Regulate Target Gene Expression Research Articles

MHRWR: Prediction of lncRNA-Disease Associations Based on Multiple Heterogeneous Networks.

In the last few years, accumulating evidences had demonstrated that long non-coding RNAs (lncRNAs) participated in the regulation of target gene expression and played an important role in biological processes and human disease development. Thus, prediction of the associations between lncRNAs and disease had become a hot research in the fields of human sophisticated diseases. Most of these methods considered the information of two networks (lncRNA, disease) while neglected other networks. In this study, we designed a multi-layer network by integrating the similarity networks of lncRNAs, diseases and genes, and the known association networks of lncRNA-disease, lncRNAs-gene, and disease-gene, and then we developed a model called MHRWR for predicting the lncRNA-disease potential associations based on random walk with restart. The performance of MHRWR was evaluated by experimentally verified lncRNA-disease associations based on leave-one-out cross validation. MHRWR obtained a reliable AUC value of 0.91344, which significantly outperformed some previous methods. To further validate the reproducibility of performance, we used the model of MHRWR to verify related lncRNAs of colon cancer, colorectal cancer and lung adenocarcinoma in the case studies. The codes of MHRWR is available on: https://github.com/yangyq505/MHRWR.

Synovial fibroblast-derived exosomal microRNA-106b suppresses chondrocyte proliferation and migration in rheumatoid arthritis via down-regulation of PDK4.

Fibroblast-derived exosomes have been reported to transfer microRNAs to recipient cells, where they regulate target gene expression, which is of interest for understanding the basic biology of inflammation, tissue homeostasis, and development of therapeutic approaches. Initial microarray-based analysis carried out in this study identified the rheumatoid arthritis (RA)-related differentially expressed gene pyruvate dehydrogenase kinase 4 (PDK4). Subsequently, the upstream regulatory microRNA-106b (miR-106b) of PDK4 was predicted with bioinformatic analyses. A collagen-induced arthritis (CIA)-induced mouse model was established, and exosomes were isolated from synovial fibroblasts (SFs) and transferred into chondrocytes to identify the role of exosomes in rheumatoid arthritis (RA). We found that PDK4 was poorly expressed in RA cartilage tissues and chondrocytes, while miR-106b was highly expressed in RA SFs and SF-derived exosomes. Notably, PDK4 was confirmed as a target gene of miR-106b. Over-expression of PDK4 promoted the proliferation and migration abilities of chondrocytes and inhibited their apoptosis as well as affected the receptor activator of nuclear factor kappa B ligand (RANKL)/RANK/osteoprotegerin (OPG) system. Meanwhile, miR-106b was delivered from SFs to chondrocytes through exosomes, which suppressed chondrocyte proliferation and migration and accelerated apoptosis as well as affected the RANKL/RANK/OPG system via down-regulation of PDK4. Furthermore, in vivo results validated that miR-106b inhibition could relieve CIA-induced RA. Taken together, SF-derived exosomal miR-106b stimulates RA initiation by targeting PDK4, indicating a physiologically validated potential approach for the prevention and treatment of RA. KEY MESSAGES: PDK4 is decreased in chondrocytes of RA, while miR-106b is increased in SFBs. PDK4 promotes proliferation and migration of chondrocytes. miR-106b could target 3'UTR of PDK4 gene. SFB-exosomal miR-106b inhibits proliferation and migration of chondrocytes. Inhibition of miR-106b attenuates RA progression in a CIA mouse model.

Construction and Comprehensive Analyses of a Competing Endogenous RNA Network in Tumor-Node-Metastasis Stage I Hepatocellular Carcinoma.

Background Long noncoding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) and interact with microRNAs (miRNAs) to regulate target gene expression, which can greatly influence tumor development and progression. Different tumor-node-metastasis (TNM) stages of hepatocellular carcinoma (HCC) defined by the American Joint Committee on Cancer (AJCC) have different clinical results. Our purpose was to comprehensively analyze differentially expressed (DE) lncRNAs, miRNAs, and mRNAs in stage I HCC and identify prognosis-associated RNAs. Methods RNA-seq data were obtained from The Cancer Genome Atlas (TCGA) database. A stage I HCC-associated miRNA-lncRNA-mRNA network was constructed. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analyses of ceRNA-associated DEmRNAs were performed using Database for Annotation, Visualization, and Integrated Discovery (DAVID) 6.8 and Clusterprofile in the R package. The protein-protein interaction (PPI) network of the above mRNAs was then constructed using STRING. Finally, the association between lncRNAs and mRNAs in the ceRNA network and prognosis of patients was further analyzed. Linear regression analysis of the above lncRNAs and mRNAs associated with overall survival was performed. Results After a comparison between HCC and adjacent nontumor tissues, 778 lncRNAs, 1608 mRNAs, and 102 miRNAs that were abnormally expressed were identified. The ceRNA network was composed of 56 DElncRNAs, 14 DEmiRNAs, and 30 DEmRNAs. Functional analysis results showed that 30 DEmRNAs were enriched in 14 GO biological process categories and 6 KEGG categories (false discovery rate (FDR) < 0.05). A PPI network was composed of 22 nodes and 58 edges. We detected 4 DElncRNAs (BPESC1, AC061975.6, AC079341.1, and CLLU1) and 6 DEmRNAs (CEP55, E2F1, E2F7, EZH2, G6PD, and SLC7A11) that had significant influences on the overall survival (OS) of stage I HCC patients (P < 0.05). lncRNA BPESC1 was positively correlated with mRNA CEP55 via miR-424, and lncRNA AC061975.6 was positively correlated with mRNA E2F1 via miR-519d. Conclusion Our study identified novel lncRNAs and mRNAs that were associated with the progression and prognosis of stage I HCC and further investigated the regulatory mechanism of lncRNA-mediated ceRNAs in the development of stage I HCC.

Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy.

Polyploid plants are more often invasive species than their diploid counterparts. As the invasiveness of a species is often linked to its production of allelopathic compounds, we hypothesize that differences in invasive ability between cytotypes may be due to their different ability to synthesize allelopathic metabolites. We test this using two cytotypes of Solidago canadensis as the model and use integrated metabolome and transcriptome data to resolve the question. Metabolome analysis identified 122 metabolites about flavonoids, phenylpropanoids and terpenoids, of which 57 were differentially accumulated between the two cytotypes. Transcriptome analysis showed that many differentially expressed genes (DEGs) were enriched in ‘biosynthesis of secondary metabolites’, ‘plant hormone signal transduction’, and ‘MAPK signaling’, covering most steps of plant allelopathic metabolite synthesis. Importantly, the differentially accumulated flavonoids, phenylpropanoids and terpenoids were closely correlated with related DEGs. Furthermore, 30 miRNAs were found to be negatively associated with putative targets, and they were thought to be involved in target gene expression regulation. These miRNAs probably play a vital role in the regulation of metabolite synthesis in hexaploid S. canadensis. The two cytotypes of S. canadensis differ in the allelopathic metabolite synthesis and this difference is associated with regulation of expression of a range of genes. These results suggest that changes in gene expression may underlying the increased invasive potential of the polyploidy.

LncRNA LUCRC Regulates Colorectal Cancer Cell Growth and Tumorigenesis by Targeting Endoplasmic Reticulum Stress Response.

Colorectal cancer (CRC) is the second most common cause of cancer-related death worldwide, and is well known for its strong invasiveness, rapid recurrence, and poor prognosis. Long non-coding RNAs (lncRNAs) have been shown to be involved in the development of various types of cancers, including colorectal cancer. Here, through transcriptomic analysis and functional screening, we reported that lncRNA LUCRC (LncRNA Upregulated in Colorectal Cancer) is highly expressed in colorectal tumor samples and is required for colorectal cancer cell proliferation, migration, and invasion in cultured cells and tumorigenesis in xenografts. LUCRC was found to regulate target gene expression of unfolded protein response (UPR) in endoplasmic reticulum (ER), such as BIP. The clinical significance of LUCRC is underscored by the specific presence of LUCRC in blood plasma of patients with colorectal cancers. These findings revealed a critical regulator of colorectal cancer development, which might serve as a therapeutic target in colorectal cancer.

Pol-miR-7133 and pol-miR-3p-9227 of Japanese flounder Paralichthys olivaceus modulate Streptococcus iniae infection through regulation of the common target gene LAMP2

MicroRNAs (miRNAs) are small, non-coding endogenous RNAs that play critical roles in diverse cellular processes through regulating target gene expression. In the present study, we identified two Japanese flounder (Paralichthys olivaceus) miRNAs, i.e., pol-miR-7133 and pol-miR-3p-9227, and examined the functions of the miRNAs and their target gene in association with the infection of Streptococcus iniae. pol-miR-7133 and pol-miR-3p-9227 were identified as miRNAs downregulated during S. iniae infection. Both miRNAs targeted the gene of lysosome-associated membrane protein 2 (LAMP2) isoform 3 of flounder (named PoLAMP23) by interaction with the 3′-untranslated region (3’-UTR) of PoLAMP2–3. Both in vivo and in vitro studies showed that PoLAMP2–3 expression negatively correlated with pol-miR-7133 and pol-miR-3p-9227 expression. Since to date no study on fish LAMP2 had been documented, we investigated the biological property of PoLAMP2–3. We found that PoLAMP2–3 expression occurred in multiple tissues and was most abundant in liver. PoLAMP2–3 is a highly acidic transmembrane protein and was observed to localize in both lysosome and cellular membrane. In vitro studies showed that overexpression of pol-miR-7133 and pol-miR-3p-9227 or interference with PoLAMP2-3 expression significantly enhanced S. iniae infection in flounder cells. Consistently, in vivo studies showed that knockdown of pol-miR-7133 and pol-miR-3p-9227, or overexpression of PoLAMP2-3, inhibited S. iniae infection in flounder, whereas knockdown of PoLAMP2-3 in flounder facilitated S. iniae infection. Together these results revealed for the first time an important immune function of fish LAMP2 and indicated that pol-miR-7133 and pol-miR-3p-9227, via LAMP2, play a vital role in anti-bacterial immunity in fish.

Severe obstructive sleep apnea is associated with circulating microRNAs related to heart failure, myocardial ischemia, and cancer proliferation.

Obstructive sleep apnea (OSA) is associated with multiple comorbid conditions including cardiovascular diseases and cancer. There is a growing interest in exploring biomarkers to understand the related mechanisms and improve the risk stratification of OSA. Circulating microRNAs (miRNAs) are single noncoding strands of nearly 22 nucleotides that posttranscriptionally regulate target gene expression. Our aim was to identify miRNA profiles associated with OSA. We studied 48 male subjects, mostly Caucasian (63%) and overweight, divided by polysomnography into the no OSA control group (n = 6), mild OSA group (n = 12), moderate OSA group (n = 15), and severe OSA group (n = 15). The study groups were matched for age, body mass index (BMI), and body fat composition. miRNA profiles were measured from peripheral whole blood using two steps: (1) microarray analysis comprising more than 2500 miRNAs in a subsample of 12 subjects (three from each group); and (2) validation phase using real-time quantitative polymerase chain reaction (RTqPCR). The microarray assessment identified 21 differentially expressed miRNAs among the groups. The RT-qPCR assessment showed that miR-1254 and miR-320e presented a gradual increase in expression parallel to OSA severity. Linear regression analysis showed that severe OSA was independently associated with miR-1254 (ß = 68.4; EP = 29.8; p = 0.02) and miR-320e (ß = 76.1; EP = 31.3; p = 0.02). Severe OSA is independently associated with miRNAs that are involved in heart failure (miR-1254), myocardial ischemia/reperfusion (miR-320e), and cell proliferation in some cancer types (miR-1254 and miR-320e). Future investigations addressing whether these miRs may provide prognostic information in OSA are needed.

MicroRNA‑21 contributes to renal cell carcinoma cell invasiveness and angiogenesis via the PDCD4/c‑Jun (AP‑1) signalling pathway.

Accumulating evidence has demonstrated that microRNAs are associated with malignant biological behaviour, including tumorigenesis, cancer progression and metastasis via the regulation of target gene expression. Our previous study demonstrated that programmed cell death protein 4 (PDCD4), which is a tumour suppressor gene, is a target of microRNA‑21 (miR‑21), which affects the proliferation and transformation capabilities of renal cell carcinoma (RCC) cells. However, the role of miR‑21 in the molecular mechanism underlying the migration, invasion and angiogenesis of RCC remains poorly understood. The effects of miR‑21 on the invasion, migration and angiogenesis of RCC cells was determined through meta‑analysis and regulation of miR‑21 expression invitro. After searching several databases, 6 articles including a total of 473patients met the eligibility criteria for this analysis. The combined results of the meta‑analysis revealed that increased miR‑21 expression was significantly associated with adverse prognosis in patients with RCC, with a pooled hazard ratio estimate of 1.740. In invitro experiments, we demonstrated that a miR‑21 inhibitor decreased the number of migrating and invading A498 and 786‑O RCC cells, along with a decrease in PDCD4, c‑Jun, matrix metalloproteinase (MMP)2 and MMP9 expression. Additionally, inhibition of miR‑21 was revealed to reduce tube formation and tube junctions in the endothelial cell line HMEC‑1 by affecting the expression of angiotensin‑1 and vascular endothelial growth factor A, whereas PDCD4 small interfering RNA exerted opposite effects on the same cells. Overall, these findings, along with evidence‑based molecular biology, demonstrated that miR‑21 expression promoted the migration, invasion and angiogenic abilities of RCC cells by directly targeting the PDCD4/c‑Jun signalling pathway. The results may help elucidate the molecular mechanism underlying the development and progression of RCC and provide a promising target for microRNA‑based therapy.

Bovine milk transcriptome analysis reveals microRNAs and RNU2 involved in mastitis.

Mastitis is a common inflammatory infectious disease in dairy cows. To understand the microRNA (miRNA) expression profile changes during bovine mastitis, we undertook a genome-wide miRNA study of normal milk and milk that tested positive on the California mastitis test for bovine mastitis (CMT+). Twenty-five miRNAs were differentially expressed (23 miRNAs upregulated and two downregulated) during bovine mastitis relative to their expression in normal milk. Upregulated mature miR-1246 probably derived from a U2 small nuclear RNA rather than an miR-1246 precursor. The significantly upregulated miRNA precursors and RNU2 were significantly enriched on bovine chromosome 19, which is homologous to human chromosome 17. A gene ontology analysis of the putative mRNA targets of the significantly upregulated miRNAs showed that these miRNAs were involved in binding target mRNA transcripts and regulating target gene expression, and a Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the upregulated miRNAs were predominantly related to cancer and immune system pathways. Three novel miRNAs were associated with bovine mastitis and were relatively highly expressed in milk. We confirmed that one of the novel mastitis-related miRNAs was significantly upregulated using a digital PCR system. The differentially expressed miRNAs were involved in human cancers, infections, and immune-related diseases. The genome-wide analysis of miRNA profiles in this study provides insight into bovine mastitis and inflammatory diseases. DATABASES: The miRNAseq generated for this study can be found in the Sequence Read Archive (SRA) under BioProject Number PRJNA421075 and SRA Study Number SRP126134 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421075).

Functional Evaluation and Mechanism Study of Kel As an Oncogenic Driver in Acute Erythroleukemia

Background Acute erythroleukemia (AEL) is defined as an distinct subtype (&lt;5%) of AML in FAB classification, characterized by predominant erythropoiesis. It is associated with a poor prognosis, with a median overall survival (OS) of 3-14 months from diagnosis. No recurrent cytogenetic abnormality is specific of AEL. Through "Oncomine" Database, we found that KEL was significantly up-regulated in AEL patients, compared with other types of AML and normal patients. It has been reported that KEL promoter exhibited a strong transcriptional erythroid activity in K562 cells, but its role in the development of AEL remains unclear. Circular RNAs (circRNAs) have been implicated in various biological processes. Here we found one circRNA transcripted from KEL gene (circ-KEL), which also had a high expression in AEL, may play a role of coordinate regulation with KEL. The present study aimed to investigate the potential modulation of KEL in the development and progression of AEL. Method In our study, we collected blood samples of 11 AEL patient, 20 other types of AML patients and 20 normal patients. qPCR and Western blot analysis were performed to examine the expression of KEL and circ-KEL. We set up the erythroid differentiation models in vitro using two AEL cells lines (K562 and HEL) , induced with 50 μM hemin from day1 to day 7. The oncogenic functions of KEL were further measured in AEL cell lines by performing RNA interfering (RNAi), immunofluorescence (IF) staining, CCK8 assay and flow cytometry. The expression levels of γ-globin and FUT1 as well as the erythroid surface markers TER119 and GPA were examined to evaluate their function in erythroid differentiation. The proliferative ability of AEL cells was determined by CCK-8 assay. AEL animal models were established using NCG mice transplanted with K562 (NC and KEL over-expression). The tumor formation rate, body weight and survival curve were investigated to evaluate the oncogenic functions of KEL in-vivo. Protein antibody microarray was used to analyze the activation of related pathways after KEL over-expression in AEL cells. Moreover, we explored the molecular mechanisms of KEL and verified the interactions among GATA1 and H3K27ac as well as the PKC/RSK2/CREB pathway by performing ChIP, RIP, dual-luciferase reporter assay and Western blotting. Result KEL was specifically higher expressed in AEL clinical samples/cells lines, consistent with the results of the database. The over-expression of KEL could up-regulate the expression of GATA1, thus promoting the erythroid differentiation of AEL cells. Moreover, protein antibody microarray results showed that the up-regulation of KEL in AEL cells leads to the activation of multiple proliferation and PDL1 related pathways. After subsequent verification, it was verified that PKC/RSK2/CREB pathway was significantly activated. Meanwhile, the expression of PDL1 was highly correlated with KEL. We found that the higher expression of KEL in AEL cells could up-regulate PDL1 expression through activating the phosphorylation of relative transcript factors on PDL1 DNA promoter. In-vivo experiment showed that KEL over-expression may accelerate the leukemia progression. In addition, we discovered that JQ1 could be used as a inhibitor of KEL, which could effectively decrease the expression of GATA1 and PDL1. A number of circRNAs have been reported to act as microRNA (miRNA) sponges, which regulate target gene expression by interacting with miRNA. Our results revealed that circ-KEL could serve as a sponge for miR-671 and up-regulate miR-617 functional target KEL, thus promote the erythroid differentiation. Conclusion Our study reveals the oncogenic role and a novel regulatory mechanism of KEL in AEL progression. For the first time, we demonstrated that KEL was specifically highly expressed in AEL cells, leading to the dysregulation of erythroid differentiation through up-regulating GATA1, and on the other hand, promoting cell proliferation via PKC/RSK2/CREB pathway. Circ-KEL which also had a high expression in AEL, may play a role of coordinate regulation with KEL. These findings may provide a promising strategy for future diagnosis, biomarker discoveries and treatment for AEL patients. Figure Disclosures No relevant conflicts of interest to declare.

The role of acetylation sites in the regulation of p53 activity.

As a "genomic guardian", p53 mainly functions as a transcription factor that regulates downstream targets responsible for cell fate control, and the activity of p53 is tightly regulated by a complex network that include an abundance of post-translational modifications. Notably, acetylation of p53 at many positions has been demonstrated to play a major role in accurate p53 regulation and cell fate determination. However, no evidence has been provided to compare the effect of acetylation at different sites on p53 regulation. Here, we constructed six acetylation-defective p53 mutants that lysine was substituted by arginine at residues 120, 164, 305, 320, 370/372/373 or 381/382/386, respectively, and determined their effects on p53 activity systematically. Our results showed that all six mutants exhibited diminished transactivation ability and selective regulation of target genes expression through distinct mechanisms. Specifically, lysine 370/372/373 and 381/382/386 mutations decreased p53 stability, and lysine 305 mutation reduced p53 phosphorylation level at serine 15, while lysine 120 and 164 mutations decreased p53 acetylation level at lysine 382. Collectively, these data indicate that acetylation of p53 at different sites has diverse regulatory effects on p53 transcriptional activity through different mechanisms.

Ferritin Light Chain (FTL) competes with long noncoding RNA Linc00467 for miR-133b binding site to regulate chemoresistance and metastasis of colorectal cancer.

Although the colorectal cancer (CRC) mortality rates are decreasing in virtue of CRC screening and improved therapeutic methods, CRC is still a leading cause of cancer deaths. One of the main causes is chemoresistance occurrence in CRC. Understanding of the molecular mechanisms of chemoresistance benefits to CRC diagnosis and treatment. In this study, gene expression was determined by western blot and qRT-PCR. The biological functions of genes in CRC cells were studied by knocking down or overexpressing the gene in CRC cells and then analyzing cell sensitivity to 5-Fu by the MTT assay and the flow cytometry, and analyzing cell migration and invasion by transwell assays. The luciferase reporter assay was used to examine microRNA regulation of target gene expression, and biotin pull-down assay was performed to detect interaction between RNA molecules. This study found that ferritin light chain (FTL) and long intergenic noncoding RNA Linc00467 were both upregulated in CRC tissues and cell lines, and inversely correlated to CRC patient survival. FTL and Linc00467 promoted CRC cells abilities to resistance against 5-fluor-ouracil (5-Fu), migration and invasion. These effects were compromised by miR-133b which targeted both FTL and Linc00467. miR-133b interacted with Linc00467 and miR-133b inhibitor prevented Linc00467 knockdown-induced alternations of FTL expression and biological functions. Both FTL and Linc00467 are oncogenes in CRC. FTL expression upregulated in CRC via Linc00467/ miR-133b axis, and leads to CRC cell resistance against 5-FU treatment and promotes CRC metastasis. FTL expression upregulated in CRC via Linc00467/miR-133b axis, and leads to CRC cell resistance to 5-FU treatment and promotes CRC metastasis.

Inhibition of microRNA-711 limits angiopoietin-1 and Akt changes, tissue damage, and motor dysfunction after contusive spinal cord injury in mice

Spinal cord injury (SCI) causes neuronal cell death and vascular damage, which contribute to neurological dysfunction. Given that many biochemical changes contribute to such secondary injury, treatment approaches have increasingly focused on combined therapies or use of multi-functional drugs. MicroRNAs (miRs) are small (20–23 nucleotide), non-protein-coding RNAs and can negatively regulate target gene expression at the post-transcriptional level. As individual miRs can potentially modulate expression of multiple relevant proteins after injury, they are attractive candidates as upstream regulators of the secondary SCI progression. In the present study we examined the role of miR-711 modulation after SCI. Levels of miR-711 were increased in injured spinal cord early after SCI, accompanied by rapid downregulation of its target angiopoietin-1 (Ang-1), an endothelial growth factor. Changes of miR-711 were also associated with downregulation of the pro-survival protein Akt (protein kinase B), another target of miR-711, with sequential activation of glycogen synthase kinase 3 and the pro-apoptotic BH3-only molecule PUMA. Central administration of a miR-711 hairpin inhibitor after SCI limited decreases of Ang-1/Akt expression and attenuated apoptotic pathways. Such treatment also reduced neuronal/axonal damage, protected microvasculature and improved motor dysfunction following SCI. In vitro, miR-711 levels were rapidly elevated by neuronal insults, but not by activated microglia and astrocytes. Together, our data suggest that post-traumatic miR-711 elevation contributes to neuronal cell death after SCI, in part by inhibiting Ang-1 and Akt pathways, and may serve as a novel therapeutic target.

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

Current literature suggests that epigenetically regulated super-enhancers (SEs) are drivers of aberrant gene expression in cancers. Many tumor types are still missing chromatin data to define cancer-specific SEs and their role in carcinogenesis. In this work, we develop a simple pipeline, which can utilize chromatin data from etiologically similar tumors to discover tissue-specific SEs and their target genes using gene expression and DNA methylation data. As an example, we applied our pipeline to human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV + OPSCC). This tumor type is characterized by abundant gene expression changes, which cannot be explained by genetic alterations alone. Chromatin data are still limited for this disease, so we used 3627 SE elements from public domain data for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We integrated the available DNA methylation and gene expression data for HPV + OPSCC samples to filter the candidate SEs to identify functional SEs and their affected targets, which are essential for cancer development. Overall, we found 159 differentially methylated SEs, including 87 SEs that actively regulate expression of 150 nearby genes (211 SE-gene pairs) in HPV + OPSCC. Of these, 132 SE-gene pairs were validated in a related TCGA cohort. Pathway analysis revealed that the SE-regulated genes were associated with pathways known to regulate nasopharyngeal, breast, melanoma, and bladder carcinogenesis and are regulated by the epigenetic landscape in those cancers. Thus, we propose that gene expression in HPV + OPSCC may be controlled by epigenetic alterations in SE elements, which are common between related tissues. Our pipeline can utilize a diversity of data inputs and can be further adapted to SE analysis of diseased and non-diseased tissues from different organisms.

Circular RNA (circRNA) and YAP in tumor: A review

&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt; Circular Ribonucleic Acid (circRNA) is a type of RNA that has been found in recent years and is a closed loop structure widely found in eukaryotic cells. &lt;strong&gt;Present situation:&lt;/strong&gt; The circRNA is stable in nature, highly conserved and tissue and disease specific, and regulates target gene expression at the transcriptional or posttranscriptional level, which is related to the occurrence and development of tumors. YAP (Yes-associated protein) is the main effector of Hippo signaling pathway. It is found that YAP level is closely related to cell proliferation and apoptosis, tissue organ size control and tumorigenesis. &lt;strong&gt;Aim:&lt;/strong&gt; to study the correlation between circRNA and YAP in tumors.&lt;/p&gt;

Comprehensive analysis of the lncRNA‑associated competing endogenous RNA network in breast cancer.

Long noncoding RNAs (lncRNAs) have been confirmed to be potential prognostic markers in a variety of cancers and to interact with microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs) to regulate target gene expression. However, the role of lncRNA-mediated ceRNAs in breast cancer (BC) remains unclear. In the present study, a ceRNA network was generated to explore their role in BC. The expression profiles of mRNAs, miRNAs and lncRNAs in 1,109 BC tissues and 113 normal breast tissues were obtained from The Cancer Genome Atlas database (TCGA). A total of 3,198 differentially expressed (DE) mRNAs, 150 differentially DEmiRNAs and 1,043 DElncRNAs were identified between BC and normal tissues. A lncRNA-miRNA-mRNA network associated with BC was successfully constructed based on the combined data obtained from RNA databases, and comprised 97 lncRNA nodes, 24 miRNA nodes and 74 mRNA nodes. The biological functions of the 74 DEmRNAs were further investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results demonstrated that the DEmRNAs were significantly enriched in two GO biological process categories; the main biological process enriched term was ‘positive regulation of GTPase activity’. By KEGG analysis, four key enriched pathways were obtained, including the ‘MAPK signaling pathway’, the ‘Ras signaling pathway’, ‘prostate cancer’, and the ‘FoxO signaling pathway’. Kaplan-Meier survival analysis revealed that six DElncRNAs (INC AC112721.1, LINC00536, MIR7-3HG, ADAMTS9-AS1, AL356479.1 and LINC00466), nine DEmRNAs (KPNA2, RACGAP1, SHCBP1, ZNF367, NTRK2, ORS1, PTGS2, RASGRP1 and SFRP1) and two DEmiRNAs (hsa-miR-301b and hsa-miR-204) had significant effects on overall survival in BC. The present results demonstrated the aberrant expression of INC AC112721.1, AL356479.1, LINC00466 and MIR7-3HG in BC, indicating their potential prognostic role in patients with BC.

Identification of Target Genes Mediated by Two-Component Regulators of Staphylococcus aureus Using RNA-seq Technology.

Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.

MicroRNA Networks Modulate Oxidative Stress in Cancer.

Imbalanced regulation of reactive oxygen species (ROS) and antioxidant factors in cells is known as “oxidative stress (OS)”. OS regulates key cellular physiological responses through signal transduction, transcription factors and noncoding RNAs (ncRNAs). Increasing evidence indicates that continued OS can cause chronic inflammation, which in turn contributes to cardiovascular and neurological diseases and cancer development. MicroRNAs (miRNAs) are small ncRNAs that produce functional 18-25-nucleotide RNA molecules that play critical roles in the regulation of target gene expression by binding to complementary regions of the mRNA and regulating mRNA degradation or inhibiting translation. Furthermore, miRNAs function as either tumor suppressors or oncogenes in cancer. Dysregulated miRNAs reportedly modulate cancer hallmarks such as metastasis, angiogenesis, apoptosis and tumor growth. Notably, miRNAs are involved in ROS production or ROS-mediated function. Accordingly, investigating the interaction between ROS and miRNAs has become an important endeavor that is expected to aid in the development of effective treatment/prevention strategies for cancer. This review provides a summary of the essential properties and functional roles of known miRNAs associated with OS in cancers.

RIG-I-like receptors direct inflammatory macrophage polarization against West Nile virus infection

RIG-I-Like Receptors (RLRs) RIG-I, MDA5, and LGP2, are vital pathogen recognition receptors in the defense against RNA viruses. West Nile Virus (WNV) infections continue to grow in the US. Here, we use a systems biology approach to define the contributions of each RLR in the innate immune response to WNV. Genome-wide RNAseq and bioinformatics analyses of macrophages from mice lacking either RLR reveal that the RLRs drive distinct immune gene activation and response polarization to mediate an M1/inflammatory signature while suppressing the M2/wound healing phenotype. While LGP2 functions to modulate inflammatory signaling, RIG-I and MDA5 together are essential for M1 macrophage polarization in vivo and the control of WNV infection through potential downstream control of ATF4 and SMAD4 to regulate target gene expression for cell polarization. These analyses reveal the RLR-driven signature of macrophage polarization, innate immune protection, and immune programming against WNV infection.

Molecular network-based identification of competing endogenous RNAs in bladder cancer.

BackgroundCircular RNAs (circRNAs) have been shown to interact with microRNAs (miRNA) as competitive endogenous RNAs (ceRNAs) to regulate target gene expression and participate in tumorigenesis. However, the role of circRNA-mediated ceRNAs in bladder cancer (BC) remains unknown. Accordingly, the aim of this study was to elucidate the regulatory mechanisms in BC based on construction of the ceRNA network.MethodsThe RNA expression profiles were obtained from public datasets in the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database, and were used to establish a circRNA-miRNA-mRNA network. The interactions among proteins were analyzed using the STRING database and hubgenes were extracted using the cytoHubba application. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed mRNAs in BC and normal tissue samples were performed to determine the functions of the intersecting mRNAs.ResultsA total of 27 circRNAs, 76 miRNAs, and 4744 mRNAs were found to be differentially expressed between BC and normal tissues. The circRNA-miRNA-mRNA ceRNA network was established based on 21 circRNAs, 14 miRNAs, and 150 mRNAs differentially expressed in BC. We also established a protein-protein interaction network and identified 10 hubgenes, which were used to construct circRNA-miRNA-hubgene regulatory modules. The most enriched biological process GO term was strand displacement (P<0.05), and the homologous recombination and Fanconi anemia pathways were significantly enriched (P<0.05) for the differentially expressed genes in BC.ConclusionsWe screened several dysregulated circRNAs and established a circRNA-associated ceRNA network by bioinformatics analysis. The identified ceRNAs are likely critical in the pathogenesis of BC and may serve as future therapeutic biomarkers.