scholarly journals Expression profiles of long noncoding RNAs and messenger RNAs in the border zone of myocardial infarction in rats

2019 ◽  
Vol 24 (1) ◽  
Author(s):  
Qingkun Meng ◽  
Zhijun Sun ◽  
Hui Gu ◽  
Jiaying Luo ◽  
Jingjing Wang ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Cytokine Receptor ◽  
Border Zone ◽  
Receptor Interaction ◽  
Messenger Rnas ◽  
Chromosomal Distribution

Abstract Background The participation of long noncoding RNAs (lncRNAs) in myocardial infarction has recently been noted. However, their underlying roles in the border zone of myocardial infarction remain unclear. This study uses microarrays to determine the profiles of lncRNAs and mRNAs in the border zone. Methods Bioinformatics methods were employed to uncover their underlying roles. Highly dysregulated lncRNAs was further validated via PCR. Results Four hundred seven lncRNAs and 752 mRNAs were upregulated, while 132 lncRNAs and 547 mRNAs were downregulated in the border zone of myocardial infarction. A circos graph was constructed to visualize the chromosomal distribution and classification of the dysregulated lncRNAs and mRNAs. The upregulated mRNAs in the border zone were most highly enriched in cytokine activity, binding, cytokine receptor binding and related processes, as ascertained through Go analysis. Pathway analysis of the upregulated mRNAs showed the most significant changes were in the TNF signaling pathway, cytokine–cytokine receptor interaction and chemokine signaling pathway and similar pathways and interactions. An lncRNA–mRNA co-expression network was established to probe into the underlying functions of the 10 most highly dysregulated lncRNAs based on their co-expressed mRNAs. In the co-expression network, we found 16 genes directly involved in myocardial infarction, including Alox5ap, Itgb2 and B4galt1. The lncRNAs AY212271, EF424788 and MRAK088538, among others, might be associated with myocardial infarction. BC166504 is probably a key lncRNA in the border zone of myocardial infarction. Conclusions The results may have revealed some aberrantly expressed lncRNAs and mRNAs that contribute to the underlying pathophysiological mechanisms of myocardial infarction.

Comprehensive analysis of long noncoding RNAs and mRNAs expression profiles and functional networks during chondrogenic differentiation of murine ATDC5 cells

2019 ◽  
Vol 51 (8) ◽  
pp. 778-790
Author(s):  
Wei Wang ◽  
Yu Ding ◽  
Yanhua Xu ◽  
Hefeng Yang ◽  
Wenjing Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pathway Analysis ◽  
Chondrogenic Differentiation ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Receptor Interaction ◽  
Messenger Rnas ◽  
Kegg Pathway Analysis

AbstractChondrogenic differentiation is a coordinated biological process orchestrated by various cell signaling pathways, involving complex pathways regulated at both transcriptional and post-transcriptional levels. Long noncoding RNAs (lncRNAs) are emerging as important regulators in the modulation of multiple cell processes. However, the potential roles of lncRNAs and their regulatory mechanisms in chondrogenic differentiation remain largely unclear. In this study, microarray was performed to detect the expression profiles of lncRNAs and messenger RNAs (mRNAs) during chondrogenic differentiation of murine chondrogenic cell line ATDC5. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explore their functions. Coding-noncoding co-expression (CNC) and competing endogenous RNA (ceRNA) networks were also constructed with bioinformatics methods. The results revealed that 1009 lncRNAs and 1206 mRNAs were differentially regulated during chondrogenic differentiation. GO and KEGG pathway analysis indicated that the principal functions of the transcripts were associated with system development and extracellular matrix-receptor interaction, TGF-β signaling, and PI3K-Akt signaling pathways. The CNC network showed that lncRNA AK136902 was positively correlated with prostaglandin F receptor (FP). The ceRNA network covered 3 lncRNAs, 121 miRNAs and 241 edges. The upregulated lncRNA AK136902, AK016344, and ENSMUST00000180767 might promote chondrogenic differentiation by acting as ceRNAs. Knockdown of lncRNA AK136902 could inhibit the mRNA expression of FP and other chondrogenic related genes, including Aggrecan and Col2a1 during chondrogenic differentiation. Our results provide a new perspective on the modulation of lncRNAs during chondrogenic differentiation.

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

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.

Differential Gene Signature and Signaling Pathways in Childhood Burkitt (BL) vs Diffuse Large B-Cell Lymphoma (DLBCL).

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4142-4142
Author(s):  
Nancy S. Day ◽  
Janet Ayello ◽  
Ian Waxman ◽  
Evan Shereck ◽  
Catherine McGuinn ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Expression Profiles ◽  
B Cell Lymphoma ◽  
Cytokine Receptor ◽  
Receptor Interaction ◽  
Signal Pathways ◽  
Type I

Abstract The prognosis and treatment of both major forms of advanced childhood B-NHL (BL and DLBCL) is similar with short and intensive multi-agent chemotherapy (Cairo/Patte et al., Blood, 2007 and Patte/Cairo et al., Blood, 2007). Despite both BL and DLBCL being germinal center derived, our recent cytogenetic results of BL vs DLBCL in the FAB LMB 96 study have demonstrated significant differences in secondary chromosomal aberrations in BL vs DLBCL and a differential prognosis based on secondary cytogenetic findings (Poirel/Cairo/Patte, Blood, 2003a). Thus, we sought to identify genes that could uniquely differentiate childhood BL vs DLBCL and discover potential genetic mechanisms of differential molecular pathogenesis and to determine the signal pathways that contribute to the genetic disparity between these two histological types of childhood B-NHL. Nine BL (7 patient samples and 2 cell lines, Raji and Ramos) and 3 DLBCL (1 patient sample and 2 cell lines, Pfeiffer and DB) were compared. Total RNA was isolated, reverse transcribed to cDNA biotinylated cRNA and hybridized to Affymetrix U133A_2 as we have previously described (Jiang/Cairo et al., Journal of Immunology, 2004). Data were analyzed using Agilent GeneSpring 7.3. Signal intensities were compared using one way ANOVA and Welch Test for statistical analysis. Two-fold changes between BL and DLBCL were considered as significant (p<0.05). KEGG Pathways were evaluated for the genes identified. There were 120 genes over-expressed and 217 genes under-expressed in BL vs DLBCL. BL expressed significantly higher level of Ki-67 (a measure of lymphoma-cell proliferation) than DLBCL (2.68F). BL also expressed higher level of the pro-apoptotic gene, p53 compared to DLBCL (1.46F). Over-expressed genes in BL vs DLBCL included TNFSF10 (11.87F), RHOQ (3.16F), PIP5K1B (5.22F) among many others. The genes significantly under-expressed in BL vs DLBCL included PIGL (0.45F), Inositol (myo)-1 (or 4)-monophosphatase 1 (IMPA1; 0.28F), cAMP-dependent regulatory type I, alpha protein kinase (PRKAR1A; 0.37F) among many others. TNFSF10 induces apoptosis in transformed and tumor cells and is known to participate in pathways including cytokine-cytokine receptor interaction and induction of apoptosis through DR3 and DR4/5 death receptors. PIP5K1B is involved in the Rho signaling pathway and PIGL catalyzes the second step of glycosylphosphatidylinositol (GPI) biosynthesis. Since activation of IL3R-mediated cAMP-dependent protein kinase leads to increased cell survival, we searched gene expression profiles in BL vs DLBCL that were involved in IL signaling pathways. The genes that were identified to be over-expressed in BL vs DLBCL included IL2RG (2.24F), IL8RB, IL18 receptor accessory protein (IL18RAP), IL18, IL18R1, and IL1R2 (natural log values of 11.11, 22.95, 2.16, 1.73 and 11.84, respectively in BL vs non-detectable values in DLBCL). Taken together, since IL1, IL2, IL8, and IL18 all belong to IL1 super family, these results suggest significant involvement of TNF (TRAIL) and IL1 super family via cytokine-cytokine receptor interaction and activation of the Rho signaling pathway in Burkitt vs DLBCL lymphomagenesis.

scholarly journals Comprehensive Analysis of Long Noncoding RNAs and Messenger RNAs Expression Profiles in Patients with Marjolin Ulcer

2018 ◽  
Vol 24 ◽  
pp. 7828-7840 ◽  
Author(s):  
Zan Liu ◽  
Licheng Ren ◽  
Jing Tian ◽  
Ning Liu ◽  
Yanke Hu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Noncoding Rnas ◽  
Comprehensive Analysis ◽  
Long Noncoding Rnas ◽  
Messenger Rnas

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals Identification of upregulated NF-κB inhibitor alpha and IRAK3 targeting lncRNA following intracranial aneurysm rupture-induced subarachnoid hemorrhage

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wei Leng ◽  
Dan Fan ◽  
Zhong Ren ◽  
Qiaoying Li
Keyword(s):  
Subarachnoid Hemorrhage ◽  
Intracranial Aneurysm ◽  
Signaling Pathway ◽  
Aneurysm Rupture ◽  
Cytokine Receptor ◽  
Gene Set Enrichment Analysis ◽  
Receptor Interaction ◽  
Regulatory Pathways ◽  
Ruptured Intracranial Aneurysm ◽  
Neurotrophin Signaling

Abstract Background This study was performed to identify genes and lncRNAs involved in the pathogenesis of subarachnoid hemorrhage (SAH) from ruptured intracranial aneurysm (RIA). Methods Microarray GSE36791 was downloaded from Gene Expression Omnibus (GEO) database followed by the identification of significantly different expressed RNAs (DERs, including lncRNA and mRNA) between patients with SAH and healthy individuals. Then, the functional analyses of DEmRNAs were conducted and weighted gene co-expression network analysis (WGCNA) was also performed to extract the modules associated with SAH. Following, the lncRNA-mRNA co-expression network was constructed and the gene set enrichment analysis (GSEA) was performed to screen key RNA biomarkers involved in the pathogenesis of SAH from RIA. We also verified the results in a bigger dataset GSE7337. Results Totally, 561 DERs, including 25 DElncRNAs and 536 DEmRNAs, were identified. Functional analysis revealed that the DEmRNAs were mainly associated with immune response-associated GO-BP terms and KEGG pathways. Moreover, there were 6 modules significantly positive-correlated with SAH. The lncRNA-mRNA co-expression network contained 2 lncRNAs (LINC00265 and LINC00937) and 169 mRNAs. The GSEA analysis showed that these two lncRNAs were associated with three pathways (cytokine-cytokine receptor interaction, neurotrophin signaling pathway, and apoptosis). Additionally, IRAK3 and NFKBIA involved in the neurotrophin signaling pathway and apoptosis while IL1R2, IL18RAP and IL18R1 was associated with cytokine-cytokine receptor interaction pathway. The expression levels of these genes have the same trend in GSE36791 and GSE7337. Conclusion LINC00265 and LINC00937 may be implicated with the pathogenesis of SAH from RIA. They were involved in three important regulatory pathways. 5 mRNAs played important roles in the three pathways.

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