mRNA High-throughput Sequencing Research Articles

Overexpression of SLAP2 inhibits triple-negative breast cancer progression by promoting macrophage M1-type polarization

Breast cancer is the most common malignant tumor in women, and triple-negative breast cancer (TNBC) is a specific subtype of breast cancer characterized by high invasiveness, high metastatic potential, ease of recurrence, and poor prognosis. Src-like adaptor protein 2 (SLAP2), which can be involved in the regulation of multiple signaling pathways, may be a key target for TNBC. The aim of this study was to investigate the effect of overexpression of SLAP2 on TNBC and to explore the underlying mechanisms. First, we constructed and transfected SLAP2 overexpressing lentivirus based on MDA-MB-231 human TNBC cell line, screened for differential downstream target genes in combination with mRNA high-throughput sequencing (RNA-Seq), and predicted their functions and enriched pathways in conjunction with bioinformatics analysis. The effects of SLAP2 overexpression on macrophage polarization, as well as on tumor proliferation and apoptosis, were assessed by tail vein injection of a stable transfection line of 4T1 cells transfected with SLAP2 overexpressing lentivirus. The effect of SLAP2 on macrophage polarization was assessed by inducing M1/M2 polarization and transfecting SLAP2 overexpressing lentivirus. Meanwhile, a transwell co-culture system was constructed between differently treated macrophages and 4T1 cells to assess the effect of SLAP2 overexpression on the malignant behavior of the cells via macrophage polarization. Overexpression of SLAP2 revealed 179 genes up-regulated and 74 genes down-regulated by mRNA high-throughput sequencing, and the enriched functions and pathways of differential genes were mainly related to immunity response. In vivo experiments revealed that overexpression of SLAP2 inhibited the growth of tumor in nude mice, decreased the expression of ki67 in tumor tissues, and increased the rate of apoptosis in tumor tissues. Meanwhile, we found that overexpression of SLAP2 promoted macrophage polarization toward M1 type and inhibited M2 type polarization in tumors. In vitro experiments further verified its effect on M1/M2 polarization by transfecting SLAP2 overexpressing lentivirus. By transwell co-culture system, we further demonstrated that overexpression of SLAP2 inhibits cell proliferation and invasion, promotes apoptosis, up-regulates the expression of Bax in cells, and down-regulates the expression of Bcl-2 in cells by promoting macrophage M1-type polarization. Overexpression of SLAP2 inhibits TNBC progression by promoting macrophage M1-type polarization.

Shikonin reactivates TSGs GADD45B and PPP3CC to block NSCLC cell proliferation and migration through JNK/P38/MAPK signaling pathways

BackgroundShikonin, a natural naphthoquinone compound extracted from the Chinese traditional herbal medicine “Lithospermum erythrorhizon”, possesses antitumor activity against various cancer types. Tumor-suppressor genes (TSGs) negatively regulate cell growth, proliferation, and differentiation, thereby inhibiting tumor formation. However, the molecular mechanism of action of shikonin on TSGs in non–small-cell lung cancer (NSCLC) remains unclear.MethodsThe inhibitory effect of shikonin on the proliferation and migration abilities of lung cancer cells were measured by Cell Counting Kit 8 (CCK8) and wound healing assays. The alteration of genes by shikonin treatment was detected by mRNA high-throughput sequencing and further confirmed by qPCR and western blotting experiments. The dominant functions of the upregulated genes were analyzed by GO and KEGG profiling.ResultsShikonin inhibited the proliferation and migration of A549 and H1299 NSCLC cells in a dose-dependent manner. mRNA high-throughput sequencing revealed a total of 1794 upregulated genes in shikonin-treated NSCLC cells. Moreover, bioinformatic analysis of GO and KEGG profiling revealed that the up-regulated genes were mostly involved in the JNK/P38/MAPK signaling pathway, among which the expression of GADD45B and PPP3CC was significantly enhanced. Finally, we confirmed that GADD45B and PPP3CC were indeed upregulated in JNK/P38/MAPK pathway.ConclusionsTaken together, these results suggested that shikonin might affect the expression of GADD45B and PPP3CC through the JNK/P38/MAPK pathway, therefore exerting an inhibitory effect on the proliferation and migration of cancer cells. To our knowledge, this is the first study reporting the role of shikonin in upregulating TSGs to activate the JNK/P38/MAPK signaling pathways in NSCLC.

Myristic acid alleviates hippocampal aging correlated with GABAergic signaling.

Previous studies have shown that myristic acid (MA), a saturated fatty acid, could promote the proliferation and differentiation of neural stem cells in vitro. However, the effect of MA on hippocampal neurons aging has not been reported in vivo. Here we employed 22-month-old naturally aged C57BL/6 mice to evaluate the effect and mechanism of MA on hippocampal aging. First, we examined a decreased exploration and spatial memory ability in aging mice using the open field test and Morris water maze. Consistently, aging mice showed degenerative hippocampal histomorphology by H&E and Nissl staining. In terms of mechanism, imbalance of GABRB2 and GABRA2 expression in aging mice might be involved in hippocampus aging by mRNA high throughput sequencing (mRNA-seq) and immunohistochemistry (IHC) validation. Then, we revealed that MA alleviated the damage of exploration and spatial memory ability and ameliorated degeneration and aging of hippocampal neurons. Meanwhile, MA downregulated GABRB2 and upregulated GABRA2 expression, indicating MA might alleviate hippocampal aging correlated with GABAergic signaling. In conclusion, our findings revealed MA alleviated hippocampal aging correlated with GABAergic signaling, which might provide insight into the treatment of aging-associated diseases.

Silencing CAMK2D Promotes the Proliferation of Spermatogonia in the Testis of Experimental Varicocele Rats.

Varicocele is regarded as the main factor that contributes to male infertility. This study aimed to explore the effect of CAMK2D on spermatogonia in the testis of experimental varicocele rats. The experimental varicocele model was established in rats and treated using different ligation methods. mRNA expression profile analysis was performed on the left testicular tissue isolated from different groups, and differentially expressed genes (DEGs) were analysed by bioinformatics methods and identified by qRT-PCR. The effect of CAMK2D, the screened DEG, on the proliferation of spermatogonia was evaluated by CCK-8 assay. The expression level of the c-kit was measured by the immunofluorescence assay and the expression levels of CAMKII, FOXO1, and β-catenin were detected by qRT-PCR and western blotting. Five DEGs (i.e., TMCC3, FLNB, CAMK2D, OPLAH, and EGR1) were screened using the comprehensive analysis of mRNA high-throughput sequencing data. TMCC3 and FLNB were significantly downregulated, and CAMK2D, OPLAH, and EGR1 were dramatically upregulated in the testicular tissue of varicocele rats. The target DEG CAMK2D was obtained through identification by using qRT-PCR. In vitro assays revealed that the proliferation of spermatogonia was significantly facilitated by the silencing of CAMK2D, which resulted in the downregulation of CAMKII, FOXO1, and β-catenin. In conclusion, silencing CAMK2D facilitated the proliferation of spermatogonia in the testis of experimental varicocele rats.

The effects of the Xijiao Dihuang decoction combined with Yinqiao powder on miRNA-mRNA profiles in mice infected with influenza a virus

BackgroundMicroRNAs (miRNAs) play vital roles in acute inflammatory and antiviral responses during influenza A virus (IAV) infection. The Xijiao Dihuang decoction combined with Yinqiao powder (XDY) is applied to remedy viral pneumonia in China and its therapeutic efficacy in pneumonic mice challenged with IAV was demonstrated; however, the underlying mechanisms remain elusive. Thus, this study aimed to explore the miRNA-mRNA profiles in the lungs of IAV-infected mice and investigate the therapeutic mechanisms of XDY involving miRNAs and associated pathways.MethodsWe detected the cellular miRNA contents in the lungs of mice treated with XDY (23 g/kg/d) for A/FM/1/47 (H1N1) (FM1) infection at 4 days postinoculation (dpi) and 7 dpi. MiRNA and mRNA high-throughput sequencing analyses, and miRNA and mRNA qRT-PCR analyses were used to detect and verify the relevant miRNAs and mRNAs. Conjoint analysis, GO enrichment analysis, and KEGG database analysis were applied to identify the miRNA-mRNA regulatory relationships.ResultsThe quantities of differentially expressed miRNAs and mRNAs were upregulated over time. The data showed that 104 miRNAs and 3485 mRNAs were differentially expressed after challenge with FM1 on day 4, while 191 miRNAs and 6126 mRNAs were differentially expressed on day 7. The GO enrichment analysis and KEGG database data showed that the differentially expressed miRNAs and mRNAs were mainly enriched in JNK activity, MAPK phosphatase activity, and the TLR, Jak-STAT and TNF signalling pathways after treatment of FM1 infection with XDY. Generally, the expression trends of differentially expressed miRNAs and mRNAs based on the qRT-PCR results exhibited good consistency with the results of the high-throughput sequencing analysis.ConclusionsMiRNAs and mRNAs were differentially expressed during FM1 infection. The therapeutic mechanisms of XDY in FM1-infected mice, might be related to regulating antiviral immunity and ameliorating excessive inflammatory responses by modulating the expression of dysregulated miRNAs and mRNAs involved in the ERK/JNK-AP-1, and IFN-β/STAT signalling pathways.

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To explore the potential lncRNAs that regulate the male sheep pituitary development and sexual maturation, we constructed immature and mature sheep pituitary cDNA libraries (three-month-old, TM, and nine-month-old, NM, respectively, n = 3) for lncRNA and mRNA high-throughput sequencing. Firstly, the expression of lncRNA and mRNA were comparatively analyzed. 2417 known lncRNAs and 1256 new lncRNAs were identified. Then, 193 differentially expressed (DE) lncRNAs and 1407 DE mRNAs were found in the pituitary between the two groups. Moreover, mRNA-lncRNA interaction network was constructed according to the target gene prediction of lncRNA and functional enrichment analysis. Five candidate lncRNAs and their targeted genes HSD17B12, DCBLD2, PDPK1, GPX3 and DLL1 that enriched in growth and reproduction related pathways were further filtered. Lastly, the interaction of candidate lncRNA TCONS_00066406 and its targeted gene HSD17B12 were validated in in vitro of sheep pituitary cells. Our study provided a systematic presentation of lncRNAs and mRNAs in male sheep pituitary, which revealed the potential role of lncRNA in male reproduction.

An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes

Drosophila Blanks is a testes-specific RNA-binding protein required for post-meiotic spermiogenesis. However, Blanks's role in regulating RNA populations in the testes remains unknown. We performed small RNA and mRNA high-throughput sequencing in blanks mutant testes and controls. We identified two miRNAs, one siRNA, and hundreds of mRNAs that are significantly upregulated or downregulated in blanks mutant testes. Pathway analysis revealed that differentially expressed mRNAs are involved in catabolic and metabolic processes, anion and cation transport, mating, and reproductive behavior. Our results reveal that Blanks plays important roles in defining testicular small RNA and mRNA profiles.

Abstract 3294: Functional annotation for alternative splicing to investigate disrupted splicing in cancer

Abstract Alternative splicing (AS) plays a key role to confer human genome complexity. The advent of mRNA high-throughput sequencing facilitates to identify precise differential alternative splicing analysis. Massive result estimated from RNA-Seq should be sorted out whether AS has functional impact or not. Previous studies investigated protein domain or nonsense-mediated decay of AS event region. However other functional sites on exon inclusion region also exist. For example, miRNA binding site, and post-translational modification of AS site already are reported to assign functional impact. Therefore we developed ASpedia (http://combio.snu.ac.kr/aspedia/) to annotation functional impact of AS event. AS events of our database were generated from human genome hg19 ENSEMBL and Refseq. ASpedia provides a database, explore system, and AS browser to annotate functional impact evidence encompassing DNA, RNA, and protein. The user could query multiple AS events from differential AS analysis result. Currently our system supports a jar execution file to convert input query file from MISO or rMATS result. The variant of splicing factor (SF) disrupts normal splicing. It could be assumed that target genes of mutated SF could be transcribed to aberrant isoforms by changed splicing machinery. Therefore we investigated the comprehensive SF variant status from TCGA somatic mutation and copy number. SF3B1 (2% in BRCA) and U2AF1 (4% in AML, and 2% in LUAD) were shown to recurrent mutation including hotspot. ELAVL2 known dispensable splicing factor to brain tissue were highly recurrent in deletion (18% in GBM). In order to examine aberrant AS events caused SF variants, we estimated exon-inclusion proportion Percent-Spliced-In (PSI) values for identifiable AS events using TCGA RNA-Seq dataset. Using differentially AS event analysis, we identified AS events that were significantly differentially spliced in the presence of a U2AF S34F/Y mutation (119 in AML). And we purposed to finding In order to investigate functional site, the differentially spliced AS events were additionally annotated using ASpedia. Finally we identified the landscape of that AS events were altered by SF variants, and we proved that a part of the events was involved in cancer-associated functions. Citation Format: Daejin Hyung, Jihyun Kim, Soo Young Cho, Charny Park. Functional annotation for alternative splicing to investigate disrupted splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3294.

Stigmasterol upregulates immediate early genes and promotes neuronal cytoarchitecture in primary hippocampal neurons as revealed by transcriptome analysis

BackgroundThe hippocampus is a vulnerable brain region that is implicated in learning and memory impairment by two pathophysiological features, that is, neurite regression and synaptic dysfunction, and stigmasterol (ST), a cholesterol-equivalent phytosterol, is known to facilitate neuromodulatory effects. PurposeTo investigate the neuromodulatory effects of ST on the development of central nervous system neurons and the molecular bases of these effects in primary hippocampal neurons. MethodsRat embryonic (E18-19) brain neurons were cultured in the absence or presence of ST (75 µM). Neuritogenic activities of ST were evident by increases in various morphometric parameters. To identify underlying affected genes, total RNA was isolated on day in vitro 12 (DIV 12) and mRNA high throughput sequencing (mRNA-Seq) was performed. Affected key genes for neuronal development were identified using bioinformatics tools and their upregulations were confirmed by immunocytochemistry. ResultsAmong the differentially expressed 17,337 RefSeq genes, 445 genes (up/down 293/157) passed the p-value < 0.05 criterion, 52 genes (up/down; 37/13) had a p-value < 0.05 and a false discovery rate (FDR) q-value of < 0.2, and 24 genes (up/down; 20/4) passed the more stringent criterion of both p < 0.05 and q < 0.05. After applying a stringent FDR q-value cutoff of < 0.2, it was found ST induced many immediate early genes (IEGs), and that a major proportion of upregulated genes were related to central nervous system (CNS) development (neurite outgrowth or synaptic transmission). In a Venn diagram for CNS development Gene Ontologies (GOs) (i.e., axon development, dendrite development, modulation of synaptic transmission), Reln emerged as a central player in these processes, and highly interconnected ‘hub’ genes, including Dcx, Egr1, Ntrk2, and Slc24a2, were revealed by gene co-expression networks. Finally, transcriptomic data was confirmed by immunocytochemistry of primary hippocampal neurons. ConclusionThe study indicates that ST upregulates genes for neuritogenesis and synaptogenesis, and suggests ST be viewed as a potential resource for improving brain functions.

Integrated analysis of miRNA, gene, and pathway regulatory networks in hepatic cancer stem cells.

BackgroundHepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. HCC has a poor prognosis associated with tumor recurrence and drug resistance, which has been attributed to the existence of hepatic cancer stem cells (HCSCs). However, the characteristics and regulatory mechanisms of HCSCs remain unclear. We therefore established a novel system to enrich HCSCs and we demonstrate that these HCSCs exhibit cancer stem cell properties.MethodsWe used miRNA and mRNA high-throughput sequencing data sets to determine molecular signatures and regulatory mechanisms in HCSCs. Paired miRNA and gene deep sequencing data in HCSCs versus HCC cells were used to identify candidate biomarkers of HCSCs. Using network analysis, we studied the relationship between miRNA and gene biomarkers, and KEGG pathway enrichment analysis was performed to study the function of candidate biomarkers.ResultsWe identified 9 up- and 9 down-regulated miRNAs and 115 up- and 402 down-regulated genes in HCSCs compared with HCC cells. A miRNA-gene network was constructed using 651 miRNA–gene interactions (between 7 up-regulated miRNAs and 274 down-regulated genes), and 103 miRNA–gene interactions (between 9 down-regulated miRNAs and 62 up-regulated genes). Pathway enrichment analysis identified five tumor invasion- and metastasis-related pathways and MAPK signaling associated with HCSCs. We further discovered two novel pathways that likely play a role in the regulation of HCSCs.ConclusionsWe identified a molecular expression signature and pathway regulatory mechanisms in HCSCs with potential diagnostic and therapeutic value.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-015-0609-7) contains supplementary material, which is available to authorized users.