scholarly journals Identification and validation of potential key long noncoding RNAs in sorafenib-resistant hepatocellular carcinoma cells

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8624
Author(s):  
Manya Wu ◽  
Xiaoyun Shen ◽  
Yanping Tang ◽  
Caifu Zhou ◽  
Haixia Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Advanced Hepatocellular Carcinoma ◽  
Ontology Term ◽  
Huh7 Cells ◽  
Hcc Cells

As the first-line treatment, sorafenib has been used for advanced hepatocellular carcinoma (HCC), but the chemoresistance commonly restricts to the clinical efficiency. In this study, we intend to investigate the genome-wide expression pattern of long noncoding RNAs (lncRNAs) in sorafenib-resistant HCC. Herein, we identified thousands of differentially expressed lncRNAs in sorafenib-resistant HCC cells by high-throughput sequencing compared to the parental. Besides, based on GO (Gene Ontology) term enrichment analysis, these differentially expressed lncRNAs are mainly related to binding and catalytic activity and biological regulation of metabolic processes in both the sorafenib-resistant Huh7 cells (Huh7-S) and sorafenib-resistant HepG2 cells (HepG2-S) compared to the parental cells. Moreover, when analyzed by KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, the differentially expressed genes were significantly related to the tight junction. Among them, the expression of TCONS_00284048 and TCONS_00006019 was consistently up-regulated in sorafenib-resistant HCC cell lines, whereas when either was knocked down, the sensitivity of Huh7-S and HepG2-S cells to sorafenib was increased. Taken together, our data demonstrate that the lncRNA expression profile is significantly altered in sorafenib-resistant HCC cells as well as differentially expressed lncRNAs may play crucial functions on HCC sorafenib resistance and HCC progression.

scholarly journals Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yaqiong Wu ◽  
Jing Guo ◽  
Tongli Wang ◽  
Fuliang Cao ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Leaf Color ◽  
Wide Range ◽  
Color Mutation

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood. Results In this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks. Conclusions This study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.

scholarly journals Expression Signatures of Long Noncoding RNAs in Left Ventricular Noncompaction

2021 ◽  
Vol 8 ◽  
Author(s):  
Qingshan Tian ◽  
Hanxiao Niu ◽  
Dingyang Liu ◽  
Na Ta ◽  
Qing Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Left Ventricular ◽  
Long Noncoding Rnas ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Left Ventricular Noncompaction ◽  
Ventricular Noncompaction

Long noncoding RNAs have gained widespread attention in recent years for their crucial role in biological regulation. They have been implicated in a range of developmental processes and diseases including cancer, cardiovascular, and neuronal diseases. However, the role of long noncoding RNAs (lncRNAs) in left ventricular noncompaction (LVNC) has not been explored. In this study, we investigated the expression levels of lncRNAs in the blood of LVNC patients and healthy subjects to identify differentially expressed lncRNA that develop LVNC specific biomarkers and targets for developing therapies using biological pathways. We used Agilent Human lncRNA array that contains both updated lncRNAs and mRNAs probes. We identified 1,568 upregulated and 1,141 downregulated (log fold-change > 2.0) lncRNAs that are differentially expressed between LVNC and the control group. Among them, RP11-1100L3.7 and XLOC_002730 are the most upregulated and downregulated lncRNAs. Using quantitative real-time reverse transcription polymerase chain reaction (RT-QPCR), we confirmed the differential expression of three top upregulated and downregulated lncRNAs along with two other randomly picked lncRNAs. Gene Ontology (GO) and KEGG pathways analysis with these differentially expressed lncRNAs provide insight into the cellular pathway leading to LVNC pathogenesis. We also identified 1,066 upregulated and 1,017 downregulated mRNAs. Gene set enrichment analysis (GSEA) showed that G2M, Estrogen, and inflammatory pathways are enriched in differentially expressed genes (DEG). We also identified miRNA targets for these differentially expressed genes. In this study, we first report the use of LncRNA microarray to understand the pathogenesis of LVNC and to identify several lncRNA and genes and their targets as potential biomarkers.

scholarly journals E2F1-Induced lncRNA BAIAP2-AS1 Overexpression Contributes to the Malignant Progression of Hepatocellular Carcinoma via miR-361-3p/SOX4 Axis

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Yan Yang ◽  
Hong Ge ◽  
De-qing Li ◽  
Ai-xia Xu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Therapeutic Target ◽  
Antisense Rna ◽  
Noncoding Rnas ◽  
Malignant Progression ◽  
Long Noncoding Rnas ◽  
Positive Interaction ◽  
Potential Therapeutic Target ◽  
Proliferation And Metastasis ◽  
Hcc Cells

Currently, plenty of researches have revealed that long noncoding RNAs (lncRNAs) can act as crucial roles during the progression of various tumors, including hepatocellular carcinoma (HCC). Here, we measured the expression of lncRNA BAIAP2 antisense RNA 1(BAIAP2-AS1) as well as its contribution to the developments of HCC. In this study, the expressions of BAIAP2-AS1 and SOX4 were distinctly upregulated in HCC cells and tissues, and high BAIAP2-AS1 may be a novel biomarker for HCC. E2F1 activated BAIAP2-AS1 expression. The silence of BAIAP2-AS1 inhibited the proliferation and metastasis of HepG2 and PLC5 cells. Assays for relationship verification showed that BAIAP2-AS1 regulated the expression of SOX4 and miR-361-3p. Rescue experiments further confirmed the positive interaction between miR-361-3p and BAIAP2-AS1 as well as between miR-361-3p and SOX4. Overall, BAIAP2-AS1 modulated the miR-361-3p/SOX4 axis to promote the development of HCC. Thus, our study offers a potential therapeutic target for treating HCC.

scholarly journals Decoding the Roles of Long Noncoding RNAs in Hepatocellular Carcinoma

2021 ◽  
Vol 22 (6) ◽  
pp. 3137
Author(s):  
Lok-Sze Wong ◽  
Chun-Ming Wong
Keyword(s):  
Hepatocellular Carcinoma ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Future Research ◽  
Research Directions ◽  
Cancer Hallmarks ◽  
Future Research Directions ◽  
Cancer Phenotypes ◽  
Functional Mechanisms

Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies worldwide. HCC is associated with several etiological factors, including HBV/HCV infections, cirrhosis, and fatty liver diseases. However, the molecular mechanism underlying HCC development remains largely elusive. The advent of high-throughput sequencing has unveiled an unprecedented discovery of a plethora of long noncoding RNAs (lncRNAs). Despite the lack of coding capacity, lncRNAs have key roles in gene regulation through interacting with various biomolecules. It is increasingly evident that the dysregulation of lncRNAs is inextricably linked to HCC cancer phenotypes, suggesting that lncRNAs are potential prognostic markers and therapeutic targets. In light of the emerging research in the study of the regulatory roles of lncRNAs in HCC, we discuss the association of lncRNAs with HCC. We link the biological processes influenced by lncRNAs to cancer hallmarks in HCC and describe the associated functional mechanisms. This review sheds light on future research directions, including the potential therapeutic applications of lncRNAs.

scholarly journals The difference in expression of long noncoding RNAs in rat semen induced by high-fat diet was associated with metabolic pathways

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3518 ◽  
Author(s):  
Tian An ◽  
Hui Fan ◽  
Yu F. Liu ◽  
Yan Y. Pan ◽  
Ying K. Liu ◽  
...  
Keyword(s):  
Male Infertility ◽  
Pathway Analysis ◽  
Metabolic Pathways ◽  
High Fat Diet ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
High Fat ◽  
Expression Levels

Background Obesity, a common metabolic disease, is a known cause of male infertility due to its associated health risk. Long noncoding RNAs (lncRNAs) have also been reported to be associated with male reproductive diseases; however, their role in the association between high-fat diet-induced obesity (DIO) and male reproduction remains unclear. Methods We used microarray analysis to compare the expression levels of lncRNAs and mRNAs in the spermatozoa of rats with DIO and normal rats. We selected a few lncRNAs that were obviously up-regulated or down-regulated, and then used RT-PCR to verify the accuracy of their expression. We then performed a functional enrichment analysis of the differentially expressed mRNAs using gene ontology and pathway analysis. Finally, target gene predictive analysis was used to explore the relationship between lncRNAs and mRNAs. Results The results revealed a statistically significant difference in the fasting blood glucose level in rats with DIO and control rats. We found that 973 lncRNAs and 2,994 mRNAs were differentially expressed in the sperm samples of the DIO rats, compared to the controls. GO enrichment analysis revealed 263 biological process terms, 39 cellular component terms, and 40 molecular function terms (p < 0.01) in the differentially expressed mRNAs. The pathway analysis showed that metabolic pathways were most enriched in protein-coding genes. Discussion To the best of our knowledge, this is the first report to show differences in the expression levels of lncRNAs and mRNAs in the sperms of rats with DIO and normal rats, and to determine the expression profile of lncRNAs in the sperm of rats with DIO. Our results have revealed a number of lncRNAs and pathways associated with obesity-induced infertility, including metabolic pathways. These pathways could be new candidates that help cope with and investigate the mechanisms behind the progression of obesity-induced male infertility.

scholarly journals Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jianguo Li ◽  
Jin Zhou ◽  
Shuangshuang Kai ◽  
Can Wang ◽  
Daijun Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Network Analysis ◽  
Primary Liver Cancer ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Long Noncoding Rnas ◽  
Coexpression Network ◽  
Functional Modules ◽  
Biological Processes ◽  
Coexpression Network Analysis

Hepatocellular carcinoma (HCC) is a primary liver cancer associated with a growing incidence and extremely high mortality. However, the pathogenic mechanism is still not fully understood. In the present study, we identified 1,631 upregulated and 1,515 downregulated genes and found that cell cycle and metabolism-related pathways or biological processes highly dysregulated in HCC. To assess the biological importance of these DEGs, we carried out weighted gene coexpression network analysis (WGCNA) to identify the functional modules potentially involved in HCC pathogenesis or progression. The five modules were detected with Dynamic Tree Cut algorithm, and GO enrichment analysis revealed that these modules exhibited different biological processes or signaling pathways, such as metabolism-related pathways, cell proliferation-related pathways, and molecules in tumor microenvironment. Moreover, we also observed two immune cells, namely, cytotoxic cells and macrophage enriched in modules grey and brown, respectively, while T helper cell-2 (Th2) was enriched in module turquoise. Among the WGCNA network, four hub long noncoding RNAs (lncRNAs) were identified to be associated with HCC prognostic outcomes, suggesting that coexpression network analysis could uncover lncRNAs with functional importance, which may be associated with prognostic outcomes of HCC patients. In summary, this study demonstrated that network-based analysis could identify some functional modules and some hub-lncRNAs, which may be critical for HCC pathogenesis or progression.

scholarly journals Long Noncoding RNAs Coregulated by Annexin A7 and JNK in Hepatocellular Carcinoma Cells Identified by Whole-Genome Expression Profiling

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Qi Deng ◽  
Lianhong Li ◽  
Yanling Jin
Keyword(s):  
Hepatocellular Carcinoma ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Jnk Signaling ◽  
Control Shrna ◽  
Enhanced Expression ◽  
And Control ◽  
Annexin A7

Knockdown of Annexin A7 (ANXA7) or C-Jun N-terminal kinase (JNK) inhibits the proliferation, migration, invasion, and lymphatic adhesion of hepatocellular carcinoma (HCC) cells, suggesting that ANXA7 and JNK signaling pathways contribute to HCC growth and lymph node metastasis (LNM). While the intervening molecular pathways are largely unknown, emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in ANXA7 and JNK signaling. To identify potential therapeutic targets for HCC, we screened for lncRNAs differentially expressed among Hca-P cells stably expressing shRNA-ANXA7, shRNA-JNK, or control-shRNA. RNA sequencing identified 216 lncRNAs differentially expressed between shRNA-ANXA7 and control-shRNA cells, of which 101 were downregulated and 115 upregulated, as well as 436 lncRNAs differentially expressed between shRNA-JNK and control-shRNA cells, of which 236 were downregulated and 200 upregulated. Fifty-six lncRNAs were differentially expressed under both ANXA7 and JNK knockdown. We selected 4 of these for verification based on putative involvement in cancer regulation according to GO and KEEG analyses of target genes. Knockdown of ANXA7 or JNK suppressed expression of NONMMUT012084.2, NONMMUT024756.2, and ENSMUST00000130486, and enhanced expression of ENSMUST00000197932. These lncRNAs are intriguing candidate targets for mechanistic analysis of HCC progression and therapeutic intervention.

scholarly journals Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 232
Author(s):  
Weiran Zheng ◽  
Haichao Hu ◽  
Qisen Lu ◽  
Peng Jin ◽  
Linna Cai ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

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