Differential mRNAs Research Articles

Exerkine irisin mitigates cognitive impairment by suppressing gut-brain axis-mediated inflammation

IntroductionExercise has been recognized to improve cognitive performance by optimizing gut flora and up-regulating exerkine irisin. ObjectiveAlthough exercise-induced irisin is beneficial to cognitive improvement, whether this benefit is achieved by optimizing gut microbiota and metabolites is not fully explored. MethodsAfter aerobic exercise and exogenous irisin interventions for 12 weeks, the 16S rRNA and metabolites in feces of 21-month-old mice were analyzed. Meanwhile, the differential miRNAs and mRNAs in hippocampal tissues were screened by high-throughput sequencing. Relevant mRNAs and proteins were evaluated by RT-PCR, Western blot, and immunofluorescence. ResultsCompared with the young control mice, irisin levels and cognitive capacity of aged mice revealed a significant reduction, while aerobic exercise and intraperitoneal injection of exogenous irisin reversed aging-induced cognitive impairment. Similarly, 147 up-regulated and 173 down-regulated metabolites were detected in aged mice, while 64 and 45 up-regulated and 225 and 187 down-regulated metabolites were detected in aged mice with exercise and irisin interventions, respectively. Moreover, during hippocampal miRNA and mRNA sequencing analysis, 9 differential gut flora and 35 differential genes were identified to be correlated with the inflammatory signaling mediated by the TLR4/MyD88 signal pathway. ConclusionAging-induced cognitive impairment is due to insulin resistance induced by TLR4/MyD88 signaling activation in hippocampal tissues mediated by gut microbiota and metabolite changes. Myokine irisin may be an important mediator in optimizing gut microbiota and metabolism for an improved understanding of mitigated aging process upon exercise interventions.

Activation of α7 Nicotinic Acetylcholine Receptor Improves Muscle Endurance by Upregulating Orosomucoid Expression and Glycogen Content in Mice.

There are presently no acknowledged therapeutic targets or official drugs for the treatment of muscle fatigue. The alpha7 nicotinic acetylcholine receptor (α7nAChR) is expressed in skeletal muscle, with an unknown role in muscle endurance. Here, we try to explore whether α7nAChR could act as a potential therapeutic target for the treatment of muscle fatigue. Results showed that nicotine and PNU-282987 (PNU), as nonspecific and specific agonists of α7nAChR, respectively, could both significantly increase C57BL6/J mice treadmill-running time in a time- and dose-dependent manner. The improvement effect of PNU on running time and ex vivo muscle fatigue index disappeared when α7nAChR deletion. RNA sequencing revealed that the differential mRNAs affected by PNU were enriched in glycolysis/gluconeogenesis signaling pathways. Further studies found that PNU treatment significantly elevates glycogen content and ATP level in the muscle tissues of α7nAChR+/+ mice but not α7nAChR-/- mice. α7nAChR activation specifically increased endogenous glycogen-targeting protein orosomucoid (ORM) expression both in vivo skeletal muscle tissues and in vitro C2C12 skeletal muscle cells. In ORM1 deficient mice, the positive effects of PNU on running time, glycogen and ATP content, as well as muscle fatigue index, were abolished. Therefore, the activation of α7nAChR could enhance muscle endurance via elevating endogenous anti-fatigue protein ORM and might act as a promising therapeutic strategy for the treatment of muscle fatigue.

Expression profile of long noncoding RNAs and comprehensive analysis of lncRNA-cisTF-DGE regulation in condyloma acuminatum

ObjectiveTo identify differentially expressed long noncoding RNAs (lncRNAs) in condyloma acuminatum (CA) and to explore their probable regulatory mechanisms by establishing coexpression networks.MethodsHigh-throughput RNA sequencing was performed to assess genome-wide lncRNA expression in CA and paired adjacent mucosal tissue. The expression of candidate lncRNAs and their target genes in larger CA specimens was validated using real-time quantitative reverse transcriptase polymerase chain reaction (RT‒qPCR). Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used for the functional enrichment analysis of these candidate lncRNAs and differential mRNAs. The coexpressed mRNAs of the candidate lncRNAs, calculated by Pearson’s correlation coefficient, were also analysed using GO and KEGG analysis. In addition, the interactions among differentially expressed lncRNAs (DElncRNAs)-cis-regulatory transcription factors (cisTFs)-differentially expressed genes (DEGs) were analysed and their network was constructed.ResultsA total of 546 lncRNAs and 2553 mRNAs were found to be differentially expressed in CA compared to the paired control. Functional enrichment analysis revealed that the DEGs coexpressed with DElncRNAs were enriched in the terms of cell adhesion and keratinocyte differentiation, and the pathways of ECM-receptor interaction, local adhesion, PI3K/AKT and TGF-ß signaling. We further constructed the network among DElncRNAs-cisTFs-DEGs and found that these 95 DEGs were mainly enriched in GO terms of epithelial development, regulation of transcription or gene expression. Furthermore, the expression of 3 pairs of DElncRNAs and cisTFs, EVX1-AS and HOXA13, HOXA11-AS and EVX1, and DLX6-AS and DLX5, was validated with a larger number of specimens using RT‒qPCR.ConclusionCA has a specific lncRNA profile, and the differentially expressed lncRNAs play regulatory roles in mRNA expression through cis-acting TFs, which provides insight into their regulatory networks. It will be useful to understand the pathogenesis of CA to provide new directions for the prevention, clinical treatment and efficacy evaluation of CA.

Silencing immune-infiltrating biomarker CCDC80 inhibits malignant characterization and tumor formation in gastric cancer

ObjectiveTumor immune infiltration leads to poor prognosis of gastric cancer patients and seriously affects the life quality of gastric cancer patients. This study was based on bioinformatics to screen prognostic biomarkers in patients with high degree of immune invasion of gastric cancer. Meanwhile, the action of biomarker CCDC80 was explored in gastric cancer by cell and tumorigenesis experiments, to provide reference for the cure of gastric cancer patients.MethodsData sets and clinical massage on gastric cancer were collected from TCGA database and GEO database. ConsensusClusterPlus was used to cluster gastric cancer patients based on the 28 immune cells infiltration in ssGSEA. R “Limma” package was applied to analyze differential mRNAs between Cluster 1 and Cluster 2. Differential expression genes were screened by single factor analysis. Stemness markers (SERPINF1, DCN, CCDC80, FBLN5, SPARCL1, CCL14, DPYSL3) were identified for differential expression genes. Prognostic value of CCDC80 was evaluated in gastric cancer. Differences in genomic mutation and tumor microenvironment immune infiltration were assessed between high or low CCDC80. Finally, gastric cancer cells (HGC-27 and MKN-45) were selected to evaluate the action of silencing CCDC80 on malignant characterization, macrophage polarization, and tumor formation.ResultsBioinformatics analysis showed that CCDC80, as a stemness marker, was significantly overexpressed in gastric cancer. CCDC80 was also related to the degree of gastric cancer immune invasion. CCDC80 was up-expressed in cells of gastric cancer. Silencing CCDC80 inhibited malignant characterization and subcutaneous tumor formation of gastric cancer cells. High expression of CCDC80 was positive correspondence with immune invasion. Silencing CCDC80 inhibited M2 polarization and promoted M1 polarization in tumor tissues. In addition, gastric cancer patients were likely to have mutations in CDH1, ACTRT1, GANAB, and CDH10 genes in the High-CCDC80 group.ConclusionSilencing CCDC80, a prognostic biomarker in patients with immune invasion of gastric cancer, could effectively inhibit the malignant characterization, M2 polarization, and tumor formation of gastric cancer.

Clinical efficacy and gene chip expression analysis of Shenzhu Guanxin recipe granules in patients with intermediate coronary lesions.

To evaluate the clinical efficacy and safety of Shenzhu Guanxin recipe granules (, SGR) in treating patients with intermediate coronary lesions (ICL), and to investigate the potential mechanism though a transcriptome sequencing approach. ICL patients with Qi deficiency and phlegm stasis were adopted and randomly assigned to a case group or a control by random number generator in a 1:1 randomization ratio to evaluate the clinical efficacy. There was no significant difference between the two groups in coronary computed tomography angiography related indexes in the two groups before and after intervention. Through the gene chip expression analysis, it is finally concluded that there are 355 differential mRNAs (190 up-regulated genes and 165 down regulated genes) when compared the SGR group and placebo group. Through protein-protein interaction network analysis of differentially expressed genes, 10 hub genes were finally obtained: CACNA2D2, CACNA2D3, DNAJC6, FGF12, SGSM2, CACNA1G, LRP6, KIF25, OXTR, UPB1. SGR combined with Western Medicine can be safely used to treat ICL patients with Qi deficiency and phlegm stasis. The possible mechanism of action and relevant gene loci and pathway were proposed.

Unveiling the Impact of ApoF Deficiency on Liver and Lipid Metabolism: Insights from Transcriptome-Wide m6A Methylome Analysis in Mice.

Lipid metabolism participates in various physiological processes and has been shown to be connected to the development and progression of multiple diseases, especially metabolic hepatopathy. Apolipoproteins (Apos) act as vectors that combine with lipids, such as cholesterol and triglycerides (TGs). Despite being involved in lipid transportation and metabolism, the critical role of Apos in the maintenance of lipid metabolism has still not been fully revealed. This study sought to clarify variations related to m6A methylome in ApoF gene knockout mice with disordered lipid metabolism based on the bioinformatics method of transcriptome-wide m6A methylome epitranscriptomics. High-throughput methylated RNA immunoprecipitation sequencing (MeRIP-seq) was conducted in both wild-type (WT) and ApoF knockout (KO) mice. As a result, the liver histopathology presented vacuolization and steatosis, and the serum biochemical assays reported abnormal lipid content in KO mice. The m6A-modified mRNAs were conformed consensus sequenced in eukaryotes, and the distribution was enriched within the coding sequences and 3' non-coding regions. In KO mice, the functional annotation terms of the differentially expressed genes (DEGs) included cholesterol, steroid and lipid metabolism, and lipid storage. In the differentially m6A-methylated mRNAs, the functional annotation terms included cholesterol, TG, and long-chain fatty acid metabolic processes; lipid transport; and liver development. The overlapping DEGs and differential m6A-modified mRNAs were also enriched in terms of lipid metabolism disorder. In conclusion, transcriptome-wide MeRIP sequencing in ApoF KO mice demonstrated the role of this crucial apolipoprotein in liver health and lipid metabolism.

Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with FecB BB genotype

Background The thyroid gland is an important endocrine gland in animals that secretes thyroid hormones and acts on various organs throughout the body. lncRNAs are long non-coding RNAs that play an important role in animal reproduction; however, there is a lack of understanding of their expression patterns and potential roles in the thyroid gland of the Small Tail Han (STH) sheep. In this study, we used RNA-Seq technology to examine the transcriptome expression pattern of the thyroid from the luteal phase (LP) and follicular phase (FP) of FecB BB (MM) STH sheep. Results We identified a total of 122 and 1287 differential expression lncRNAs (DELs) and differential expression mRNAs (DEGs), respectively, which were significantly differentially expressed. These DELs target genes and DEGs can be enriched in several signalling pathways related to the animal reproduction process. Conclusions The expression profiles of DELs and DEGs in thyroid glands provide a more comprehensive resource for elucidating the reproductive regulatory mechanisms of STH sheep.

Molecular prognostic of nine parthanatos death-related genes in glioma, particularly in COL8A1 identification.

Post-operative progression and chemotherapy resistance are the main causes of treatment failure in glioma patients. There is a lack of ideal prediction models for post-operative glioma patient progression and drug sensitivity. We aimed to develop a prognostic model of parthanatos mRNA biomarkers for glioma outcomes. A total of 11 parthanatos genes were obtained from ParthanatosCluster database. ConsensusClusterPlus and R "Limma" package were used to cluster The Cancer Genome Atlas (TCGA)-glioma cohort and analyze the differential mRNAs. Univariate Cox regression analysis, random survival forest model, and least absolute shrinkage and selection operator (LASSO) regression analysis were used to determine the nine ParthanatosScore prognostic genes combination. ParthanatosScore was verified by 656 patients and 979 patients in TCGA and CGCA-LGG/GBM datasets. Differences in genomic mutations, tumor microenvironments, and functional pathways were assessed. Drug response prediction was performed using pRRophetic. Kaplan-Meier survival analysis was analyzed. Finally, COL8A1 was selected to evaluate its potential biological function and drug sensitivity of temozolomide and AZD3759 in glioma cells. ParthanatosScore obtained a combination of nine glioma prognostic genes, including CD58, H19, TNFAIP6, FTLP3, TNFRSF11B, SFRP2, LOXL1, COL8A1, and FABP5P7. In the TCGA-LGG/GBM dataset, glioma prognosis was poor in high ParthanatosScore. Low-score glioma patients were sensitive to AZD3759_1915, AZD5582_1617, AZD8186_1918, Dasatinib_1079, and Temozolomide_1375, while high-score patients were less sensitive to these drugs. Compared with HA cells, COL8A1 was significantly over-expressed in LN229 and U251 cells. Silencing COL8A1 inhibited the malignant characterization of LN229 and U251 cells. Temozolomide and AZD3759 also promoted parthanatos gene expression in glioma cells. Temozolomide and AZD3759 inhibited COL8A1 expression and cell viability and promoted apoptosis in glioma cells and PGM cells. ParthanatosScore can accurately predict clinical prognosis and drug sensitivity after glioma surgery. Silencing COL8A1 inhibited the malignant characterization. Temozolomide and AZD3759 inhibited COL8A1 expression and cell viability and promoted apoptosis and parthanatos gene expression, which is a target to improve glioma.

N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells

ABSTRACT N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.

Transcriptome analysis reveals pituitary lncRNA, circRNA and mRNA affecting fertility in high- and low-yielding goats.

The pituitary gland serves as the central endocrine regulator of growth, reproduction, and metabolism and plays a crucial role in the reproductive process of female animals. Transcriptome analysis was conducted using pituitary gland samples from Leizhou goats with varying levels of fecundity to investigate the effects of long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA regulation on pituitary hormone secretion and its association with goat fecundity. The analysis aimed to identify lncRNAs, circRNAs, and mRNAs that influence the fertility of Leizhou goats. GO and KEGG enrichment analyses were performed on differentially expressed lncRNAs, circRNAs, and mRNAs and revealed considerable enrichment in pathways, such as regulation of hormone secretion, germ cell development, and gonadotropin-releasing hormone secretion. The pituitary lncRNAs (ENSCHIT00000010293, ENSCHIT00000010304, ENSCHIT00000010306, ENSCHIT00000010290, ENSCHIT00000010298, ENSCHIT00000006769, ENSCHIT00000006767, ENSCHIT00000006921, and ENSCHIT00000001330) and circRNAs (chicirc_029285, chicirc_026618, chicirc_129655, chicirc_018248, chicirc_122554, chicirc_087101, and chicirc_078945) identified as differentially expressed regulated hormone secretion in the pituitary through their respective host genes. Additionally, differential mRNAs (GABBR2, SYCP1, HNF4A, CBLN1, and CDKN1A) influenced goat fecundity by affecting hormone secretion in the pituitary gland. These findings contribute to the understanding of the molecular mechanisms underlying pituitary regulation of fecundity in Leizhou goats.

Analysis of the mechanism of curcumin against osteoarthritis using metabolomics and transcriptomics

Curcumin, a polyphenolic compound derived from the turmeric plant (Curcuma longa), has been extensively studied for its anti-inflammatory and anti-proliferative properties. The safety and efficacy of curcumin have been thoroughly validated. Nevertheless, the underlying mechanism for treating osteoarthritis remains ambiguous. This study aims to reveal the potential mechanism of curcumin in treating osteoarthritis by using metabolomics and transcriptomics. Firstly, we validated the effect of curcumin on inflammatory factors in human articular chondrocytes. Secondly, we explored the cellular metabolism mechanism of curcumin against osteoarthritis using cell metabolomics. Thirdly, we assessed the differences in gene expression of human articular chondrocytes through transcriptomics. Lastly, to evaluate the essential targets and elucidate the potential mechanism underlying the therapeutic effects of curcumin in osteoarthritis, we conducted a screening of the proteins within the shared pathway of metabolomics and transcriptomics. Our results demonstrated that curcumin significantly decreased the levels of inflammatory markers, such as IL-β, IL-6, and TNF-α, in human articular chondrocytes. Cell metabolomics identified 106 differential metabolites, including beta-aminopropionitrile, 3-amino-2-piperidone, pyrrole-2-carboxaldehyde, and various other components. The transcriptomic analysis yielded 1050 differential mRNAs. Enrichment analysis showed that the differential metabolites and mRNAs were significantly enriched in seven pathways, including glycine, serine, and threonine metabolism; pentose and glucuronate interconversions; glycerolipid metabolism; histidine metabolism; mucin-type o-glycan biosynthesis; inositol phosphate metabolism; and cysteine and methionine metabolism. A total of 23 key targets were identified to be involved in these pathways. We speculate that curcumin may alleviate osteoarthritis by targeting key proteins involved in glycine, serine, and threonine metabolism; inhibiting pyruvate production; and modulating glycolysis.

Astragalus membranaceus and Salvia miltiorrhiza ameliorate diabetic kidney disease via the “gut-kidney axis”

BackgroundThe combination of Astragalus membranaceus and Salvia miltiorrhiza (AS) is an effective prescription for treating diabetic kidney disease (DKD) in traditional Chinese medicine. Its efficacy in treating DKD has been confirmed, but the potential regulatory mechanism has not yet been fully clarified. PurposeTo explore the mechanism by which AS regulates the "gut-metabolism-transcription" coexpression network under the action of the "gut-kidney axis" to ameliorate DKD. MethodsSD rats were used to establish the DKD model by injecting STZ. After AS intervention, the structure and function of the kidney and colon were observed. We sequenced the gut microbiota utilizing 16S rDNA, identified serum differential metabolites using LC‒MS/MS, and observed renal mRNA expression by RNA seq. The "gut-metabolism-transcription" coexpression network was further constructed, and the target bacteria, target metabolites, and target genes of AS were ultimately screened and validated. ResultsAS improved renal pathology and functional damage and increased the abundance of Akkermansia, Akkermansia_muciniphila, Lactobacillus and Lactobacillus_murinus. Fourteen target metabolites of AS were identified, which were mainly concentrated in 19 KEGG pathways, including sphingolipid metabolism and glycerophospholipid metabolism. Sixty-three target mRNAs of AS were identified. The top 20 pathways were closely related to glycolipid metabolism, and 14 differential mRNAs were expressed in these pathways. Correlation analysis showed that Akkermansia, Akkermansia muciniphila, Lactobacillus and Lactobacillus murinus were closely associated with sphingolipid metabolism, glycerophospholipid metabolism, arachidonic acid metabolism, ascorbate and aldarate metabolism and galactose metabolism. Moreover, the target metabolites and target mRNAs of AS were also enriched in five identical pathways of sphingolipid metabolism, glycerophospholipid metabolism, arachidonic acid metabolism, ascorbate and aldarate metabolism and galactose metabolism, including 8 different metabolites, such as sphingosine, and 5 different genes, such as Kng1. The 8 metabolites had high AUC prediction values, and the validation of the 5 genes was consistent with the sequencing results. ConclusionOur research showed that AS can improve DKD via the "gut-kidney axis". Akkermansia muciniphila and Lactobacillus murinus were the main driving bacteria, and five pathways related to glycolipid metabolism, especially sphingolipid metabolism and glycerophospholipid metabolism, may be important follow-up reactions and regulatory mechanisms.

B-383 Exosomal PRPSAP1 in Plasma Predicts Microvascular Invasion in Hepatocellular Carcinoma

Abstract Background Microvascular invasion (MVI), a critical predictor of postoperative tumor recurrence in hepatocellular carcinoma (HCC), is only detectable by histopathological examination of the surgical specimen. Prediction of MVI before surgery is of great significance to prognosis, especially by non-invasive means. Here, we report that exosome-derived mRNA in plasma can be promising biomarkers for MVI preoperatively. Methods Patients with initially suspected HCC who were undergoing hepatectomy were prospectively recruited with preoperative peripheral blood collection and followed up. Exosomal mRNA profiling was performed using RNA sequencing in the discovery cohort, and the edgeR package in R software was used to screen out significantly differential expression exosomal mRNAs between MVI and non-MVI groups. Multiplex droplet digital PCR (ddPCR) technology was utilized to verify filtered exosomal mRNAs in the validation cohort. Results A total of 131 HCC patients were enrolled with 37 in the discovery cohort and 94 in the validation cohort. RNA-sequencing data identified six candidate exosomal mRNAs (ZC3H3, RSAD2, PRPSAP1, HOXA2, CHPM4A and KCTD10) as potential predictors for MVI. In the validation cohort, expression levels of PRPSAP1 and HOXA2 were slightly higher and the expression level of CHMP4A was slightly lower in the MVI group than the non-MVI one, which were consistent with the discovery cohort though without statistically significant difference (P > 0.05). Further analysis between MVI number>5 and non-MVI patients validated that the expression level of exosomal PRPSAP1 was significantly higher in MVI number>5 patients (0.147 vs 0.070, P = 0.035). Altogether, exosomal PRPSAP1 in plasma was a promising biomarker predicting MVI for HCC patients. Conclusion We validated for the first time that high level expression of exosome-derived PRPSAP1 can preoperatively predict MVI, especially with the number >5, to improve prognosis.

Hsa-miR-148a-3p promotes malignant behavior of breast cancer cells by downregulating DUSP1

To investigate the role of Hsa-miR-148a-3p in regulating biological behaviors of breast cancer cells and explore the mechanism. TCGA database was used to identify the differential miRNAs and mRNAs in breast cancer, and the protein-protein interaction (PPI) network was constructed using String and Cytoscape to screen the top 10 hub genes and construct the miRNA-TOP10hub network. RT-qPCR was used to detect the expressions of Hsa-miR-148a-3p and DUSP1 in breast cancer tissues and cell lines. The effects of Hsa-miR-148a-3p mimic and inhibitor on proliferation, migration, invasion and apoptosis of MCF-7 cells were analyzed, and luciferase reporter gene experiment was performed to verify the binding of Hsa-miR-148a-3p to DUSP1. The effect of Hsa-miR-148a-3p overexpression on breast cancer cell xenograft growth was evaluated in nude mice. Kaplan-Meier survival curve analysis was used to analyze the survival of the tumor-bearing mice, and the expression level of DUSP1 in the xenografts was detected using immunohistochemistry. A total of 54 differential miRNAs and 799 differential mRNAs were identified in breast cancer; 3716 target genes were intersected with the differential mRNA, resulting in 150 intersected genes. The top 10 hub genes were downregulated in breast cancer tissues in the PPI network. Double luciferase reporter gene experiment confirmed that Hsa-miR-148a-3p was capable of binding to DUSP1. Hsa-miR-148a-3p was up-regulated and DUSP1 was down-regulated significantly in breast cancer tissues and cells (P<0.01). In breast cancer cells, Hsa-miR-148a-3p mimic strongly promoted cell proliferation, migration and invasion and inhibited cell apoptosis (P<0.01). Hsa-miR-148a-3p overexpression obviously promoted xenograft growth in nude mice (P<0.01), shortened survival time of the mice (P<0.01), and reduced the expression of DUSP1 in the xenografts (P<0.01). Hsa-miR-148a-3p promotes malignant behavior of breast cancer cells by inhibiting the expression of DUSP1.

Integrated Analysis of Long Non-Coding RNA Expression Profiles in Glaesserella parasuis-Induced Meningitis: New Insight into Pathogenesis

Glaesserella parasuis (G. parasuis) can elicit meningitis in pigs; however, the pathogenic mechanisms of meningitis induced by G. parasuis remain unclear. Long non-coding RNAs (lncRNAs) have been proven to play key roles in a variety of physiological and pathological processes. However, whether lncRNAs are involved in meningitis triggered by G. parasuis has not been investigated. In this study, we performed an integrative analysis of lncRNAs expression profiles in the porcine brain infected with G. parasuis using RNA-seq. The results showed that lncRNA expressions in G. parasuis-induced meningitis were modified, and a total of 306 lncRNAs exhibited significant differential expression, in which 176 lncRNAs were up-regulated and 130 lncRNAs were down-regulated. KEGG enrichment analysis demonstrated that the differentially expressed target mRNAs of affected lncRNAs in G. parasuis-infected porcine brain were mainly involved in the cell adhesion molecules (CAMs), Jak-STAT signaling pathway, PI3k-Akt signaling pathway, and TNF signaling pathway. The expression relationship between the most affected differential lncRNAs and their differential target mRNAs was visualized by a co-expression network. A protein-protein interaction network consisting of 12 differential targets was constructed using STRING analysis. In addition, differential expressions of important lncRNAs were validated by qRT-PCR. lncRNA ALDBSSCT0000007362, ALDBSSCT0000001959, ALDBSSCT0000005529, MSTRG.2939.1, and MSTRG.32374.1 showed the same expression pattern with the lncRNA sequencing data. Our results demonstrated that G. parasuis could modify the lncRNA expression profiles in the porcine brain. To the best of our knowledge, this is the first report revealing the integrative analysis of lncRNA expression profiles in G. parasuis-induced meningitis, which could enhance important information to understand the inflammatory functions of lncRNAs involved in swine meningitis, and also provide a foundation for finding out novel strategies to prevent and treat meningitis in piglets triggered by G. parasuis.

Identification and verification of a prognostic signature based on a miRNA-mRNA interaction pattern in colon adenocarcinoma.

The expression characteristics of non-coding RNA (ncRNA) in colon adenocarcinoma (COAD) are involved in regulating various biological processes. To achieve these functions, ncRNA and a member of the Argonaute protein family form an RNA-induced silencing complex (RISC). The RISC is directed by ncRNA, especially microRNA (miRNA), to bind the target complementary mRNAs and regulate their expression by interfering with mRNA cleavage, degradation, or translation. However, how to identify potential miRNA biomarkers and therapeutic targets remains unclear. Here, we performed differential gene screening based on The Cancer Genome Atlas dataset and annotated meaningful differential genes to enrich related biological processes and regulatory cancer pathways. According to the overlap between the screened differential mRNAs and differential miRNAs, a prognosis model based on a least absolute shrinkage and selection operator-based Cox proportional hazards regression analysis can be established to obtain better prognosis characteristics. To further explore the therapeutic potential of miRNA as a target of mRNA intervention, we conducted an immunohistochemical analysis and evaluated the expression level in the tissue microarray of 100 colorectal cancer patients. The results demonstrated that the expression level of POU4F1, DNASE1L2, and WDR72 in the signature was significantly upregulated in COAD and correlated with poor prognosis. Establishing a prognostic signature based on miRNA target genes will help elucidate the molecular pathogenesis of COAD and provide novel potential targets for RNA therapy.

Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for hepatocellular carcinoma using integrated bioinformatic analysis

Objective: By applying bioinformatic techniques, this study aims to explore potential biomarkers associated with hepatoma carcinoma (HCC) through comprehensive analyses. Methods: We downloaded two RNA microarray datasets related to HCC by accessing the Gene Expression Omnibus (GEO) database and employing specific keywords. Subsequently, all data were retrieved and processed to analyze the differential miRNAs and mRNAs within these datasets. Moreover, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted, followed by the construction of protein-protein interaction (PPI) network. Utilizing diverse software and online platforms, we created volcano maps, GO analysis diagrams, KEGG analysis diagrams, protein interaction network diagrams, and miRNA-mRNA interaction analysis diagrams. Results: 13 differential miRNAs and 256 differential mRNAs were extracted from the two datasets. The GO annotation encompasses over 1,000 entries, comprising 345 biological process (BP) entries, over 490 cellular component (CC) entries, and 165 molecular function (MF) entries. Additionally, 116 signaling pathways were identified from the general set pathway of the KEGG. Conclusions: This study utilized bioinformatics research methods to construct a miRNA-mRNA interaction network by further collating, refining and analyzing the data obtained from miRNA chips and mRNA chips. Through the mining of potential biomarkers of HCC, new insights have been proposed for future experimental research.

MiRNA-103-3p-Hlf regulates apoptosis and autophagy by targeting hepatic leukaemia factor in heart failure.

Cardiomyocyte apoptosis is an important factor leading to the occurrence and development of heart failure (HF), which is associated with high mortality of patients with cardiovascular diseases. This study aims to investigate the underlying mechanisms of HF in terms of expression and regulation patterns using bioinformatics and experimental validation. Two HF datasets were collected: a dataset GSE112056 downloaded from the GEO database (including mRNA and miRNA sequencing data) and another is the laboratory-owned mRNA dataset. Differential mRNAs and miRNAs in the two datasets were screened using the raw Bayesian approach method. Gene Ontology was used to perform functional enrichment analysis of the differential mRNAs and co-expression network analysis of the differential mRNAs, combined with nuclear transcription factors in the differential miRNAs and mRNAs for target gene prediction. A HF cell model was constructed using mouse cardiomyocytes (HL-1), and the role and mechanism of miRNA-103-3p-Hlf (hepatic leukaemia factor) in the process of HF was verified by cell transfection, luciferase reporter gene, WB, and qPCR. We found that Hlf gene expression was decreased in the HF model group and strongly correlated with FYCO1 (FYVE and coiled-coil domain-containing protein 1) gene, a phenomenon enriched in apoptotic autophagy-related pathways. MiR-103-3p expression was up-regulated in the HF model group, and its targeting correlation with Hlf was confirmed by luciferase activity assay. In the HL-1 cell model, miR-103-3p significantly promoted apoptosis and inhibited autophagy in HL-1 cells (all P<0.05), and overexpression of the Hlf gene reversed this phenomenon, inhibiting apoptosis and promoting autophagy in HL-1 cells (all P<0.05). MiR-103-3p affects myocardial cells apoptosis and autophagy by targeting Hlf, playing as a potential therapeutic biomarker for HF progression.

Differentially Expressed Circulating Long-Noncoding RNAS in Premature Infants with Respiratory Distress Syndrome.

Recent studies have addressed the association between lung development and long-noncoding RNAs (lncRNAs). But few studies have investigated the role of lncRNAs in neonatal respiratory distress syndrome (RDS). Thus, this study aimed to compare the expression profile of circulating lncRNAs between RDS infants and controls. 10 RDS infants and 5 controls were enrolled. RDS patients were further divided into mild and severe RDS subgroups. Blood samples were collected for the lncRNA expression profile. Subsequently, differentially expressed lncRNAs were screened out. Bioinformatics analysis was applied to establish a co-expression network of differential lncRNAs and mRNAs, and predict the underlying biological functions. A total of 135 differentially expressed lncRNAs were identified, including 108 upregulated and 27 downregulated lncRNAs (fold-change>2 and P<0.05) among the three groups (non-RDS, mild RDS and severe RDS groups). Of these lncRNAs, four were selected as showing higher fold changes and validated by qRT-PCR. ENST00000470527.1, ENST00000504497.1, ENST00000417781.5, and ENST00000440408.5 were increased not only in the plasma of total RDS patients but also in the severe RDS subgroup. Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses showed that differentially expressed lncRNAs may play important roles in RDS through regulating PI3KAkt, RAS, MAPK, and TGF-β signaling pathways. The present results found that ENST00000470527.1, ENST00000504497.1, ENST00000417781.5, and ENST00000440408.5 may be invol ved in RDS. This could provide new insight into research of the potential pathophysiological mechanisms of preterm RDS.

Revealing common differential mRNAs, signaling pathways, and immune cells in blood, glomeruli, and tubulointerstitium of lupus nephritis patients based on transcriptomic data

Lupus nephritis (LN) is a potentially fatal autoimmune disease. The purpose of this study was to find potential key molecular markers of LN to aid in the early diagnosis and management of the disease. Datasets GSE99967_blood, GSE32591_glomeruli, and GSE32591_tubulointerstitium were included in this study. Differentially expressed mRNAs (DEmRNAs) were identified between the normal control and LN groups using the limma package in R. Common DEmRNAs in the three datasets were taken. Subsequently, functional enrichment analysis, immune correlation analysis, receiver operating characteristic (ROC) curve analysis and real-time polymerase chain reaction (RT-PCR) verification were performed. In this study, 11 common DEmRNAs were obtained and all of them were up-regulated. In protein–protein interaction (PPI) networks, we found that MX dynamin like GTPase 1 (MX1) and radical S-adenosyl methionine domain containing 2 (RSAD2) had the highest interaction score (0.997). Functional enrichment analysis revealed that MX1 and RSAD2 were enriched in influenza A and hepatitis C signaling pathways. The area under the curve (AUC) values of interferon-induced protein 44 (IFI44) and MX1 in GSE32591_glomeruli and GSE32591_tubulointerstitium datasets are 1, which is worthy of further study on their diagnostic value and molecular mechanism. The xCell analysis showed abnormal distribution of granulocyte-macrophage progenitor (GMP) cells in blood, glomeruli, and tubulointerstitium. Pearson’s correlation analysis found that GMP cells were significantly correlated with lactotransferrin (LTF) and cell cycle. Identification of common DEmRNAs and key pathways in the blood, glomeruli, and tubulointerstitium of patients with LN provides potential research directions for exploring the molecular mechanisms of the disease.