Expression Profile of Long Noncoding RNAs in Human Earlobe Keloids: A Microarray Analysis

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.

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

BMC Plant Biology ◽

10.1186/s12870-019-2141-z ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

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.

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Characterization and validation of long noncoding RNAs as new candidates in prostate cancer

10.21203/rs.3.rs-36555/v3 ◽

2020 ◽

Author(s):

Shengyang Ge ◽

Yuanyuan Mi ◽

Xiaojun Zhao ◽

Qingfeng Hu ◽

Yijun Guo ◽

...

Keyword(s):

Prostate Cancer ◽

Expression Profiles ◽

Survival Curve ◽

Noncoding Rnas ◽

Hazard Ratio ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Clinical Samples ◽

High Hazard Ratio ◽

High Hazard

Abstract Background: Long noncoding RNAs (lncRNAs) have been proved to be an important regulator in gene expression. In almost all kinds of cancers, lncRNAs participated in the process of pathogenesis, invasion, and metastasis. Meanwhile, compared with the large amounts of patients, there is rare knowledge about the role of lncRNAs in prostate cancer (PCa). Material/Method: In this study, lncRNA expression profiles of prostate cancer were detected by Agilent microarray chip, 5 pairs of case and control specimens were involved in. Differentially expressed lncRNAs were screened out by volcano plot for constructing lncRNA-miRNA-mRNA central network. Then, the top ten up-regulated and down-regulated lncRNAs were validated by qRT-PCR in another 5 tumor specimens and 7 para-cancerous/benign contrasts. Furthermore, we searched for the survival curve of the top 10 upregulated and downregulated lncRNAs. Results: A total of 817 differentially expressed lncRNAs were filtered out by the criteria of fold change (FC) and t-test p < 0.05. Among them, 422 were upregulated, whereas 395 were downregulated in PCa tissues. Gene ontology and KEGG pathway analyses showed that many lncRNAs were implicated in carcinogenesis. lnc-MYL2-4:1 (FC = 0.00141, p = 0.01909) and NR_125857 (FC = 59.27658, p = 0.00128) had the highest magnitude of change. The subsequent qPCR confirmed the expression of NR_125857 was in accordance with the clinical samples. High expression of PCA3, PCAT14 and AP001610.9 led to high hazard ratio while low expression of RP11-279F6.2 led to high hazard ratio. Conclusions: Our study detected a relatively novel complicated map of lncRNAs in PCa, which may have the potential to investigate for diagnosis, treatment and follow-up in PCa. Our study revealed the expression of NR_125857 in human PCa tissues was most up-regulated. Further studies are needed to investigate to figure out the mechanisms in PCa.

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Long Noncoding RNAs and Messenger RNAs Expression Profiles Potentially Regulated by ZBTB7A in Nasopharyngeal Carcinoma

BioMed Research International ◽

10.1155/2019/7246491 ◽

2019 ◽

Vol 2019 ◽

pp. 1-16

Author(s):

Fei Liu ◽

Jiazhang Wei ◽

Yanrong Hao ◽

Fengzhu Tang ◽

Wei Jiao ◽

...

Keyword(s):

Nasopharyngeal Carcinoma ◽

Fatty Acid Synthase ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Messenger Rnas ◽

Regulatory Pathways ◽

Different Levels

Our previous studies showed that ZBTB7A played an important role in promoting nasopharyngeal carcinoma (NPC) progression. However, molecular mechanisms of different levels of ZBTB7A are still unclear. It is necessary to search molecular markers which are closely connected with ZBTB7A. We selected NPC sublines CNE2 with stably transfecting empty plasmid (negative control, NC) and short hair RNA (shRNA) plasmid targeting ZBTB7A as research objectives. Microarray was used to screen differentially expressed long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) via shRNA-CNE2 versus NC-CNE2. Quantitative PCR (qPCR) was used to validate lncRNAs and mRNAs from the sublines, chronic rhinitis, and NPC tissues. Bioinformatics was used to analyze regulatory pathways which were connected with ZBTB7A. The 1501 lncRNAs (long noncoding RNAs) and 1275 differentially expressed mRNAs were upregulated or downregulated over 2-fold. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the upregulated or downregulated carbohydrate and lipid metabolisms probably involved in carcinogenicity of shRNA-CNE2 (P-value cut-off was 0.05). In order to find the molecular mechanisms of ZBTB7A, we validated 12 differentially expressed lncRNAs and their nearby mRNAs by qPCR. Most of the differentially expressed mRNAs are closely connected with carbohydrate and lipid metabolisms in multiply cancers. Furthermore, part of them were validated in NPC and rhinitis tissues by qPCR. As a result, NR_047538, ENST00000442852, and fatty acid synthase (FASN) were closely associated with NPC. ZBTB7A had a positive association with NR_047538 and negative associations with ENST00000442852 and FASN. The results probably provide novel candidate biomarkers for NPC progression with different levels of ZBTB7A.

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Characterization and validation of long noncoding RNAs as new candidates in prostate cancer

Cancer Cell International ◽

10.1186/s12935-020-01615-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Shengyang Ge ◽

Yuanyuan Mi ◽

Xiaojun Zhao ◽

Qingfeng Hu ◽

Yijun Guo ◽

...

Keyword(s):

Prostate Cancer ◽

Expression Profiles ◽

Survival Curve ◽

Noncoding Rnas ◽

Hazard Ratio ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Clinical Samples ◽

High Hazard Ratio ◽

High Hazard

Abstract Background Long noncoding RNAs (lncRNAs) have been proved to be an important regulator in gene expression. In almost all kinds of cancers, lncRNAs participated in the process of pathogenesis, invasion, and metastasis. Meanwhile, compared with the large amounts of patients, there is rare knowledge about the role of lncRNAs in prostate cancer (PCa). Material/Method In this study, lncRNA expression profiles of prostate cancer were detected by Agilent microarray chip, 5 pairs of case and control specimens were involved in. Differentially expressed lncRNAs were screened out by volcano plot for constructing lncRNA-miRNA-mRNA central network. Then, the top ten up-regulated and down-regulated lncRNAs were validated by qRT-PCR in another 5 tumor specimens and 7 para-cancerous/benign contrasts. Furthermore, we searched for the survival curve of the top 10 upregulated and downregulated lncRNAs. Results A total of 817 differentially expressed lncRNAs were filtered out by the criteria of fold change (FC) and t-test p < 0.05. Among them, 422 were upregulated, whereas 395 were downregulated in PCa tissues. Gene ontology and KEGG pathway analyses showed that many lncRNAs were implicated in carcinogenesis. lnc-MYL2-4:1 (FC = 0.00141, p = 0.01909) and NR_125857 (FC = 59.27658, p = 0.00128) had the highest magnitude of change. The subsequent qPCR confirmed the expression of NR_125857 was in accordance with the clinical samples. High expression of PCA3, PCAT14 and AP001610.9 led to high hazard ratio while low expression of RP11-279F6.2 led to high hazard ratio. Conclusions Our study detected a relatively novel complicated map of lncRNAs in PCa, which may have the potential to investigate for diagnosis, treatment and follow-up in PCa. Our study revealed the expression of NR_125857 in human PCa tissues was most up-regulated. Further studies are needed to investigate to figure out the mechanisms in PCa.

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RNA sequencing identifies two novel liver-specific long noncoding RNAs with potential diagnostic value in hepatocellular carcinoma

Biomarkers in Medicine ◽

10.2217/bmm-2020-0825 ◽

2021 ◽

Author(s):

Chao Tan ◽

Xi Zeng ◽

Meile Mo ◽

Xiaoyun Ma ◽

Qiuli Liang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Rna Sequencing ◽

Reverse Transcription ◽

Expression Profiles ◽

Noncoding Rnas ◽

Area Under The Curve ◽

Long Noncoding Rnas ◽

Normal Tissues ◽

Quantitative Reverse Transcription Pcr ◽

Reverse Transcription Pcr

Aim: To explore the expression profiles of long noncoding RNAs (lncRNAs) and identify novel lncRNAs as biomarkers for early diagnosis and therapy of hepatocellular carcinoma (HCC). Materials & methods: Expression profiles of lncRNAs and mRNAs in five paired HCC and adjacent normal tissues were obtained by RNA sequencing. Eight lncRNAs, including two novel liver-specific lncRNAs (NONHSAT059247.2 and NONHSAT013897.2), were validated in another 74 pairs of HCC and adjacent normal tissues by quantitative reverse transcription PCR. Results: The results of quantitative reverse transcription PCR showed that NONHSAT252133.1, NONHSAT112116.2 and NONHSAT242657.1 were significantly upregulated in HCC tissues, whereas NONHSAT169790.1, NONHSAT059247.2 and NONHSAT013897.2 were significantly downregulated. Two liver-specific lncRNAs demonstrated excellent diagnostic performance: NONHSAT059247.2 (area under the curve = 0.941, 95% CI: 0.902–0.979, p < 0.0001), NONHSAT013897.2 (area under the curve = 0.944, 95% CI: 0.906–0.983, p < 0.0001). Conclusion: The liver-specific lncRNAs NONHSAT059247.2 and NONHSAT013897.2, may provide new biomarkers for the future study on diagnosis, therapy, and mechanisms of HCC.

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Unraveling the Expression Profiles of Long Noncoding RNAs in Rat Cardiac Hypertrophy and Functions of lncRNA BC088254 in Cardiac Hypertrophy Induced by Transverse Aortic Constriction

Cardiology ◽

10.1159/000443370 ◽

2016 ◽

Vol 134 (2) ◽

pp. 84-98 ◽

Cited By ~ 12

Author(s):

Xiaoying Li ◽

Lei Zhang ◽

Jiangjiu Liang

Keyword(s):

Cardiac Hypertrophy ◽

Myocardial Hypertrophy ◽

Heart Diseases ◽

Expression Profiles ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Transverse Aortic Constriction ◽

Rt Pcr ◽

Aortic Constriction

Long noncoding RNAs (lncRNAs), although initially considered as genomic transcription noise, have been demonstrated to play pivotal roles in multiple biological processes and are increasingly recognized as contributors to the pathology of cancer, neurodegenerative diseases, diabetes, heart diseases, and inflammation. However, studies on the roles of lncRNAs in angiocardiopathy, particularly in cardiac hypertrophy, are still preliminary. In our study, differentially expressed lncRNAs in rat cardiac hypertrophy induced by transverse aortic constriction (TAC) were identified by microarray analysis and validated using quantitative real-time polymerase chain reaction (RT-PCR). Briefly, we identified 6,969 lncRNAs, among which 80 lncRNAs were significantly upregulated and 172 lncRNAs were significantly downregulated. Quantitative RT-PCR was used to validate the differential expression of 5 lncRNAs in myocardial tissue RNA. Further, pathway analysis indicated that 25 pathways corresponded to upregulated transcripts and 20 pathways corresponded to downregulated transcripts. Third, by coexpression network analysis, we found a correlation between BC088254 and phb2 (prohibitin 2) and verified this expression by RT-PCR and Western blot. This is the first study to reveal differentially expressed lncRNAs in rat cardiac hypertrophy induced by TAC, indicating potential lncRNA mechanisms of action in myocardial hypertrophy. We also found that lncRNA BC088254 may have a certain role in myocardial hypertrophy induced by TAC and functional relevance between lncRNA BCO88254 and phb2, but the relationship between these two factors is unclear.

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Transcriptome Analysis of Long Noncoding RNAs in Toll-Like Receptor 3-Activated Mesenchymal Stem Cells

Stem Cells International ◽

10.1155/2016/6205485 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Shihua Wang ◽

Xiaoxia Li ◽

Robert Chunhua Zhao

Keyword(s):

Stem Cells ◽

Mesenchymal Stem Cells ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Length Distribution ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Therapeutic Effects ◽

Wide Range

Mesenchymal stem cells (MSCs) possess great immunomodulatory capacity which lays the foundation for their therapeutic effects in a variety of diseases. Recently, toll-like receptors (TLR) have been shown to modulate MSC functions; however, the underlying molecular mechanisms are poorly understood. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are an important class of regulators involved in a wide range of biological processes. To explore the potential involvement of lncRNAs in TLR stimulated MSCs, we performed a comprehensive lncRNA and mRNA profiling through microarray. 10.2% of lncRNAs (1733 out of 16967) and 15.1% of mRNA transcripts (1760 out of 11632) were significantly differentially expressed (absolute fold-change≥5 ,Pvalue≤0.05) in TLR3 stimulated MSCs. Furthermore, we characterized the differentially expressed lncRNAs through their classes and length distribution and correlated them with differentially expressed mRNA. Here, we are the first to determine genome-wide lncRNAs expression patterns in TLR3 stimulated MSCs by microarray and this work could provide a comprehensive framework of the transcriptome landscapes of TLR3 stimulated MSCs.

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A Novel Analysis of the Differentiated Expression of Long Noncoding RNAs Profiles in Human Prostate Cancer

10.21203/rs.3.rs-36555/v1 ◽

2020 ◽

Author(s):

Chuanyu Sun ◽

Shengyang Ge ◽

Yuanyuan Mi ◽

Qingfeng Hu ◽

Yijun Guo ◽

...

Keyword(s):

Prostate Cancer ◽

Cancer Biology ◽

Expression Profiles ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Clinical Samples ◽

Clinical Value ◽

Pathway Analyses ◽

Almost All

Abstract Background: Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. Increasing numbers of evidences have indicated that lncRNAs play an important role in the pathogenesis, invasion, and metastasis in almost all kinds of cancers. But, compared with the large amounts of patients, there is rare reports that showed the differential expression of lncRNAs in prostate cancer. Methods: In this study, lncRNA expression profiles were screened in PCa, by using 5 pairs of clinical specimens in PCa and matched non-PCa tissues with lncRNA chip. To affirm further clinical value, we extended the samples consisting of another 5 tumor specimens and 7 para-cancerous/benign contrasts by qRT-PCR in top 10 up-regulated and down-regulated lncRNAs. Results: A total of 817 lncRNAs were differentially expressed between PCa tumor and para-cancerous tissues (Fold Change ≥2.0, p < 0.05): 422 were upregulated, whereas 395 were downregulated in PCa tissues. Gene ontology and KEGG pathway analyses showed that many lncRNAs were implicated in carcinogenesis. Among differentially expressed lncRNAs, lnc-MYL2-4:1 (FC = 0.00141, p = 0.01909) and NR_125857 (FC = 59.27658, p = 0.00128) had the highest magnitude of change. The subsequent qPCR confirmed the expression of NR_125857 accorded with the clinical samples.Conclusions: Our study detected a relatively novel complicated map of lncRNAs in PCa, which may have the potential to investigate for diagnosis, treatment and follow-up in PCa. Our study revealed the expression of NR_125857 in human PCa tissues was most up-regulated. Further study of these meaningful candidates are need to research deep mechanisms.

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