Differential Expression Profiles Of lncRNAs Research Articles

Transcriptome Sequencing of lncRNAs, circRNAs, miRNAs, mRNAs, and Interaction Network Constructing in Acute Exacerbation of Idiopathic Pulmonary Fibrosis.

Idiopathic pulmonary fibrosis (IPF) patients who suffer from acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) are at increased risk of respiratory deterioration and death. Non-coding RNAs (ncRNAs) play a vital role in AE-IPF, but studies of crosstalk between transcripts of IPF based on Traditional Chinese Medicine (TCM) syndrome type are relatively few. The construction of long non-coding RNAs (lncRNA)/circular RNAs (circRNA)-microRNAs (miRNA)-mRNA interaction networks can promote understanding RNA interaction in different syndrome types of AE-IPF. The study aimed to identify the difference in RNA transcription expression between IPF patients with "lung heat and collateral stasis (LHCS)" and "lung deficiency with collateral stasis (LDCS)" syndromes, further to construct the potential RNA networks. Five IPF patients with LHCS and five IPF patients with LDCS were recruited in this study to perform RNA sequencing and miRNA sequencing. Further analysis was carried out on the differential expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs among patients with LHCS and LDCS. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. The lncRNA/circRNA-miRNA-mRNA competing endogenous RNAs (ceRNAs) network was constructed, and the key regulatory molecules were analyzed. For LHCS and LDCS, we identified 69 lncRNAs, 150 circRNAs, 27 miRNAs, and 56 mRNAs. Differential expression analysis through GO and KEGG highlights that differentially expressed mRNAs have significant associations with pathways such as tight junction and Hepatitis C. Within the ceRNA network, all nodes have a direct or indirect association with LHCS progression. The hsa-miR-150-5p core sub-network is composed of 1 lncRNA, 6 circRNAs, 1 miRNA, and 5 mRNAs. From the ceRNA sub-network analysis, NR_120628/hsa-miR-150-5p/E2F3 and hsa-circ-0053515/hsa-miR-150-5p/E2F3 emerged as the pivotal ceRNA pairs. This study highlights that the NR_120628/hsa-miR-150-5p/E2F3 and hsa-circ-0053515/hsa-miR-150-5p/E2F3 axes could be central in the regulation of LHCS, providing valuable insights into potential directions for subsequent research on LHCS. Chinese clinical trial registry (CHiCTR23007405). Registered on July 27, 2023. https://www.chictr.org.cn/.

LncRNA-mRNA co-expression analysis revealed 8 core lncRNAs in rheumatoid arthritis of collagen-induced arthritis rats

BackgroundsRheumatoid arthritis (RA) is a chronic inflammatory and autoimmune disease. Current studies suggest that long noncoding RNAs (lncRNAs) may be key regulators in pathogenesis.MethodsAnalyzed lncRNAs and mRNAs using microarrays to find key differentially expressed lncRNAs in RA. GO and KEGG enrichment analysis together with coding non-coding co-expression (CNC) network was used for comprehensive analysis. Verify that their expression levels are consistent with the chip results by qRT-PCR.ResultsThere are 268 differentially expressed lncRNAs (DELs) and 286 differentially expressed mRNAs (DEMs). We found 8 core lncRNAs through the CNC network. Eight highly significantly differentially expressed lncRNAs corrected with microarray profiles. The functions and associated pathways of significantly differentially expressed lncRNAs were predicted by GO and KEGG analysis. They may be involved in the pathogenesis of RA.ConclusionThe differential expression profiles of lncRNAs and mRNAs in the collagen-induced arthritis rat model preliminarily predicted functions through comprehensive analysis. However, its exact role and specific mechanism remain to be further studied.

Identification of lncRNA-miRNA-mRNA networks in late-onset pre-eclampsia

Objective: Long non-coding RNAs (lncRNAs) are implicated in multiple pathophysiological processes in placenta-related disorders; however, their expression and function in late-onset pre-eclampsia (LOPE) remain unclear. This study aimed to investigate the expression of lncRNAs in LOPE, construct a competing endogenous RNA (ceRNA) network, and identify the pathways associated with LOPE pathogenesis. Methods: We performed lncRNA and mRNAs microarray profiling to identify the differential expression profiles of lncRNAs and mRNAs in LOPE compared to those in normal pregnancy. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate differentially expressed genes. Subsequently, we generated an interaction network between lncRNAs, (micro-RNAs) miRNAs, and mRNAs based on the Pearson’s correlation coefficient between lncRNAs and mRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to understand the functional significance of differentially expressed lncRNAs (DElncRNAs) in LOPE. Results: We identified 29 DElncRNAs (25 upregulated and four downregulated) and 212 differentially expressed mRNAs (DEmRNAs; 203 upregulated and nine downregulated) in LOPE placentas. Within them, six lncRNAs and four mRNAs were verified by qRT-PCR. GO and KEGG analyses revealed the potential pathways affected by these mRNAs, such as positive regulation of leukocyte chemotaxis, chemokine signaling pathway, and response to hypoxia. Finally, we constructed a ceRNA network including three DElncRNAs and 124 DEmRNAs, whose competing interactions may be mediated by 17 miRNAs. Two DElncRNAs, ENST00000515376 and ENST00000520544, were found to be hub genes, as they interacted with most miRNAs and mRNAs. ENST00000515376 is most likely related to the metabolic process of arachidonic acid, whereas ENST00000520544 is more likely related to the coagulation system, such as the regulation of blood coagulation and platelet degranulation. Conclusion: Differential expression profile of lncRNAs and the lncRNA-miRNA-mRNA network in LOPE provide potential therapeutic targets for this disease.

RNA-sequencing analysis reveals the long noncoding RNA profile in the mouse myopic retina.

Aim: Myopia is a prevalent public health problem. The long noncoding RNA (lncRNA) mechanisms for dysregulated retinal signaling in the myopic eye have remained elusive. The aim of this study was to analyze the expression profiles and possible pathogenic roles of lncRNAs in mouse form-deprived myopia (FDM) retinas. Methods: A mouse FDM model was induced and retinas from the FDM right eyes and the contralateral eyes were collected for RNA sequencing. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and lncRNA-mRNA coexpression network analyses were conducted to explore the biological functions of the differentially expressed lncRNAs. In addition, the levels of differentially expressed lncRNAs in the myopic retinas were validated by quantitative real-time PCR (qRT–PCR). Fluorescence in situ hybridization (FISH) was used to detect the localization of lncRNAs in mouse retinas. Results: FDM eyes exhibited reduced refraction and increased ocular axial length compared to control fellow eyes. RNA sequencing revealed that there were 655 differentially expressed lncRNAs between the FDM and control retinas. Functional enrichment analysis indicated that the differentially expressed RNAs were mostly enriched in cellular processes, cytokine-cytokine receptor interactions, retinol metabolism, and rhythmic processes. Differentially expressed lncRNAs were validated by qRT–PCR. Additionally, RNA FISH showed that XR_384718.4 (Gm35369) localized in the ganglion cell (GCL) and inner nuclear layers (INL). Conclusion: This study identified the differential expression profiles of lncRNAs in myopic mouse retinas. Our results provide scientific evidence for investigations of myopia and the development of putative interventions in the future.

LncRNA RAD51-AS1 Regulates Human Bone Marrow Mesenchymal Stem Cells via Interaction with YBX1 to Ameliorate Osteoporosis.

Long noncoding RNA (lncRNA) is a new key regulatory molecule in the occurrence of osteoporosis, but its research is still in the primary stage. In order to study the role and mechanism of lncRNA in the occurrence of osteoporosis, we reannotated the GSE35956 datasets, compared and analyzed the differential expression profiles of lncRNAs between bone marrow mesenchymal stem cells (hBMSCs) from healthy and osteoporotic patients, and then screened a lncRNA RAD51-AS1 with low expression in hBMSCs from osteoporotic patients, and its role in the occurrence of osteoporosis has not been studied. We confirmed that the expression level of lncRNA RAD51-AS1 in hBMSCs from patients with osteoporosis was significantly lower than those from healthy donors. A nuclear cytoplasmic separation experiment and RNA fluorescence in situ hybridization showed that RAD51-AS1 was mainly located in the nucleus. RAD51-AS1 knockdown significantly inhibited the proliferation and osteogenic differentiation of hBMSCs and significantly increased their apoptosis, while RAD51-AS1 overexpression significantly promoted the proliferation, osteogenic differentiation, and ectopic bone formation of hBMSCs. Mechanistically, we found that RAD51-AS1 banded to YBX1 and then activated the TGF-β signal pathway by binding to Smad7 and Smurf2 mRNA to inhibit their translation and transcription up-regulated PCNA and SIVA1 by binding to their promoter regions. In conclusion, RAD51-AS1 promoted the proliferation and osteogenic differentiation of hBMSCs by binding YBX1, inhibiting the translation of Smad7 and Smurf2, and transcriptionally up-regulated PCNA and SIVA1.

Plasmodium manipulates the expression of host long non-coding RNA during red blood cell intracellular infection

BackgroundParasites interact with their host through “direct” and/or “indirect” mechanisms. Plasmodium, for example, either mediates direct physical interactions with host factors or triggers the immune system of the host indirectly, leading to changes in infectious outcomes. Long non-coding RNAs (lncRNAs) participate in regulating biological processes, especially host–pathogen interactions. However, research on the role of host lncRNAs during Plasmodium infection is limited.MethodsA RNA sequencing method (RNA-seq) was used to confirm the differential expression profiles of lncRNAs in Plasmodium yeolii 17XL (P.y17XL)-infected BALB/c mice. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to elucidate the potential functions of Plasmodium-induced genes. Subsequently, the effect of specific lncRNAs on the modulation of immune-related signaling pathways in malaria was determined by fluorescence-activated cell sorting, western blot and enzyme-linked immunosorbent assay.ResultsThe data showed that in P.y17XL-infected BALB/c mice, Plasmodium upregulated the expression of 132 lncRNAs and downregulated the expression of 159 lncRNAs. Differentially expressed lncRNAs clearly associated with malaria infection were annotated, including four novel dominant lncRNAs: ENMSUSG00000111521.1, XLOC_038009, XLOC_058629 and XLOC_065676. GO and KEGG pathway analyses demonstrated that these four differentially expressed lncRNAs were associated with co-localized/co-expressed protein-coding genes that were totally enriched in malaria and with the transforming growth factor beta (TGF-β) signaling pathway. Using the models of P.y17XL-infected BALB/c mice, data certified that the level of TGF-β production and activation of TGF-β/Smad2/3 signaling pathway were obviously changed in malaria infection.ConclusionsThese differentially expressed immune-related genes were deemed to have a role in the process of Plasmodium infection in the host via dendritic/T regulatory cells and the TGF-β/Smad2/3 signaling pathway. The results of the present study confirmed that Plasmodium infection-induced lncRNA expression is a novel mechanism used by Plasmodium parasites to modify host immune signaling. These results further enhance current understanding of the interaction between Plasmodium and host cells.Graphical

The role and possible mechanism of the long noncoding RNA LINC01260 in nonalcoholic fatty liver disease

ObjectiveTo investigate the differential expression profile of lncRNAs in the nonalcoholic fatty liver disease (NAFLD) model induced by oleic acid (OA) and to further explore the role of LINC01260 (ENST00000255183) in NAFLD, providing theoretical support for the clinical value of lncRNAs in NAFLD.MethodsOA (50 μg/mL) was used to induce steatosis in normal human LO2 hepatocytes for 48 h and was verified by Oil red O staining. Differential expression profiles of lncRNAs were obtained by eukaryotic circular sequencing (RNA/lncRNA/circRNA-seq) techniques. A gain-of-function (GOF) strategy for LINC01260 was adopted, Oil red O staining and semiquantitative analysis were combined to explore whether the GOF of LINC01260 affects LO2 cell steatosis. CeRNA-based bioinformatics analysis of lncRNAs was performed, and the enriched mRNAs were further verified. RXRB siRNAs were applied and verify its role in LINC01260 regulated OA-induced hepatocytes steatosis.ResultsLipid droplets of different sizes were observed in the cells of the OA group. Absorbance in the OA group was significantly increased after isopropanol decolorization (P < 0.05). Compared with those in the control group, there were 648 lncRNAs with differential expression greater than 1 time in the OA group, of which 351 were upregulated and 297 were downregulated. Fluorescence quantitative PCR showed that the expression of LINC01260 in the OA group was downregulated by 0.35 ± 0.07-fold (P < 0.05). The formation of lipid droplets in LO2 cells of the LINC01260 GOF group decreased significantly (P < 0.05). CeRNA analysis indicated that the mRNA levels of RXRB, RNPEPL1, CD82, MADD and KLC2 were changed to different degrees. Overexpression of LINC01260 significantly induced RXRB transcription (P < 0.05) and translation, and RXRB silence attenuated the lipids decrease induced by LINC01260 overexpression.ConclusionThe OA-induced NAFLD cell model has a wide range of lncRNA differential expression profiles. LINC01260 participates in the regulation of the lipid droplet formation process of NAFLD, and its overexpression can significantly inhibit the steatosis process of LO2 cells. Mechanistically, LINC01260 may act as a ceRNA to regulate the expression of RXRB, thereby affecting the adipocytokine signaling pathway.

Comprehensive Analysis of Competing Endogenous RNA Network Focusing on Long Noncoding RNA Involved in Cirrhotic Hepatocellular Carcinoma.

The role of long noncoding RNAs- (lncRNAs-) associated competing endogenous RNA (ceRNA) in the field of hepatocellular carcinoma (HCC) biology is well established, but the involvement of lncRNAs competing interactions in the progression of liver cirrhosis to HCC is still unclear. We aimed to explore the differential expression profiles of lncRNAs, microRNAs (miRNA), and messenger RNAs (mRNAs) to construct a functional ceRNA network in cirrhotic HCC. The lncRNA, miRNA, and mRNA expression datasets were obtained from Gene Expression Omnibus and The Cancer Genome Atlas. Based on miRanda and TargetScan, the HCC-specific ceRNA network was constructed to illustrate the coexpression regulatory relationship of lncRNAs, miRNAs, and mRNAs. The potential prognostic indicators in the network were confirmed by survival analysis and validated by qRT-PCR. A total of 74 lncRNAs, 36 intersection miRNAs, and 949 mRNAs were differentially expressed in cirrhotic HCC samples compared with cirrhosis samples. We constructed a ceRNA network, including 47 lncRNAs, 35 miRNAs, and 168 mRNAs. Survival analysis demonstrated that 2 lncRNAs (EGOT and SERHL), 4 miRNAs, and 40 mRNAs were significantly associated with the overall survival of HCC patients. Two novel regulatory pathways, EGOT-miR-32-5p-XYLT2 axis and SERHL-miR-1269a/miR-193b-3p-BCL2L1/SYK/ARNT/CHST3/LPCAT1 axis, were built up and contribute to the underlying mechanism of HCC pathogenesis. The higher-expressed SERHL was associated with a higher risk of all-cause death. The expressions of SERHL-miR-1269a-BCL2L1 were significantly different using qRT-PCR in vitro studies. lncRNAs EGOT and SERHL might serve as effective prognostic biomarkers and potential therapeutic targets in cirrhotic HCC treatment.

Dynamic assessing silica particle-induced pulmonary fibrosis and associated regulation of long non-coding RNA expression in Wistar rats

BackgroundExposure to respirable crystalline silica (RCS) can induce accelerated silicosis (AS), a form of silicosis that is more progressive and severe form of silicosis. In this project we aimed to assess processes of silicosis in rats exposed to RCS with focus on the regulation of long noncoding RNAs (lncRNAs).ResultsThe results showed that RCS induced acute inflammatory response as indicated by the appearance of inflammatory cells in the lung from the first day and peaked on day 7 of exposure. The fibroblasts appeared along with the inflammatory cells decreasing gradually on day 14. Extensive fibrosis appeared in the lung tissue, and silicon nodules were getting larger on day 28. Interestingly, the number of altered lncRNAs increased with the exposure time with 193, 424, 455, 421 and 682 lncRNAs on day 1, 7, 14, 21, and 28 after exposure, respectively. We obtained 285 lncRNAs with five significant temporal expression patterns whose expressions might correlate with severity of silicosis. KEGG analysis showed that lncRNAs from short time-series expression miner (STEM)-derived data mainly involved in 17 pathways such as complement and coagulation cascades.ConclusionsThe differential expression profiles of lncRNAs may be potential biomarkers in silicosis through modulating expressions of their relevant genes in lungs of rat and thus warrant further investigation.

Identification and coregulation pattern analysis of long noncoding RNAs following subacute spinal cord injury

Long noncoding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in posttranscriptional and transcriptional regulation in eukaryotic cells. However, the characteristics of many lncRNAs, particularly their expression patterns in the lesion epicenter of spinal tissues following subacute spinal cord injury (SCI), remain unclear. In this study, we determined the expression profiles of lncRNAs in the lesion epicenter of spinal tissues after traumatic SCI and predicted latent regulatory networks. Standard Allen's drop surgery was conducted on mice, and hematoxylin and eosin staining was used to observe the damaged area. High‐throughput sequencing was performed to identify the differential expression profiles of lncRNAs. Quantitative real‐time polymerase chain reaction was conducted to evaluate the quality of the sequencing results. Bioinformatics analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, coexpression analysis, and protein–protein interaction analysis, were performed. Targeted binding of lncRNA–miRNA–mRNA was predicted by TargetScan and miRanda. A total of 230 differentially expressed lncRNAs were identified and preliminarily verified, and some potential regulatory networks were constructed. These findings improve our understanding of the mechanisms underlying subacute SCI; differentially expressed lncRNAs are closely involved in pathophysiological processes by regulating multiple pathways. Further studies are essential for revealing the exact mechanism underlying competing endogenous RNA pathways in vivo and in vitro.

Integrated analysis of ceRNA network in hepatocellular carcinoma using bioinformatics analysis.

Background:Long noncoding RNAs (lncRNAs) can work as microRNA (miRNA) sponges through a competitive endogenous RNA (ceRNA) mechanism. LncRNAs and miRNAs are important components of competitive endogenous binding, and their expression imbalance in hepatocellular carcinoma (HCC) is closely related to tumor development, diagnosis, and prognosis. This study explored the potential impact of the ceRNA regulatory network in HCC on the prognosis of HCC patients.Methods:We thoroughly researched the differential expression profiles of lncRNAs, miRNAs, and mRNAs from 2 HCC Gene Expression Omnibus datasets (GSE98269 and GSE60502). Then, a dysregulated ceRNA network was constructed by bioinformatics. In addition, hub genes in the ceRNA network were screened by Cytoscape, these hub genes functional analysis was performed by gene set enrichment analysis, and the expression of these hub genes in tumors and their correlation with patient prognosis were verified with Gene Expression Profiling Interactive Analysis.Results:A ceRNA network was successfully constructed in this study including 4 differentially expressed (DE) lncRNAs, 7 DEmiRNAs, and 166 DEmRNAs. Importantly, 4 core genes (CCNA2, CHEK1, FOXM1, and MCM2) that were significantly associated with HCC prognosis were identified.Conclusions:Our study provides comprehensive and meaningful insights into HCC tumorigenesis and the underlying molecular mechanisms of ceRNA. Furthermore, the specific ceRNAs can be further used as potential therapeutic targets and prognostic biomarkers for HCC.

Novel Insights into the Potential Diagnostic Value of Circulating Exosomal IncRNA-Related Networks in Large Artery Atherosclerotic Stroke.

Exosomes show diagnostic and therapeutic promise as carriers of ncRNAs in diseases. LncRNAs in exosomes have been identified as being stable and avoided degradation by nucleolytic enzymes. Although lncRNAs have been confirmed to be important in cancers, no studies for exo-lncRNAs have been reported in LAA stroke. High-throughput sequencing was performed to detect the differential expression profiles of lncRNAs in five paired plasma-derived exosome samples from patients with LAA stroke and controls (matched on vascular risk factors). Exo-lncRNA-associated networks were predicted with a combination of multiple databases. The expression of the selected genes in the networks was confirmed by qRT-PCR in a validation set (LAA vs. controls = 30:30). Furthermore, ROC analysis was used to evaluate the diagnostic performance of the lncRNA-related networks. A total of 1,020 differentially expressed lncRNAs were identified in LAA stroke patients. GO and KEGG pathway analyses indicated that their target genes are involved in atherosclerosis-related pathways, including inflammation, cell adhesion, and cell migration. qRT-PCR confirmed that the expression trend of differential expressed genes was consistent with RNA-seq. Furthermore, the AUCs of the lnc_002015-related network and lnc_001350-related network were 0.959 and 0.97, respectively, in LAA stroke. Our study showed the differential expression of lncRNAs in plasma exosomes and presented related diagnostic networks for LAA stroke for the first time. The results suggested that exosomal lncRNA-related networks could be potential diagnostic tools in LAA stroke.

Preliminary RNA-microarray analysis of long non-coding RNA expression in abnormally invasive placenta.

Long non-coding RNAs (lncRNAs) are reported to have important roles in placental development and function, but the role of lncRNAs in abnormally invasive placenta (AIP) remains elusive. In the present study, the differential expression profiles of lncRNAs were analyzed to identify novel targets for further study of AIP. A total of 10 lncRNAs were chosen for validation by reverse transcription-quantitative PCR. To further determine the functions of dysregulated lncRNAs and their corresponding mRNAs, functional enrichment analysis, coexpression analysis were performed. A total of 329 lncRNAs and 179 mRNAs were identified to be differently expressed between the invasive and control group. Gene ontology analysis revealed that the 10 most significantly enriched functions included upregulated mRNAs and the most significantly enriched term was related to the proteinaceous extracellular matrix (ECM). In the pathway analysis, the two most significantly enriched pathways were the TGF-β signaling pathway for upregulated mRNAs and the pentose phosphate pathway for downregulated mRNAs. Furthermore, for certain dysregulated lncRNAs, their associated mRNAs were also dysregulated. Of note, BMP and activin membrane-bound inhibitor and TGF-β-induced, as the target genes of the TGF-β pathway, were indicated to be closely related to the ECM and invasive placental cells. Their nearby lncRNAs G008916 and vault RNA2-1 were also significantly dysregulated. In conclusion, significant lncRNAs with the potential to serve as biomarkers for AIP were identified.

LINC00473 regulated apoptosis, proliferation and migration but could not reverse cell cycle arrest of human bone marrow mesenchymal stem cells induced by a high-dosage of dexamethasone.

Dysfunction of bone marrow mesenchymal stem cells (BMSCs) is involved in the pathogenesis of steroid-induced osteonecrosis of the femoral head (SONFH). Long noncoding RNAs (lncRNAs) contribute to biological effects exerted on BMSCs by regulating the expression of genes. However, most recent studies have focused on the role of lncRNAs in modulating the imbalance between osteogenic and adipogenic differentiation but not apoptosis, proliferation, cell cycle and migration of BMSCs, especially in Dex-treated BMSCs. In this study, we conducted a microarray analysis to investigate the differential expression profiles of lncRNAs between human BMSCs (hBMSCs) obtained from patients with SONFH and control patients with femoral neck fracture. The microarray analysis showed that a total of 48 differentially expressed lncRNAs were identified in hBMSCs between the two groups, including 24 upregulated lncRNAs and 24 downregulated lncRNAs. Among of them, LINC00473 was found to be significantly downregulated. In the following study, we found that 10-6 mol/L Dex significantly inhibited proliferation, arrested cell cycle at the G1 phase, increased caspase-3 activity, induced apoptosis and impeded the migration of hBMSCs, while downregulation of the expression of LINC00473 produced results that were in line with the results of the microarray analysis in a time-dependent manner. Interestingly, upregulation of LINC00473 attenuated the negative effects caused by 10-6 mol/L Dex on hBMSCs, except for cell cycle arrest. Furthermore, it should be noted that LINC00473 had no effect on the proliferation and cell cycle of hBMSCs in the absence of Dex. Collectively, our data revealed that LINC00473 attenuated apoptosis, promoted the proliferation and migration of Dex-induced hBMSCs, which are not involved in interference with the cell cycle of hBMSCs.

Microarray analysis of long non-coding RNA expression profiles in Marfan syndrome.

Long non-coding RNAs (lncRNAs) serve a crucial role in every aspect of cell biological functions as well as in a variety of diseases, including cardiovascular disease, cancer and nervous system disease. However, the differential expression profiles of lncRNAs in Marfan syndrome (MFS) have not been reported. The aim of the present study was to identify potential target genes behind the pathogenesis of MFS by analyzing microarray profiles of lncRNA in aortic tissues from individuals with MFS and normal aortas (NA). The differentially expressed lncRNA profiles between MFS (n=3) and NA (n=4) tissues were analyzed using microarrays. Bioinformatics analyses were used to further investigate the candidate lncRNAs. Reverse transcription-quantitative (RT-qPCR) was applied to validate the results. In total, the present study identified 294 lncRNAs (245 upregulated and 49 downregulated) and 644 mRNAs (455 upregulated and 189 downregulated) which were differential expressed between MFS and NA tissues (fold change ≥1.5; P<0.05). Gene Ontology enrichment analysis indicated that the differentially expressed mRNAs were involved in cell adhesion, elastic fiber assembly, extracellular matrix (ECM) organization, the response to virus and the inflammatory response. Kyoto Encyclopedia of Gene and Genomes pathway analysis indicated that the differentially expressed mRNAs were mainly associated with focal adhesion, the ECM-receptor interaction, the mitogen-activated protein kinase signaling pathway and the tumor necrosis factor signaling pathway. The lncRNA-mRNA coexpression network analysis further elucidated the interaction between the lncRNAs and mRNAs. A total of five lncRNAs (uc003jka.1, uc003jox.1, X-inactive specific transcript, linc-lysophosphatidic acid receptor 1 and linc-peptidylprolyl isomerase domain and WD repeat containing 1) with the highest degree of coexpression were selected and confirmed using RT-qPCR. In the present study, expression profiles of lncRNA and mRNA in MFS were revealed using microarray analysis. These results provided novel candidates for further investigation of the molecular mechanisms and effective targeted therapies for MFS.

Lnc-BAZ2B promotes M2 macrophage activation and inflammation in children with asthma through stabilizing BAZ2B pre-mRNA

Dysregulation of long noncoding RNAs (lncRNAs) is associated with a variety of human diseases; however, whether they have a role in childhood asthma is unknown. We sought to determine the differential expression profiles of lncRNAs in PBMCs of children with asthma and the mechanisms underlying the effects of lncRNAs on the pathogenesis of asthma. The differential expression profiles of lncRNAs were analyzed by transcriptome microarray. The effects and mechanisms by which lncRNAs influence macrophage activation were detected by real-time quantitative PCR, Western blot, RNase protection assay, and chromatin immunoprecipitation assay. The roles played by lncRNAs in asthma were tested in a cockroach allergen extract (CRE)-induced mouse model. We identified 719 lncRNAs that were differentially expressed in PBMCs of children with asthma, 502 of which were upregulated and 217 were downregulated. An lncRNA of unknown function, lnc-BAZ2B, was dominantly expressed in monocytes and significantly upregulated in children with asthma. lnc-BAZ2B promotes M2 macrophage activation by enhancing BAZ2B expression and exacerbated lung inflammation in an M2 macrophage-associated CRE-induced asthma model. Mechanistically, lnc-BAZ2B promoted the expression of its cis target gene BAZ2B by stabilizing its pre-mRNA. BAZ2B, a reader of H3K14ac modification, enhanced the transcription of IRF4 and promoted M2 macrophage activation. lnc-BAZ2B expression was correlated with that of BAZ2B in PBMCs from children with asthma. Baz2b knockdown could alleviate asthma severity in a CRE-induced asthma model. lnc-BAZ2B promotes M2 macrophage activation and inflammation in children with asthma and may serve as a potential therapeutic and diagnostic target in children with asthma.

Comprehensive Analysis of lncRNA Expression Pattern and lncRNA–miRNA–mRNA Network in a Rat Model With Cavernous Nerve Injury Erectile Dysfunction

BackgroundLong noncoding RNAs (lncRNAs) are differentially expressed in erectile dysfunction (ED) associated with aging and diabetes mellitus; however, the lncRNA expression profile in cavernous nerve (CN) injury–related ED (CNI-ED) is unknown. AimTo investigate the dysregulated lncRNAs, microRNAs (miRNAs), and mRNA expression in CNI-ED and construct a potential lncRNA–miRNA–mRNA network. Methods22 male Sprague–Dawley (SD) rats were divided into bilateral CN crush (BCNC) and Sham groups. Using second-generation high-throughput sequencing technology, we analyzed the expression profiles of lncRNA, miRNA, and mRNA of the 2 groups. 17 differentially expressed lncRNAs were selected and further validated by quantitative real-time polymerase chain reaction (RT-qPCR). The lncRNA–miRNA–mRNA network, Gene Ontology (GO) term enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using Cytoscape. OutcomesIntra-cavernosal pressure, mean arterial pressure, smooth muscle content, and the expression of miRNA, mRNA, and lncRNA were measured. ResultsThe BCNC group showed decreased intra-cavernosal/mean arterial pressure as well as decreased smooth muscle/collagen ratios compared with the Sham group. The RNA sequencing results revealed dysregulated expressions of 65 lncRNA, 14 miRNA, and 750 mRNA in the BCNC group based on the following criteria: fold change >2 and P < .05. Among the 17 lncRNAs further selected based on mean count number >4 in both groups, 3 lncRNAs (TCONS_00028173, TCONS_00049985, and TCONS_00058429) were further validated for differential expression by RT-qPCR. GO analysis suggests that these 3 lncRNAs could regulate various processes such as myotube differentiation and muscle cell differentiation. Furthermore, the KEGG pathway analysis showed that the mRNAs in the competing endogenous RNA (ceRNA) network are involved in pathways, including axon guidance and vascular endothelial growth factor signaling pathway. Clinical TranslationOur findings may provide new information on molecular pathophysiology of CNI-ED and suggest further research to find a more effective therapy for CNI-ED. Strengths & LimitationsThis study is the first to identify the lncRNA expression pattern and propose a ceRNA network in a rat model with cavernous nerve injury–related erectile dysfunction. However, analogous studies are needed to confirm these findings in humans. In addition, we constructed the network by only confirming the lncRNA. ConclusionOur study reveals differential expression profiles of lncRNAs, miRNAs, and mRNAs between the BCNC and Sham groups and suggests that these differentially expressed lncRNAs may play critical roles in CNI-ED by regulating apoptosis and fibrosis in the corpus cavernosum via targeting mRNAs or miRNAs.Cong R, Wang Y, Wang Y. Comprehensive Analysis of lncRNA Expression Pattern and lncRNA–miRNA–mRNA Network in a Rat Model With Cavernous Nerve Injury Erectile Dysfunction. J Sex Med 2020;17:1603–1617.

Integrative analysis of an lncRNA‑associated competing endogenous RNA network in human trabecular meshwork cells under oxidative stress.

Long non-coding RNAs (lncRNAs) are a group of non-coding transcripts of >200 nucleotides. They can act as competing endogenous RNAs (ceRNAs) and suppress microRNA (miRNA) function by preventing them from binding to and interacting with target mRNAs. However, the specific role of the lncRNA-associated ceRNA network in the pathogenesis of glaucoma has not yet been elucidated. To study this, data were downloaded from the Gene Expression Omnibus database (GSE126170), which contained three human trabecular meshwork cell (HTMC) samples treated with 300 µm hydrogen peroxide and three control samples treated with vehicle. Differentially expressed lncRNAs and mRNAs of HTMCs were obtained using the R package limma. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of differentially expressed mRNAs were performed using the R package clusterProfiler. Finally, the ceRNA network was constructed using the mircode, miRDB, miRTarBase and TargetScan databases, and visualized using Cytoscape v3.6.1. The results showed that 70 lncRNAs and 558 mRNAs were identified to be significantly dysregulated (|log2FoldChange| >1 and adjusted P<0.05) in HTMCs under oxidative stress compared to those in HTMCs under control conditions. Moreover, 24 lncRNAs, 24 miRNAs and 40 mRNAs were closely connected, and were part of the ceRNA network. Among these, the expression levels of 19 lncRNAs were upregulated, and those of 5 lncRNAs were downregulated. To conclude, using bioinformatics analysis, the differential expression profiles of lncRNAs were reported and a lncRNA-associated ceRNA network in HTMCs under oxidative stress was constructed. These results may bring to light a new pathological mechanism or a potential therapeutic target for glaucoma.

RNA sequencing and functional analyses reveal regulation of novel drought-responsive, long-non-coding RNA in Zanthoxylum bungeanum Maxim

Plant stress tolerance is a complex process involving transcriptional and post-transcriptional regulation of gene expression. Many recent studies have shown that LncRNAs play important roles in plant stress responses and thus create new opportunities for genetic plant breeding. In this study, RNA-seq analysis of Zanthoxylum bungeanum leaves under PEG-simulated drought stress was carried out and differential expression profiles of LncRNAs were obtained. We identified five drought-response-up-regulated LncRNAs (DRURs) and five drought-response-down-regulated LncRNAs (DRDRs). Speculating that these LncRNAs participate in the regulation of Z. bungeanum’s PEG-simulated drought stress response, to confirm their function, we predicted miRNAs in LncRNAs and predicted the miRNA target genes. Forty-four miRNAs were identified from the 10 LncRNAs and the target genes of miRNA were shown to involve numerous signaling pathways and metabolic pathways, including plant-pathogen interaction, plant hormone signal transduction, MAPK signaling, cell growth and death, and amino acid biosynthesis. Results suggest the 10 drought-responsive LncRNAs may be involved in the regulation of membrane stability in mitochondria and chloroplasts and so help maintain normal operation of photosynthesis and respiration. They also, activate the JA, ABA, auxin, ethylene, GA and MAPK signaling pathways.

A Novel lnc-RNA, Named lnc-ORA, Is Identified by RNA-Seq Analysis, and Its Knockdown Inhibits Adipogenesis by Regulating the PI3K/AKT/mTOR Signaling Pathway.

Obesity is closely associated with numerous adipogenic regulatory factors, including coding and non-coding genes. Long noncoding RNAs (lncRNAs) play a major role in adipogenesis. However, differential expression profiles of lncRNAs in inguinal white adipose tissue (iWAT) between wild-type (WT) and ob/ob mice, as well as their roles in adipogenesis, are not well understood. Here, a total of 2809 lncRNAs were detected in the iWAT of WT and ob/ob mice by RNA-Sequencing (RNA-Seq), including 248 novel lncRNAs. Of them, 46 lncRNAs were expressed differentially in WT and ob/ob mice and were enriched in adipogenesis signaling pathways as determined by KEGG enrichment analysis, including the PI3K/AKT/mTOR and cytokine–cytokine receptor interaction signaling pathways. Furthermore, we focused on one novel lncRNA, which we named lnc-ORA (obesity-related lncRNA), which had a seven-fold higher expression in ob/ob mice than in WT mice. Knockdown of lnc-ORA inhibited preadipocyte proliferation by decreasing the mRNA and protein expression levels of cell cycle markers. Interestingly, lnc-ORA knockdown inhibited adipocyte differentiation by regulating the PI3K/AKT/mTOR signaling pathway. In summary, these findings contribute to a better understanding of adipogenesis in relation to lncRNAs and provide novel potential therapeutic targets for obesity-related metabolic diseases.