Differentially Expressed mRNAs Research Articles

CircRNAs deregulation in exosomes derived from BEAS-2B cells is associated with vascular stiffness induced by PM2.5

As an environmental pollutant, ambient fine particulate matter (PM2.5) was linked to cardiovascular diseases. The molecular mechanisms underlying PM2.5-induced extrapulmonary disease has not been elucidated clearly. In this study the ambient PM2.5 exposure mice model we established was to explore adverse effects of vessel and potential mechanisms. Long-term PM2.5 exposure caused reduced lung function and vascular stiffness in mice. And chronic PM2.5 induced migration and epithelial-mesenchymal transition (EMT) phenotype in BEAS-2B cells. After PM2.5 treatment, the circRNAs and mRNAs levels of exosomes released by BEAS-2B cells were detected by competing endogenous RNA (ceRNA) array, which contained 1664 differentially expressed circRNAs (DE-circRNAs) and 308 differentially expressed mRNAs (DE-mRNAs). By bioinformatics analysis on host genes of DE-circRNAs, vascular diseases and some pathways related to vascular diseases including focal adhesion, tight junction and adherens junction were enriched. Then, ceRNA network was constructed, and DE-mRNAs in ceRNA network were conducted functional enrichment analysis by Ingenuity Pathway Analysis, which indicated that hsa_circ_0012627, hsa_circ_0053261 and hsa_circ_0052810 were related to vascular endothelial dysfunction. Furthermore, it was verified experimentally that ExoPM2.5 could induce endothelial dysfunction by increased endothelial permeability and decreased relaxation in vitro. In present study, we investigated in-depth knowledge into the molecule events related to PM2.5 toxicity and pathogenesis of vascular diseases.

Mechanisms of Immune-Related Long Non-Coding RNAs in Spleens of Mice Vaccinated with 23-Valent Pneumococcal Polysaccharide Vaccine (PPV23).

The 23-valent pneumococcal vaccine (PPV23) is a classical common vaccine used to prevent pneumococcal disease. In past decades, it was thought that vaccination with this vaccine induces humoral immunity, thereby reducing the disease associated with infection with 23 common serotypes of Streptococcus pneumoniae (Sp). However, for this polysaccharide vaccine, the mechanism of immune response at the transcriptional level has not been fully studied. To identify the lncRNAs (long noncoding RNAs) and mRNAs in spleens related to immunity after PPV23 vaccination in mice, high-throughput RNA sequencing of spleens between a PPV23 treatment group and a control group were performed and evaluated in this study. The RNA-seq results identified a total of 41,321 mRNAs and 34,375 lncRNAs, including 55 significantly differentially expressed (DE) mRNAs and 389 DE lncRNAs (p < 0.05) between the two groups. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to T-cell costimulation, positive regulation of alpha-beta T-cell differentiation, the CD86 biosynthetic process, and the PI3K-Akt signaling pathway, indicating that the polysaccharide component antigens of PPV23 might activate a cellular immune response during the PPV23 immunization process. Moreover, we found that Trim35 (tripartite motif containing 35), a target gene of lncRNA MSTRG.9127, was involved in regulating immunity. Our study provides a catalog of lncRNAs and mRNAs associated with immune cells' proliferation and differentiation, and they deserve further study to deepen the understanding of the biological processes in the regulation of PPV23 during humoral immunity and cellular immunity.

Genome-Wide Landscape of mRNAs, lncRNAs, and circRNAs during Testicular Development of Yak.

Testicular development is a tightly regulated process in mammals. Understanding the molecular mechanisms of yak testicular development will benefit the yak breeding industry. However, the roles of different RNAs, such as mRNA, lncRNA, and circRNA in the testicular development of yak, are still largely unclear. In this study, transcriptome analyses were performed on the expression profiles of mRNAs, lncRNAs, and circRNAs in testis tissues of Ashidan yak at different developmental stages, including 6-months-old (M6), 18-months-old (M18), and 30-months-old (M30). A total of 30, 23, and 277 common differentially expressed (DE) mRNAs, lncRNAs, and circRNAs were identified in M6, M18, and M30, respectively. Furthermore, functional enrichment analysis showed that the common DE mRNAs during the entire developmental process were mainly involved in gonadal mesoderm development, cell differentiation, and spermatogenesis processes. Additionally, co-expression network analysis identified the potential lncRNAs related to spermatogenesis, e.g., TCONS_00087394 and TCONS_00012202. Our study provides new information about changes in RNA expression during yak testicular development, which greatly improves our understanding of the molecular mechanisms regulating testicular development in yaks.

Identification of lncRNA-miRNA-mRNA networks in circulating exosomes as potential biomarkers for systemic sclerosis.

This study aimed to analyze potential biomarkers for systemic sclerosis (SSc) by constructing lncRNA-miRNA-mRNA networks in circulating exosomes (cirexos). Differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in SSc cirexos were screened using high-throughput sequencing and detected with real-time quantitative PCR (RT-qPCR). Differentially expressed genes (DEGs) were analyzed using the DisGeNET, GeneCards, GSEA4.2.3, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Receiver operating characteristic (ROC) curves, correlation analyses, and a double-luciferase reporter gene detection assay were used to analyze competing endogenous RNA (ceRNA) networks and clinical data. In this study, 286 DEmRNAs and 192 DElncRNAs were screened, of which 18 DEGs were the same as the SSc-related genes. The main SSc-related pathways included extracellular matrix (ECM) receptor interaction, local adhesion, platelet activation, and IgA production by the intestinal immune network. A hub gene, COL1A1, was obtained by a protein-protein interaction (PPI) network. Four ceRNA networks were predicted through Cytoscape. The relative expression levels of COL1A1, ENST0000313807, and NON-HSAT194388.1 were significantly higher in SSc, while the relative expression levels of hsa-miR-29a-3p, hsa-miR-29b-3p, and hsa-miR-29c-3p were significantly lower in SSc (P < 0.05). The ROC curve showed that the ENST00000313807-hsa-miR-29a-3p-COL1A1 network as a combined biomarker of SSc is more valuable than independent diagnosis, and that it is correlated with high-resolution CT (HRCT), Scl-70, C-reactive protein (CRP), Ro-52, IL-10, IgM, lymphocyte percentage, neutrophil percentage, albumin divided by globulin, urea, and RDW-SD (P < 0.05). Double-luciferase reporter gene detection showed that ENST00000313807 interacts with hsa-miR-29a-3p, which interacts with COL1A1. The ENST00000313807-hsa-miR-29a-3p-COL1A1 network in plasma cirexos represents a potential combined biomarker for the clinical diagnosis and treatment of SSc.

FZD1/KLF10-hsa-miR-4762-5p/miR-224-3p-circular RNAs axis as prognostic biomarkers and therapeutic targets for glioblastoma: a comprehensive report

BackgroundThe circular RNA (circRNA) plays a vital role in the pathogenesis of tumors as a competitive endogenous RNA (ceRNA). Given the high aggressiveness and fatality rate of glioblastoma (GBM) as well as poor prognosis, it is necessary to construct a circRNA-related ceRNA network for further studies on the mechanism of GBM and identify possible biomarkers as well as therapeutic drugs.MethodsThree datasets from the gene expression omnibus (GEO) database were downloaded to distinguish differential circRNAs, microRNAs, and messenger RNAs respectively in GBM. With the help of GEPIA2, circBank, CSCD, TargetScan, miRDB, and miRTarBase databases, we established a circRNAs-related ceRNA network in GBM. Functional enrichments were employed to profile the most relevant mRNAs to indirectly clarify the mechanisms of the ceRNA network. Based on the expression profile data and survival information of GBM patients from the GEO and the cancer genome atlas (TCGA) databases, we performed survival analysis to select prognostic mRNAs and constructed a novel circRNA-miRNA-mRNA central regulatory subnetwork. The DGIdb database was used to find potential drug–gene interactions.ResultsThe datasets obtained from the GEO and TCGA databases were analyzed, and 504 differentially expressed mRNAs (DEmRNAs), 71 differentially expressed microRNAs (DEmiRNAs), and 270 differentially expressed circRNAs (DEcircRNAs) were screened out. The novel ceRNA regulatory network included 22 circRNAs, 11 miRNAs, and 15 mRNAs. FZD1 and KLF10 were significantly correlated with the overall survival rate of patients with GBM (P < 0.05). The final survival subnetwork contained six circRNAs, two miRNAs, and two mRNAs. Two small-molecule compounds and one antibody could be used as therapeutic drugs for GBM. Interestingly, the Wnt signaling pathway appeared in both KEGG and GO functional terms.ConclusionsResults of this study demonstrate that FZD1 and KLF10 may exert regulatory functions in GBM, and the ceRNA-mediated network could be a therapeutic strategy for GBM.

Investigating the molecular mechanisms of delirium-like neuropsychiatric disorder induced by electromagnetic pulse based on bioinformatics analysis

Electromagnetic pulse (EMP), a unique type of electromagnetic radiation, may induce diverse neuropsychiatric disorders, such as irritability, hyperkinesis, retardation of learning and memory. However, the underlying mechanism of EMP exposure on neuronal injury has not been elucidated. Here, we aimed to delineate the regulatory expression networks based on high-throughput sequencing data to explore the possible molecular mechanisms related to EMP-induced delirium-like neuropsychiatric disorder in rats. It’s shown that EMP exposure induced anxiety, cognitive decline and short-term memory impairment. The expression profiles of the long noncoding RNAs (lncRNAs) and mRNAs, along with their biological function and regulatory network, were explored in rats after EMP exposure. We identified 41 differentially expressed lncRNAs (DELs) and 266 differentially expressed mRNAs (DEMs) between EMP and sham groups. Sixty-one co-expression relationships between 18 DELs and 56 DEMs were mostly associated with synapse- and metabolic-related pathways. We predicted 51 DEL-miRNA pairs and 290 miRNA-mRNA pairs using the miRanda database to constructed a DEL-miRNA-DEM network. LncRNA AABR07042999.1 and mRNA Tph2, Slc6a4, Dbh and Th were upregulated, and the contents of serotonin, dopamine and norepinephrine were increased in both PFC and HIP after EMP exposure. The current study provided a better understanding of the ceRNA network, which might reveal the pathological mechanism and provide more treatment options for the EMP-induced neurobehavioral disorder.

Sequences and Genome-Wide Analysis of mRNA and microRNA Expression in Tea (Camellia sinensis) Leaves in Response to Epicoccum sorghinum Infection

Due to our lack of understanding of the host-pathogen epidemiology and the absence of effective control measures, tea leaf spot, caused by the fungus Epicoccum sorghinum, continues to reduce the productivity and quality of tea leaves in plantations in Guizhou Province, southwestern China. Here, samples of tea ( Camellia sinensis [L.] O Kuntze) leaves either infected or uninfected by E. sorghinum were used as the study model. The mRNA and microRNA (miRNA) sequences in tea leaves from the two treatments were determined using the Illumina NovaSeq 6000 and the Illumina HiSeq 2500 platforms, respectively. In total, 33,932 genes or transcripts from tea leaves were annotated. In response to infection by E. sorghinum, 1,068 or 467 of the differentially expressed mRNAs (DEmRNAs) were up- or downregulated, respectively, and the DEmRNAs containing peroxidase 21 and LRR receptor-like serine/threonine-protein kinase ERECTA were enriched in terms of defense response. Meanwhile, 1,889 miRNAs were identified from infected or uninfected leaves. Nine or seven of the differentially expressed miRNAs (DEmiRNAs) were up- or downregulated, respectively. The DEmiRNAs MIR5303j-p5, MIR6173-p5, miR858-3p, and novel-miR0377-3p were predicted to bind to DEmRNAs. Fifteen DEmRNAs annotated into transcription factor proteins enriched with respect to the plant-pathogen interaction pathway were predicted to be bound by the DEmiRNA miR858-3p. The sequences and abundances of the mRNAs and miRNAs from tea leaves infected by E. nigrum, and the prediction of the interaction between DEmiRNAs and DEmRNAs could contribute to our understanding of this plant-pathogen interaction. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

A landscape of Long non-coding RNAs reveals the leading transcriptome alterations in murine aorta during aging

Considerable studies have given convincing evidence of a forefront position for vascular aging in preventing cardiovascular disease. Various functions of Long non-coding RNAs (lncRNAs) are becoming increasingly distinct in aging-related diseases. This study aims at a better insight into the expression profile and mechanisms of lncRNAs in vascular senescence. High-throughput sequencing was used to detect the differential expression (DE) of lncRNAs and mRNAs in the aorta of 96 W and 8 W-old mice, while 1423 lncRNAs and 80 mRNAs were differentially expressed. By performing GO and KEGG enrichment analysis, we found that DE lncRNAs were mainly involved in purine metabolism and cGMP-PKG signaling pathways. In addition, a co-expression functional network of DE lncRNAs and DE mRNAs was constructed, and ENSMUST00000218874 could interact with 41 DE mRNAs, suggesting that it may play an essential role in vascular senescence. This study reveals DE lncRNAs in naturally aging vascular, which may provide new ideas and targets for aging-related cardiovascular diseases.

Bioinformatics-based identification of lipid- and immune-related biomarkers in abdominal aortic aneurysms

BackgroundAbdominal aortic aneurysm (AAA) manifest as a natural inflammatory process with permanent dilation and terminal rupture. Nevertheless, the pathogenesis of AAA remains a mystery, and treatment is still controversial. Lipid metabolism and immune system are involved in AAA progression, which has been well documented. However, lipid- and immune-related (LIR) biomarkers need to be further elucidated. MethodsThe AAA-related datasets were retrieved from the GEO database, and the datasets were analyzed for differential gene expression by NetworkAnalyst. GO and KEGG pathway enrichment analysis of differentially expressed mRNA (DE-mRNA) was performed using Metscape, and LIR DE-mRNA was further screened. AAA rat model was constructed using porcine pancreatic elastase to verify the differential expression of LIR DE-mRNA. ResultsThe GSE47472 and GSE57691 datasets respectively identified 614 (containing 381 down-regulated and 233 up-regulated DE-mRNAs) and 384 (containing 218 down-regulated and 164 up-regulated DE-mRNAs) DE-mRNAs. Intersection and union of DE-mRNAs were 13 and 983, respectively. The main terms involved in the union of DE-mRNAs included “immune system process”, “metabolic process”, “Chemokine signaling pathway”, “hematopoietic cell lineage” and “Cholesterol metabolism”. In vivo experiments revealed that LIR DE-mRNAs of PDIA3, TYROBP, and HSPA1A were significantly low expression in AAA abdominal aortic tissues, and HCK and SERPINE1 were significantly high expression, which is consistent with the bioinformatics analysis. ConclusionsPDIA3, TYROBP, HSPA1A, HCK and SERPINE1 may serve as LIR biomarkers of AAA, which provides new insights and theoretical guidance for the future treatment, early prevention and progression of AAA.

Non-Association of Driver Alterations in PTEN with Differential Gene Expression and Gene Methylation in IDH1 Wildtype Glioblastomas

During oncogenesis, alterations in driver genes called driver alterations (DAs) modulate the transcriptome, methylome and proteome through oncogenic signaling pathways. These modulatory effects of any DA may be analyzed by examining differentially expressed mRNAs (DEMs), differentially methylated genes (DMGs) and differentially expressed proteins (DEPs) between tumor samples with and without that DA. We aimed to analyze these modulations with 12 common driver genes in Isocitrate Dehydrogenase 1 wildtype glioblastomas (IDH1-W-GBs). Using Cbioportal, groups of tumor samples with and without DAs in these 12 genes were generated from the IDH1-W-GBs available from "The Cancer Genomics Atlas Firehose Legacy Study Group" (TCGA-FL-SG) on Glioblastomas (GBs). For all 12 genes, samples with and without DAs were compared for DEMs, DMGs and DEPs. We found that DAs in PTEN were unassociated with any DEM or DMG in contrast to DAs in all other drivers, which were associated with several DEMs and DMGs. This contrasting PTEN-related property of being unassociated with differential gene expression or methylation in IDH1-W-GBs was unaffected by concurrent DAs in other common drivers or by the types of DAs affecting PTEN. From the lists of DEMs and DMGs associated with some common drivers other than PTEN, enriched gene ontology terms and insights into the co-regulatory effects of these drivers on the transcriptome were obtained. The findings from this study can improve our understanding of the molecular mechanisms underlying gliomagenesis with potential therapeutic benefits.

Analysis of long noncoding RNAs and messenger RNAs expression profiles in the hearts of mice with acute viral myocarditis.

Acute viral myocarditis (AVMC) is a common acute myocardial inflammation caused by viral infections, which can lead to severe cardiac dysfunction. Several long noncoding RNAs (lncRNAs) with aberrant expression have been identified in the pathogenesis of AVMC. However, the expression profiles and functions of lncRNAs in AVMC have not been fully elucidated. In the present study, we constructed AVMC mouse models by intraperitoneal injection of coxsackievirus B3 (CVB3) and performed RNA sequencing (RNA-seq) on heart tissues to investigate the differences in lncRNAs and messenger RNAs (mRNAs) expression profiles. Based on the cutoff criteria of adjusted p-values (padj) <0.05 and |log2FoldChange| >1, a total of 1122 differentially expressed lncRNAs (DElncRNAs) and 3186 differentially expressed mRNAs (DEmRNAs) were screened, including 734 upregulated and 388 downregulated lncRNAs, 1821 upregulated and 1365 downregulated mRNAs. RT-qPCR analysis validated that the expression patterns of 12 randomly selected genes (6 DElncRNAs and 6 DEmRNAs) were highly consistent with those in RNA-seq, proving the reliability of the RNA-seq data. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that differentially expressed genes were mainly involved in metabolic and immune-related processes. Furthermore, co-expression networks between DElncRNAs and DEmRNAs in cytokine-cytokine receptor interaction, MAPK signaling pathway, and PI3K-Akt signaling pathway were constructed to study the molecular interactions of these molecules. Our study, for the first time, reveals the expression profiles of lncRNAs and mRNAs associated with AVMC, which may shed light on the roles of lncRNAs in disease pathogenesis and aid in discovering new therapeutic targets.

A porcine model of early-onset scoliosis combined with thoracic insufficiency syndrome: Construction and transcriptome analysis

BackgroundEarly-onset scoliosis (EOS) is a scoliosis deformity caused by various reasons before the age of 10 years and is often combined with thoracic insufficiency syndrome (TIS) causing patients with difficulty in securing lung growth in the thoracic cage. Currently, there is a shortage of effective large animal models for evaluating EOS + TIS in therapeutic studies. Consequently, we propose to construct a porcine EOS + TIS model and evaluate its transcriptome changes by RNA sequencing. MethodsPiglets were constructed using unilateral posterior spine-tethering and ipsilateral rib-tethering in the EOS + TIS model, and X-ray and computed tomography (CT) were performed to assess growth changes in the spine, thoracic cage and lungs. The H&E and Masson staining was performed for pathological analysis of lung tissue. After RNA sequencing of lung tissues, data were analyzed for differential expression of mRNA, functional enrichment analysis (GO, KEGG and GSEA) and protein–protein interaction (PPI) network construction, and differential expression of hub gene was verified by RT-qPCR. ResultsIn the model group, growth (body weight and length) of piglets was significantly delayed; fusion of ribs occurred and cobb angle changes in the coronal and sagittal planes were significantly enlarged; total lung volume (TLV) was significantly reduced, especially at the T7-T10 level. Pathological analysis revealed that, in the model lung tissue, the alveolar wall of was poorly perfused, the alveolar space was enlarged, the number and size of alveoli were significantly reduced, and it was accompanied by collagen fiber deposition. Moreover, a total of 432 differentially expressed mRNAs (DE-mRNAs) were identified in model lung tissues, which contained 262 down-regulated and 170 up-regulated DE-mRNAs, and they were mainly involved in the regulation of immunity, inflammation, cell cycle and extracellular matrix. A PPI network containing 71 nodes and 158 edges was constructed based on all DE-mRNAs, and JUN, CCL2, EGR1, ATF3, BTG2, DUSP1 and THBS1 etc. were hub gene. ConclusionsOverall, we constructed a porcine model that was capable of replicating the common clinical features of EOS + TIS such as rib fusion, asymmetric thoracic cage, increased cobb angle, decreased TLV, and pulmonary hypoplasia. Also, we revealed transcriptomic changes in the EOS + TIS model that may cause pulmonary hypoplasia.

ULBP2 is a biomarker related to prognosis and immunity in colon cancer.

The study aimed to determine whether ULBP2 was associated with prognosis and immune infiltration in colon cancer (CC) and provided important molecular basis inorderto early non-invasive diagnosis and immunotherapy of CC. Using The Cancer Genome Atlas database (TCGA) and ImmPort database, we extracted messenger RNA (mRNA) data of CC and immune-related genes, then we used "limma" package, "survival" package, and Venn overlap analysis to obtain the differentially expressed mRNA (DEmRNA) associated with prognosis and immunity of CC patients. "pROC" package was used to analyze receiver operating characteristics (ROC) of target gene. We used chi-square test and two-class logistics model to identify clinicopathological parameters that correlated with target gene expression. In order to determine the effects of target gene expression and clinicopathological parameters on survival, univariate and multivariate cox regression analyses were performed. We analyzed the related functions and signaling pathways of target gene by enrichment analysis. Finally, the correlation between target gene and tumor immune infiltrating was explored by ssGSEA and spearman correlation analysis. Results showed that ULBP2 was a target gene associated with immunity and prognosis in CC patients. CC patients with higher ULBP2 expression had poor outcomes. In terms of ROC, ULBP2 had an area under the curve (AUC) of 0.984. ULBP2 was associatedwith T stage, N stage, and pathologic stage of CC patients, and served as an independent predictor of overall survival in CC patients. Functional enrichment analysis revealed ULBP2 was obviously enriched in pathways connected with carcinogenesis and immunosuppression. The expression of ULBP2 was significantly associated with tumor immune cells and immune checkpoints according to ssGSEA and spearman correlation analysis. To conclude, our study suggested that ULBP2 was associated with tumor immunity, and might be a biomarker associated with the diagnosis and prognosis of CC patients, and a potential target of CC immunotherapy.

Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep.

In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue. We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2). We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep.

Characterization of the lncRNA-miRNA-mRNA regulatory network to reveal potential functional competing endogenous RNAs in traumatic brain injury.

Traumatic brain injury (TBI) is one of the most common acute central nervous system injury diseases. Given the medical and socio-economic burdens of TBI patients, the pathogenesis in TBI and the latent intervention targets needed to be further illuminated. Long non-coding RNAs (lncRNAs) had been revealed to play a vital role in the regulation of pathogenesis after TBI. However, the mutual communication and adjustment of lncRNA associated competing for endogenous RNA (ceRNA) networks in TBI have not been explored to date. In this study, we systematically sequenced the whole transcriptome of lncRNAs, miRNAs, and mRNAs between sham and TBI groups and a total of 939 differentially expressed (DE) lncRNAs, 46 DE miRNAs, and 1,951 DE mRNAs were obtained. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein interaction relationship analyses were conducted for DE mRNAs to identify hub DE genes in TBI. Based on the criteria of bioinformatics prediction, the lncRNA associated ceRNA network covering 201 lncRNAs, 22 miRNAs, and 79 mRNAs was constructed. This study provides a novel perspective on the molecular mechanism of lncRNA in TBI and identifies certain lncRNAs as potential therapeutic targets against TBI.

Transcriptome-wide analysis reveals the molecular mechanisms of cannabinoid type II receptor agonists in cardiac injury induced by chronic psychological stress.

Background: Growing evidence has supported that chronic psychological stress would cause heart damage, However the mechanisms involved are not clear and effective interventions are insufficient. Cannabinoid type 2 receptor (CB2R) can be a potential treatment for cardiac injury. This study is aimed to investigate the protective mechanism of CB2R agonist against chronic psychological stress-induced cardiac injury. Methods: A mouse chronic psychological stress model was constructed based on a chronic unpredictable stress pattern. Mice were performed a three-week psychological stress procedure, and cardiac tissues of them were collected for whole-transcriptome sequencing. Overlap analysis was performed on differentially expressed mRNAs (DE-mRNAs) and ER stress-related genes (ERSRGs), and bioinformatic methods were used to predict the ceRNA networks and conduct pathway analysis. The expressions of the DE-ERSRGs were validated by RT-qPCR. Results: In the comparison of DE mRNA in Case group, Control group and Treatment group, three groups of ceRNA networks and ceRNA (circ) networks were constructed. The DE-mRNAs were mainly enriched in chromatid-relevant terms and Hematopoietic cell lineage pathway. Additionally, 13 DE-ERSRGs were obtained by the overlap analysis, which were utilized to establish a ceRNA network with 15 nodes and 14 edges and a ceRNA (circ) network with 23 nodes and 28 edges. Furthermore, four DE-ERSRGs (Cdkn1a, Atf3, Fkbp5, Gabarapl1) in the networks were key, which were mainly enriched in response to extracellular stimulus, response to nutrient levels, cellular response to external stimulus, and FoxO signaling pathway. Finally, the RT-qPCR results showed almost consistent expression patterns of 13 DE-ERSRGs between the transcriptome and tissue samples. Conclusion: The findings of this study provide novel insights into the molecular mechanisms of chronic psychological stress-induced cardiac diseases and reveal novel targets for the cardioprotective effects of CB2R agonists.

Identification of prognostic genes signature and construction of ceRNA network in pirarubicin treatment of triple-negative breast cancer.

The altered long non-coding RNA (lncRNA), circular RNA (circRNA) and mRNA expression in triple-negative breast cancer (TNBC) after pirarubicin (THP) treatment can be a critical factor in the development of tumor. Here, we identify a set of lncRNA, circRNA, and mRNA that can reveal the molecular target and molecular mechanism of THP, and can be used to predict the prognostic characteristics of TNBC. Affymetrix GeneChip sequencing was performed to determine whether lncRNA, circRNA, and mRNA were changed in MDA-MB-231 cells after THP treatment, and qRT-PCR was used to verify the accuracy of GeneChip results. Bioinformatics methods were used to analyze the differentially expressed (DE) lncRNA, circRNA and mRNA, and the co-expression network and ceRNA network were constructed. The STRING database, Kaplan-meier Mapper database, GEPIA database, and Tumor Immunity Estimation Resource were used to screen hub genes with clinical value and important significance. THP 5μM could significantly inhibit proliferation, migration and invasion of MDA-MB-231 cells for 24h. 1547 DE lncRNAs, 4992 DE circRNAs, and 5777 DE mRNAs were identified. The reliability of the GeneChip was verified by qRT-PCR. An mRNA-lncRNA/circRNA co-expression network was constructed based on the Pearson correlation coefficient. Finally, we established a new ceRNA network, including three circRNAs, five miRNAs, and three mRNAs. The mRNAs are associated with immune infiltration. The mRNAs and miRNAs are significantly associated with survival outcomes in TNBC. The results reveal the molecular target and mechanism of THP treatment of TNBC. These ceRNA network can be used as molecular targets for the treatment of TNBC patients and as molecular biomarkers to predict patient prognosis.

An integrative analysis of an lncRNA-mRNA competing endogenous RNA network to identify functional lncRNAs in uterine leiomyomas with RNA sequencing.

Objective: To explore the functions of mRNAs and lncRNAs in the occurrence of uterine leiomyomas (ULs) and further clarify the pathogenesis of UL by detecting the differential expression of mRNAs and lncRNAs in 10 cases of UL tissues and surrounding normal myometrial tissues by high-throughput RNA sequencing. Methods: The tissue samples of 10 patients who underwent hysterectomy for UL in Lianyungang Maternal and Child Health Hospital from January 2016 to December 2021 were collected. The differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified and further analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The protein-protein interaction network (PPI) was constructed in Cytoscape software. Functional annotation of the nearby target cis-DEmRNAs of DElncRNAs was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/). Meanwhile, the co-expression network of DElncRNA-DEmRNA was constructed in Cytoscape software. Results: A total of 553 DElncRNAs (283 upregulated DElncRNAs and 270 downregulated DElncRNAs) and 3,293 DEmRNAs (1,632 upregulated DEmRNAs and 1,661 downregulated DEmRNAs) were obtained. GO pathway enrichment analysis revealed that several important pathways were significantly enriched in UL such as blood vessel development, regulation of ion transport, and external encapsulating structure organization. In addition, cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and complement and coagulation cascades were significantly enriched in KEGG pathway enrichment analysis. A total of 409 DElncRNAs-nearby-targeted DEmRNA pairs were detected, which included 118 DElncRNAs and 136 DEmRNAs. Finally, we found that the top two DElncRNAs with the most nearby DEmRNAs were BISPR and AC012531.1. Conclusion: These results suggested that 3,293 DEmRNAs and 553 DElncRNAs were differentially expressed in UL tissue and normal myometrium tissue, which might be candidate-identified therapeutic and prognostic targets for UL and be considered as offering several possible mechanisms and pathogenesis of UL in the future.

Uncovering potential diagnostic biomarkers of acute myocardial infarction based on machine learning and analyzing its relationship with immune cells

BackgroundAcute myocardial infarction (AMI) is a common cardiovascular disease. This study aimed to mine biomarkers associated with AMI to aid in clinical diagnosis and management.MethodsAll mRNA and miRNA data were downloaded from public database. Differentially expressed mRNAs (DEmRNAs) and differentially expressed miRNAs (DEmiRNAs) were identified using the metaMA and limma packages, respectively. Functional analysis of the DEmRNAs was performed. In order to explore the relationship between miRNA and mRNA, we construct miRNA-mRNA negative regulatory network. Potential biomarkers were identified based on machine learning. Subsequently, ROC and immune correlation analysis were performed on the identified key DEmRNA biomarkers.ResultsAccording to the false discovery rate < 0.05, 92 DEmRNAs and 272 DEmiRNAs were identified. GSEA analysis found that kegg_peroxisome was up-regulated in AMI and kegg_steroid_hormone_biosynthesis was down-regulated in AMI compared to normal controls. 5 key DEmRNA biomarkers were identified based on machine learning, and classification diagnostic models were constructed. The random forests (RF) model has the highest accuracy. This indicates that RF model has high diagnostic value and may contribute to the early diagnosis of AMI. ROC analysis found that the area under curve of 5 key DEmRNA biomarkers were all greater than 0.7. Pearson correlation analysis showed that 5 key DEmRNA biomarkers were correlated with most of the differential infiltrating immune cells.ConclusionThe identification of new molecular biomarkers provides potential research directions for exploring the molecular mechanism of AMI. Furthermore, it is important to explore new diagnostic genetic biomarkers for the diagnosis and treatment of AMI.

Whole transcriptome sequencing reveals core genes related to spermatogenesis in Bactrian camels.

Bactrian camels survive and reproduce better in extreme climatic conditions than other domestic animals can. However, the reproductive efficiency of camels under their natural pastoral conditions is low. Several factors affect mammalian reproductive performance, including testicular development, semen quality, libido, and mating ability. Testis is a main reproductive organ of the male and is responsible for producing spermatozoa and hormones. However, our understanding of the expression patterns of the genes in camel testis is minimal. Thus, we performed total RNA-sequencing to investigate the gene expression pattern. As a result, 1,538 differential expressed mRNAs (DEmRNAs), 702 differential expressed long non-coding RNAs (DElncRNAs), and 61 differential expressed microRNAs (DEmiRNAs) were identified between pubertal and adult Bactrian camel testes. Then the genomic features, length distribution, and other characteristics of the lncRNAs and mRNAs in the Bactrian camel testis were investigated. Target genes of the DEmiRNAs and DEmRNAs were further subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Genes, such as AMHR2, FGF1, ACTL7A, GATA4, WNT4, ID2, LAMA1, IGF1, INHBB, and TLR2, were mainly involved in the TGF-β, PI3K-AKT, Wnt, GnRH, and Hippo signaling pathways which relate to spermatogenesis. Some of the DEmiRNAs were predicted to be associated with numerous DElncRNAs and DEmRNAs through competing endogenous RNA (ceRNA) regulatory network. At last, the candidate genes were validated by RT-qPCR, dual fluorescent reporter gene, and a fluorescence in situ hybridization (FISH) assay. This research provides high-throughput RNA sequencing data of the testes of Bactrian camels across different developmental stages. It lays the foundation for further investigations on lncRNAs, miRNAs, and mRNAs that involved in Bactrian camel spermatogenesis.