scholarly journals Long Noncoding RNA Expression Signatures of Metastatic Nasopharyngeal Carcinoma and Their Prognostic Value

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Wei Zhang ◽  
Lin Wang ◽  
Fang Zheng ◽  
Ruhai Zou ◽  
Changqing Xie ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Disease Progression ◽  
Noncoding Rna ◽  
Prognostic Value ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Lncrna Expression ◽  
Genome Wide ◽  
Independent Panel ◽  
Metastatic Nasopharyngeal Carcinoma

Long noncoding RNAs (lncRNAs) have recently been found to play important roles in various cancer types. The elucidation of genome-wide lncRNA expression patterns in metastatic nasopharyngeal carcinoma (NPC) could reveal novel mechanisms underlying NPC carcinogenesis and progression. In this study, lncRNA expression profiling was performed on metastatic and primary NPC tumors, and the differentially expressed lncRNAs between these samples were identified. A total of 33,045 lncRNA probes were generated for our microarray based on authoritative data sources, including RefSeq, UCSC Knowngenes, Ensembl, and related literature. Using these probes, 8,088 lncRNAs were found to be significantly differentially expressed (≥2-fold). To identify the prognostic value of these differentially expressed lncRNAs, four lncRNAs (LOC84740, ENST00000498296, AL359062, and ENST00000438550) were selected; their expression levels were measured in an independent panel of 106 primary NPC samples via QPCR. Among these lncRNAs, ENST00000438550 expression was demonstrated to be significantly correlated with NPC disease progression. A survival analysis showed that a high expression level of ENST00000438550 was an independent indicator of disease progression in NPC patients (P=0.01). In summary, this study may provide novel diagnostic and prognostic biomarkers for NPC, as well as a novel understanding of the mechanism underlying NPC metastasis and potential targets for future treatment.

scholarly journals Genome-Wide Analysis of mRNA and Long Noncoding RNA Profiles in Chronic Actinic Dermatitis

2017 ◽  
Vol 2017 ◽  
pp. 1-15 ◽  
Author(s):  
Dongyun Lei ◽  
Lechun Lv ◽  
Li Yang ◽  
Wenjuan Wu ◽  
Yong Liu ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Differentially Expressed ◽  
Pathogenetic Mechanism ◽  
Bioinformatics Analyses ◽  
Inflammatory Lesions ◽  
Qrt Pcr ◽  
Exposed Skin ◽  
Genome Wide ◽  
Chronic Actinic Dermatitis ◽  
Solid Foundation

Chronic actinic dermatitis (CAD), a photosensitive dermatosis, is characterized by inflammatory lesions, especially on sun-exposed skin. However, its pathogenesis remains unclear. In this study, second-generation RNA sequencing and comprehensive bioinformatics analyses of mRNAs and long noncoding RNAs (lncRNAs) were performed to determine the transcriptome profiles of patients with CAD. A total 6889 annotated lncRNAs, 341 novel lncRNAs, and 65091 mRNAs were identified. Interestingly, patients with CAD and healthy controls showed distinct transcriptome profiles. Indeed, 198 annotated (81.48%) and 45 novel (18.52%) lncRNAs were differentially expressed between the two groups. GO, KEGG, and RGSEA analyses of lncRNAs showed that inflammatory and immune response related pathways played crucial roles in the pathogenetic mechanism of CAD. In addition, we unveiled key differentially expressed lncRNAs, including lncRNA RP11-356I2.4 which plays a role probably by regulating TNFAIP3 and inflammation. qRT-PCR data validated the differentially expressed genes. The newly identified lncRNAs may have potential roles in the development of CAD; these findings lay a solid foundation for subsequent functional exploration of lncRNAs and mRNAs as therapeutic targets for CAD.

scholarly journals Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

2019 ◽  
Vol 20 (21) ◽  
pp. 5419 ◽  
Author(s):  
Gao-Feng Zhou ◽  
Li-Ping Zhang ◽  
Bi-Xian Li ◽  
Ou Sheng ◽  
Qing-Jiang Wei ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Hormones ◽  
Target Genes ◽  
Expression Patterns ◽  
Poncirus Trifoliata ◽  
Differentially Expressed ◽  
Boron Deficiency ◽  
Trifoliate Orange ◽  
Genome Wide ◽  
A Genome

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

scholarly journals Genome-wide analysis of lncRNAs and mRNAs expression during the differentiation of abdominal preadipocytes in chicken

2016 ◽  
Author(s):  
Tao Zhang ◽  
Xiangqian Zhang ◽  
Kunpeng Han ◽  
Genxi Zhang ◽  
Jinyu Wang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Rna Sequencing ◽  
Early Stage ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Valuable Resource ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
And Function ◽  
Jinghai Yellow Chicken

AbstractlncRNAs regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in preadipocytes differentiation of chicken. Here, we identified lncRNAs in preadipocytes of different differentiation stages by RNA-sequencing using Jinghai Yellow chicken. A total of 1,300,074,528 clean reads and 27,023 lncRNAs were obtained from twenty samples. 3095 genes (1,336 lncRNAs and 1,759 mRNAs) were differentially expressed among different stages, of which the number of DEGs decreased with the differentiation, demonstrating that the early stage might be most important for chicken preadipocytes differentiation. Furthermore, 3,095 DEGs were clustered into 8 clusters with their expression patterns by K-means clustering. We identified six stage-specific modules related to A0, A2 and A6 stages using weighted co-expression network analysis. Many well-known/novel pathways associated with preadipocytes differentiation were found. We also identified highly connected genes in each module and visualized them by cytoscape. Many well-known genes related to preadipocytes differentiation were found such as IGFBP2 and JUN. Yet, the majority of high connected genes were unknown in chicken preadipocytes. This study provides a valuable resource for chicken lncRNA study and contributes to batter understanding the biology of preadipocytes differentiation in chicken.

scholarly journals Long non-coding RNA, LINC01614 as a potential biomarker for prognostic prediction in breast cancer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7976 ◽  
Author(s):  
Yaozong Wang ◽  
Baorong Song ◽  
Leilei Zhu ◽  
Xia Zhang
Keyword(s):  
Breast Cancer ◽  
Prognostic Value ◽  
Cox Regression ◽  
Expression Profiles ◽  
Differential Expression Analysis ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Lncrna Expression ◽  
Normal Tissues ◽  
Potential Biomarker

Background Dysregulated long non-coding RNAs (lncRNAs) may serve as potential biomarkers of cancers including breast cancer (BRCA). This study aimed to identify lncRNAs with strong prognostic value for BRCA. Methods LncRNA expression profiles of 929 tissue samples were downloaded from TANRIC database. We performed differential expression analysis between paired BRCA and adjacent normal tissues. Survival analysis was used to identify lncRNAs with prognostic value. Univariate and multivariate Cox regression analyses were performed to confirm the independent prognostic value of potential lncRNAs. Dysregulated signaling pathways associated with lncRNA expression were evaluated using gene set enrichment analysis. Results We found that a total of 398 lncRNAs were significantly differentially expressed between BRCA and adjacent normal tissues (adjusted P value <= 0.0001 and |logFC| >= 1). Additionally, 381 potential lncRNAs were correlated Overall Survival (OS) (P value < 0.05). A total of 48 lncRNAs remained when differentially expressed lncRNAs overlapped with lncRNAs that had prognostic value. Among the 48 lncRNAs, one lncRNA (LINC01614) had stronger prognostic value and was highly expressed in BRCA tissues. LINC01614 expression was validated as an independent prognostic factor using univariate and multivariate analyses. Higher LINC01614 expression was observed in several molecular subgroups including estrogen receptors+, progesterone receptors+ and human epidermal growth factor receptor 2 (HER2)+ subgroup, respectively. Also, BRCA carrying one of four gene mutations had higher expression of LINC01614 including AOAH, CIT, HER2 and ODZ1. Higher expression of LINC01614 was positively correlated with several gene sets including TGF-β1 response, CDH1 signals and cell adhesion pathways. Conclusions A novel lncRNA LINC01614 was identified as a potential biomarker for prognosis prediction of BRCA. This study emphasized the importance of LINC01614 and further research should be focused on it.

scholarly journals Long noncoding RNA expression profile of mouse cementoblasts under compressive force

2019 ◽  
Vol 89 (3) ◽  
pp. 455-463 ◽  
Author(s):  
Hao Liu ◽  
Yiping Huang ◽  
Yingying Zhang ◽  
Yineng Han ◽  
Yixin Zhang ◽  
...  
Keyword(s):  
Expression Profile ◽  
Long Noncoding Rna ◽  
Functional Annotation ◽  
Noncoding Rna ◽  
Compressive Loading ◽  
Compressive Force ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Lncrna Expression ◽  
Qrt Pcr

ABSTRACT Objectives: To investigate the long noncoding RNA (lncRNA) expression profile of cementoblasts under compressive force. Materials and Methods: Mouse cementoblasts were exposed to compression (1.5 g/cm2) for 8 hours. RNA sequencing (RNA-seq) was performed to compare the transcriptomes of the compressed and control cells. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate five of the differentially expressed lncRNAs of interest. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also performed. Results: A total of 70 lncRNAs and 521 mRNAs were differentially regulated in cementoblasts subjected to compressive loading. Among the differentially expressed lncRNAs, 57 were upregulated and 13 downregulated. The expression levels of the five selected lncRNAs (Prkcz2, Hklos, Trp53cor1, Gdap10, and Ak312-ps) were validated by qRT-PCR and consistent with the RNA-seq results. GO functional annotation demonstrated upregulation of genes associated with cellular response to hypoxia and apoptotic processes during compressive loading. KEGG analysis identified the crucial pathways involving the hypoxia-inducing factor-1α, forkhead box O, and mammalian target of rapamycin signaling pathways. Conclusions: Mechanical compression changes the lncRNA expression profile of cementoblasts, providing important references for further investigation into the role and regulation of lncRNAs in compressed cementoblasts and root resorption during orthodontic treatment.

scholarly journals Prognostic value of early radiological response to first‐line platinum‐containing chemotherapy in patients with metastatic nasopharyngeal carcinoma

2019 ◽  
Vol 9 (3) ◽  
pp. 920-930
Author(s):  
Guo‐Ying Liu ◽  
Wang‐Zhong Li ◽  
Kang‐Qiang Peng ◽  
Xing Lv ◽  
Liang‐Ru Ke ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Prognostic Value ◽  
First Line ◽  
Metastatic Nasopharyngeal Carcinoma ◽  
Radiological Response
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