obtained from the Gene Expression Omnibus website. Weighted gene co-expression network analysis and principal component analysis identified 12 lncRNAs of interest. Then, univariate, least absolute shrinkage and selection operator Cox regression and multivariate Cox hazard regression analysis identified two lncRNAs (LINC00996 and LINC00525) that were formulated to construct a risk score system to predict survival. Receiver operating characteristic analysis certificated the superior performance in predicting 3-year overall survival (area under the curve = 0.829). The similar prognostic values of the two-lncRNA signature were also observed in the tested The Cancer Genome Atlas dataset. Furthermore, two other lncRNAs (LINC00324 and LINC01128) were differentially expressed between CD138+ plasma cells from normal donors and MM patients and were verified to be associated with cancer stage in the Gene Expression Omnibus dataset. A lncRNA-mediated competing endogenous RNA network, including 2 lncRNAs, 12 mitochondrial RNAs, and 103 target messenger RNAs, was constructed. In conclusion, we developed a two-lncRNA expression signature to predict the prognosis of MM and constructed a key lncRNA-based competing endogenous RNA network in MM. These lncRNAs were associated with survival and are probably involved in the occurrence and progression of MM.

SUBMITTER: Zhou S

PROVIDER: S-EPMC7481452 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma.

Zhou Sijie S Fang Jiuyuan J Sun Yan Y Li Huixiang H

Frontiers in genetics 20200827

Long non-coding RNAs (lncRNAs) are non-protein-coding RNAs longer than 200 nucleotides. Accumulating evidence demonstrates that lncRNA is a potential biomarker for cancer diagnosis and prognosis. However, there are no prognostic biomarkers and lncRNA models for multiple myeloma (MM). Hence, it is necessary to screen novel lncRNA that can potentially participate in the initiation and progression of MM and consequently construct a risk score system for the disease. Raw microarray datasets were obt ...[more]

PMID: 33193574

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Project description:Researchers have been exploring the molecular mechanisms underlying the control of periodontal ligament stem cell (PDLSC) osteogenic differentiation. Recently, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) were shown to function as competitive endogenous RNAs (ceRNAs) to regulate the effect of microRNAs (miRNAs) on their target genes during cell differentiation. However, comprehensive identification and integrated analysis of lncRNAs and circRNAs acting as ceRNAs during PDLSC osteogenic differentiation have not been performed.PDLSCs were derived from healthy human periodontal ligament and cultured separately with osteogenic induction and normal media for 7 days. Cultured PDLSCs were positive for STRO-1 and CD146 and negative for CD31 and CD45. Osteo-induced PDLSCs showed increased ALP (alkaline phosphatase) activity and up-regulated expression levels of the osteogenesis-related markers ALP, Runt-related transcription factor 2 and osteocalcin. Then, a total of 960 lncRNAs and 1456 circRNAs were found to be differentially expressed by RNA sequencing. The expression profiles of eight lncRNAs and eight circRNAs were measured with quantitative real-time polymerase chain reaction and were shown to agree with the RNA-seq results. Furthermore, the potential functions of lncRNAs and circRNAs as ceRNAs were predicted based on miRanda and were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. In total, 147 lncRNAs and 1382 circRNAs were predicted to combine with 148 common miRNAs and compete for miRNA binding sites with 744 messenger RNAs. These mRNAs were predicted to significantly participate in osteoblast differentiation, the MAPK pathway, the Wnt pathway and the signaling pathways regulating pluripotency of stem cells. Among them, lncRNAs coded as TCONS_00212979 and TCONS_00212984, as well as circRNA BANP and circRNA ITCH, might interact with miRNA34a and miRNA146a to regulate PDLSC osteogenic differentiation via the MAPK pathway.This study comprehensively identified lncRNAs/circRNAs and first integrated their potential ceRNA function during PDLSC osteogenic differentiation. These findings suggest that specific lncRNAs and circRNAs might function as ceRNAs to promote PDLSC osteogenic differentiation and periodontal regeneration.

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Dataset Information

Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma.

Publications

Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma.

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