Interference With ACSL1 Gene in Bovine Adipocytes: Transcriptome Profiling of mRNA and lncRNA Related to Unsaturated Fatty Acid Synthesis

The enzyme long-chain acyl-CoA synthetase 1 (ACSL1) is essential for lipid metabolism. The ACSL1 gene controls unsaturated fatty acid (UFA) synthesis as well as the formation of lipid droplets in bovine adipocytes. Here, we used RNA-Seq to determine lncRNA and mRNA that regulate UFA synthesis in bovine adipocytes using RNA interference and non-interference with ACSL1. The corresponding target genes of differentially expressed (DE) lncRNAs and the DE mRNAs were found to be enriched in lipid and FA metabolism-related pathways, according to GO and KEGG analyses. The differentially expressed lncRNA- differentially expressed mRNA (DEL-DEM) interaction network indicated that some DELs, such as TCONS_00069661, TCONS_00040771, TCONS_ 00035606, TCONS_00048301, TCONS_001309018, and TCONS_00122946, were critical for UFA synthesis. These findings assist our understanding of the regulation of UFA synthesis by lncRNAs and mRNAs in bovine adipocytes.

TET3 Promotes HCC Proliferation And Metastasis Via lncRNA ARAP1-AS1

Background: Aberrations of DNA methylation and proteins involved in DNA methylation process have been demonstrated to be correlated with tumor malignancy and prognosis of patients. The present study aims to investigate the preliminary mechanism underlying the biological functions of a DNA demethylation enzyme TET3 during HCC proliferation and metastasis.Methods: CCK8 assay, colony formation assay and transwell assay were performed to monito cell proliferation, migration and invasion. RNA-sequencing (RNA-seq) was applied to screen the differentially expressed mRNA upon TET3 overexpression to investigate the downstream mediators of TET3 during HCC progression. The expression of TET3 or ARAP1-AS1 was examined by western blot or quantitative real-time PCR (qRT-PCR).Results: First, TET3 expression was increased in HCC tumor tissues and positively correlated with poor prognosis of HCC patients. Next, TET3 was found to promote the proliferation and metastasis of HCC cells. RNA-seq was then performed and unveiled lncRNA ARAP1-AS1, a well identified onco-lncRNA in several cancer types, as a candidate downstream mediator of TET3. The following results indicated that TET3 increased ARAP1-AS1 expression. And rescue experiments indicated that ARAP1-AS1 knockdown impaired the proliferation of HCC cells induced by TET3 overexpression.Conclusion: TET3 promoted the proliferation and metastasis of HCC cells by regulating the expression of lncRNA ARAP1-AS1.

The m6A RNA Modification Modulates Gene Expression and Fibrosis-Related Pathways in Hypertrophic Scar

Purpose: To systematically analyze the overall m6A modification pattern in hyperplastic scars (HS).Methods: The m6A modification patterns in HS and normal skin (NS) tissues were described by m6A sequencing and RNA sequencing, and subsequently bioinformatics analysis was performed. The m6A-related RNA was immunoprecipitated and verified by real-time quantitative PCR.Results: The appearance of 14,791 new m6A peaks in the HS sample was accompanied by the disappearance of 7,835 peaks. The unique m6A-related genes in HS were thus associated with fibrosis-related pathways. We identified the differentially expressed mRNA transcripts in HS samples with hyper-methylated or hypo-methylated m6A peaks.Conclusion: This study is the first to map the m6A transcriptome of human HS, which may help clarify the possible mechanism of m6A-mediated gene expression regulation.

Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states

BackgroundMany long non-coding RNAs (lncRNAs) have been extensively identified in many higher eukaryotic species. The function of lncRNAs has been reported to play important roles in diverse biological processes, including developmental regulation and behavioral plasticity. However, there are no reports of systematic characterization of long non-coding RNAs in the fire ant Solenopsis invicta.ResultsIn this study, we performed a genome-wide analysis of lncRNAs in the brains of S. invicta from RNA-seq. In total, 1,393 novel lncRNA transcripts were identified in the fire ant. In contrast to the annotated lncRNA transcripts having at least two exons, novel lncRNAs are monoexonic transcripts with a shorter length. Besides, the transcriptome from virgin alate and dealate mated queens were analyzed and compared. The results showed 295 differentially expressed mRNA genes (DEGs) and 65 differentially expressed lncRNA genes (DELs) between virgin and mated queens, of which 17 lncRNAs were highly expressed in the virgin alates and 47 lncRNAs were highly expressed in the mated dealates. By identifying the DEL:DEG pairs with high association in their expression (Spearman’s |rho| > 0.8 and p-value < 0.01), many DELs were co-regulated with DEGs after mating. Furthermore, several remarkable lncRNAs (MSTRG.6523, MSTRG.588, and nc909) that were found to associate with particular coding genes may play important roles in the regulation of brain gene expression in reproductive transition in fire ants.ConclusionThis study provides the first genome-wide identification of S. invicta lncRNAs in the brains in different reproductive states and will contribute to a fuller understanding of the transcriptional regulation underpinning reproductive changes.

Chrysin Induced Cell Apoptosis Through H19/let-7a/COPB2 Axis in Gastric Cancer Cells and Inhibited Tumor Growth

BackgroundChrysin is a natural flavone that is present in honey and has exhibited anti-tumor properties. It has been widely studied as a therapeutic agent for the treatment of various types of cancers. The objectives of this present study were to elucidate how chrysin regulates non-coding RNA expression to exert anti-tumor effects in gastric cancer cells.MethodsThrough the use of RNA sequencing, we investigated the differential expression of mRNAs in gastric cancer cells treated with chrysin. Furthermore, COPB2, H19 and let-7a overexpression and knockdown were conducted. Other features, including cell growth, apoptosis, migration and invasion, were also analyzed. Knockout of the COPB2 gene was generated using the CRISPR/Cas9 system for tumor growth analysis in vivo.ResultsOur results identified COPB2 as a differentially expressed mRNA that is down-regulated following treatment with chrysin. Moreover, the results showed that chrysin can induce cellular apoptosis and inhibit cell migration and invasion. To further determine the underlying mechanism of COPB2 expression, we investigated the expression of the long non-coding RNA (lncRNA) H19 and microRNA let-7a. Our results showed that treatment with chrysin significantly increased let-7a expression and reduced the expression of H19 and COPB2. In addition, our results demonstrated that reduced expression of COPB2 markedly promotes cell apoptosis. Finally, in vivo data suggested that COPB2 expression is related to tumor growth.ConclusionsThis study suggests that chrysin exhibited anti-tumor effects through a H19/let-7a/COPB2 axis.

LncRNA expression profile, functional analysis and potential biomarkers in children with pancreaticobiliary maljunction

Background The present study was aimed to investigate the expression profile of long non-coding RNAs (lncRNAs) and its potential as biomarker for pancreaticobiliary maljunction (PBM). Methods The differential expression of lncRNA and messenger RNA (mRNA) from 15 pediatric patients with PBM and 15 control subjects were analyzed with microArray and validated with quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Gene Ontology enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were used to investigate the biological functions of these genes. The area under curve (AUC) of receiver operating characteristic (ROC) curve was used to predict the biomarker of lncRNA in PBM. Results There were 2915 mRNAs and 173 lncRNAs upregulated, 2121 mRNAs and 316 lncRNAs downregulated in PBM cases, respectively. The enriched GO associated with differentially expressed mRNA were extracellular matrix, extracellular region and kinetochore. The most enriched pathway of Protein digestion and absorption was associated with cancer and PI3K-Akt signaling. Cis- and Trans-target gene analysis indicated that mRNAs were predicted to be regulated by one lncRNA and one mRNA corresponded to several lncRNAs. The results showed that the expression trends of NR_110876, NR_132344, XR_946886 and XR_002956345 were consistent with the microarray results, and the difference was statistically significant NR_132344, XR_946886 and XR_002956345 (P < 0.05).The AUC of ROC curve was significant only for XR_946886 (0.837, P < 0.001). Conclusion The present study indicated that lncRNAs were involved the pathogenesis of common bile duct in PBM and XR_946886 would be biomarkers for PMB.

Expression Status and Prognostic Roles of m6A-related Genes in Multiple Myeloma: YTHDF2 as the independent prognostic factor

Background: N6-methyladenosine is the most abundant RNA modification, which plays a prominent role in multiple biology processes, including tumorigenesis. Multiple myeloma (MM) is the second most frequent hematological cancer. However, the expression status and value of m6A-related genes in multiple myeloma remain elusive.Methods: m6A-related gene expression data and clinical information of MM patients were obtained from the Gene Expression Omnibus (GEO) database. Based on differentially expressed analysis, protein-protein interaction (PPI) analysis, Pearson correlation analysis, Kaplan-Meier survival analysis and Cox regression analysis, the prognostic m6A-associated genes were identified. The receiver operation characteristic (ROC) curves were used to verify the prognostic and diagnostic efficiency. The molecular mechanisms were investigated by differentially expressed mRNA and microRNA analyses with the help of online database ENCORI and POSTAR.Results: Among 22 m6A-related genes, HNRNPC, RBM15B, RBM15, YTHDF3, YTHDF2, HNRNPA2B1 and IGF2BP2 were significantly upregulated, while ZC3H13, FTO, IGF2BP3, ALKBH5 and YTHDC1 were significantly downregulated in MM patients. The high expression of HNRNPC, HNRNPA2B1, YTHDF2 and the low expression of ZC3H13 were associated with adverse survival. Furthermore, the expression level of YTHDF2 was the independent prognostic factor of MM. ROC curves suggested the great prediction performance for MM patients. Differentially expressed mRNA and microRNA analyses indicated the probable involvement of miR-205/YTHDF2/EGR1 axis.Conclusions: Our study first systematically analyzed the expression status of m6A-related genes in multiple myeloma, identified HNRNPC, HNRNPA2B1, YTHDF2 and ZC3H13 that could be the potential prognostic biomarkers, especially YTHDF2, which may be implicated in the miR-205/YTHDF2/EGR1 axis.

Prediction of Lymph-Node Metastasis in Cancers Using Differentially Expressed mRNA and Non-coding RNA Signatures

Accurate prediction of lymph-node metastasis in cancers is pivotal for the next targeted clinical interventions that allow favorable prognosis for patients. Different molecular profiles (mRNA and non-coding RNAs) have been widely used to establish classifiers for cancer prediction (e.g., tumor origin, cancerous or non-cancerous state, cancer subtype). However, few studies focus on lymphatic metastasis evaluation using these profiles, and the performance of classifiers based on different profiles has also not been compared. Here, differentially expressed mRNAs, miRNAs, and lncRNAs between lymph-node metastatic and non-metastatic groups were identified as molecular signatures to construct classifiers for lymphatic metastasis prediction in different cancers. With this similar feature selection strategy, support vector machine (SVM) classifiers based on different profiles were systematically compared in their prediction performance. For representative cancers (a total of nine types), these classifiers achieved comparative overall accuracies of 81.00% (67.96–92.19%), 81.97% (70.83–95.24%), and 80.78% (69.61–90.00%) on independent mRNA, miRNA, and lncRNA datasets, with a small set of biomarkers (6, 12, and 4 on average). Therefore, our proposed feature selection strategies are economical and efficient to identify biomarkers that aid in developing competitive classifiers for predicting lymph-node metastasis in cancers. A user-friendly webserver was also deployed to help researchers in metastasis risk determination by submitting their expression profiles of different origins.