Long non-coding RNA-guided regulation in organisms

Qi, Wenchuan; Xu, Shumin; Li, Ling

doi:10.1007/s11427-013-4558-1

Cited by 11 publications

(6 citation statements)

References 93 publications

(52 reference statements)

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“…Long noncoding RNAs (lncRNAs) are a group of endogenous cellular RNAs of more than 200 bp long that encoded by mammalian genome, which couldnot encode proteins for the lack of an open reading frame (Li, Tian, Yang, & Gong, ). LncRNAs may function as signals, guides, decoys, and scaffolds in diverse vital physiological and pathological processes (Bonasio & Shiekhattar, ; Mathieu, Belhocine, Dao, Puthier, & Spicuglia, ; Qi, Song, & Li, ; Ulitsky & Bartel, ). In particular, studies on cancer have proved that lncRNAs actively participated in the regulaton of cancer development and progression, such as cancer growth, metastasis, and recurrence (e.g., H19 (Liang et al, ), HOTAIR (Zhang et al, ), MALAT‐1 (Li, Zou, Xie, et al, ).…”

Section: Introductionmentioning

confidence: 99%

Long noncoding RNAs in cancer‐immunity cycle

Wang²,

et al. 2018

Journal Cellular Physiology

111

113

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The imbalance of immune status in cancer microenvironment plays an important role in the development and progression of cancer. Immunotherapy based on this has become an important field of cancer research in recent years. Many studies on long noncoding RNA (lncRNA) in cancer have focus on its regulation in cancer development and metastasis. Recent studies have suggested that lncRNAs play crucial roles in different phases of cancer immunity, including antigen releasing, antigen presentation, immune activation, immune cells migration, infiltrating into cancer tissues, and killing cancer cells. The functional studies of lncRNAs in cancer immuntity revealed the complicated molecular mechanisms in cancer immunity from a new point of view, which may provide novel potential targets for cancer immunotherapies. Based on the classical cancer-immunity cycle theory, we review the recent studies on the functions and mechanisms of immune-related lncRNAs in different stages of cancer immunity, to summarize the relationship between lncRNAs, and cancer immunity and to provide a framework for further research.

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Section: Introductionmentioning

confidence: 99%

Long noncoding RNAs in cancer‐immunity cycle

Wang²,

et al. 2018

Journal Cellular Physiology

111

113

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“…While more than 70% of the human genome is reportedly transcribed into different types of RNA, less than 2% encodes protein . LncRNAs have been validated in many human tissues and cells and may function in diverse, vital physiological and pathological processes, especially during tumor development …”

Section: Introductionmentioning

confidence: 99%

Long noncoding RNA RP11‐547D24.1 regulates proliferation and migration in papillary thyroid carcinoma: Identification and validation of a novel long noncoding RNA through integrated analysis of TCGA database

et al. 2019

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Long noncoding RNAs (lncRNAs) are known to be key regulators of numerous biological processes, and substantial evidence supports that abnormal lncRNA expression plays a significant role in tumorigenesis and tumor progression. However, the mechanism by which lncRNAs function in thyroid carcinoma are still unclear. To investigate the role of lncRNAs in the tumorigenesis of papillary thyroid carcinoma (PTC), we analyzed lncRNA data in The Cancer Genome Atlas RNA‐Seq database. A comparison of lncRNAs in cancerous thyroid tissues and normal tissues revealed hundreds of differentially expressed lncRNAs. Of 7589 lncRNAs identified in 561 thyroid cancer cases (503 cancerous tissues and 58 normal tissues), the expression levels of 144 were found to be aberrant (|log2 fold change| >2 and adjusted P < 0.05). The top 10 lncRNAs with the most significant differences were LINC01977, RP11‐363E7.4, RP3‐483K16.4, RP11‐547D24.1, RUNDC3A‐AS1, AC093609.1, CTD‐2008L17.2, HAGLROS, UNC5B‐AS1, and LINC01354. In addition, CTD‐2008L17.2, HAGLROS, AC093609.1, UNC5B‐AS1, and RUNDC3A‐AS1 were shown to play vital roles in determining the histological cancer type. Furthermore, RP11‐547D24.1 and UNC5B‐AS1 could distinguish patients with different stages of PTC. The lncRNA RP11‐547D24.1 was validated by loss‐of‐function assays, revealing that downregulation of this lncRNA regulates thyroid tumor cell proliferation and apoptosis, invasion, and migration. This study demonstrates the potential for using lncRNAs to interpret the pathogenesis and development of PTC.

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“…Many functional lncRNAs show tissue-specific expression patterns and distinct subcellular localizations [ 9 , 11 , 13 , 14 ]. Growing evidence suggests that lncRNAs are important modulators of gene expression via their interaction with DNA, RNA, or protein [ 15 – 25 ], while determining the function of individual lncRNAs remains a challenge. Some lncRNAs have been shown to regulate osteogenic differentiation of MSCs [ 26 – 31 ].…”

Section: Introductionmentioning

confidence: 99%

Differential long noncoding RNA/mRNA expression profiling and functional network analysis during osteogenic differentiation of human bone marrow mesenchymal stem cells

et al. 2017

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BackgroundMesenchymal stem cells (MSCs) are the most promising cell types for bone regeneration and repair due to their osteogenic potential. MSC differentiation is precisely regulated and orchestrated by the mechanical and molecular signals from the extracellular environment, involving complex pathways regulated at both the transcriptional and post-transcriptional levels. However, the potential role of long noncoding RNA (lncRNA) in the osteogenic differentiation of human MSCs remains largely unclear.MethodsHere, we undertook the survey of differential coding and noncoding transcript expression profiling and functional network analysis during osteogenic differentiation of human bone marrow mesenchymal stem cells (BMSCs) using human whole transcriptome microarray. The key pathways, mRNAs, and lncRNAs controlling osteogenic differentiation of BMSCs were identified by further bioinformatic analysis. The role of lncRNA in the osteogenic differentiation of MSCs was verified by lncRNA overexpression or knockdown methods.ResultsA total of 1269 coding transcripts with 648 genes significantly upregulated and 621 genes downregulated, and 1408 lncRNAs with 785 lncRNAs significantly upregulated and 623 lncRNAs downregulated were detected along with osteogenic differentiation. Bioinformatic analysis identified that several pathways may be associated with osteogenic differentiation potentials of BMSCs, such as the MAPK signaling pathway, the Jak-STAT signaling pathway, the Toll-like receptor signaling pathway, and the TGF-beta signaling pathway, etc. Bioinformatic analysis also revealed 13 core regulatory genes including seven mRNAs (GPX3, TLR2, BDKRB1, FBXO5, BRCA1, MAP3K8, and SCARB1), and six lncRNAs (XR_111050, NR_024031, FR374455, FR401275, FR406817, and FR148647). Based on the analysis, we identified one lncRNA, XR_111050, that could enhance the osteogenic differentiation potentials of MSCs.ConclusionsThe potential regulatory mechanisms were identified using bioinformatic analyses. We further predicted the interactions of differentially expressed coding and noncoding genes, and identified core regulatory factors by co-expression networks during osteogenic differentiation of BMSCs. Our results could lead to a better understanding of the molecular mechanisms of genes and lncRNAs, and their cooperation underlying MSC osteogenic differentiation and bone formation. We identified that one lncRNA, XR_111050, could be a potential target for bone tissue engineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s13287-017-0485-6) contains supplementary material, which is available to authorized users.

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Long non-coding RNA-guided regulation in organisms

Cited by 11 publications

References 93 publications

Long noncoding RNAs in cancer‐immunity cycle

Long noncoding RNAs in cancer‐immunity cycle

Long noncoding RNA RP11‐547D24.1 regulates proliferation and migration in papillary thyroid carcinoma: Identification and validation of a novel long noncoding RNA through integrated analysis of TCGA database

Differential long noncoding RNA/mRNA expression profiling and functional network analysis during osteogenic differentiation of human bone marrow mesenchymal stem cells

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