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Project description:Purpose: Hyperlipidemia has been shown to contribute to reduced implant osseointegration, but the underlying mechanism remains poorly understood. Recently, non-coding RNAs (ncRNAs) have been established as key regulators of various pathophysiological processes. Therefore, the current study aims to examine the expression profiles of mRNAs and ncRNAs in femoral tissues around surgical implants in a murine hyperlipidemia model via RNA sequencing.Materials and method: Twenty adult male Wistar rats were equally divided between an experimental group and a control group, which were fed a high-fat diet and a normal diet, respectively. Titanium root-form implants was inserted into both femoral shafts of each rat in eight weeks. Bone tissues were collected at day 10 after the insertion of the implants and subsequently used for RNA extraction and sequencing. The sequenced reads were refined, assembled and annotated to obtain mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) transcripts. The levels of all types of RNA molecules in both animal groups were quantified and differentially expressed candidates were identified. The function of the identified RNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. LncRNA-miRNA-mRNA and circRNA-miRNA-mRNA co-expression network of differentially expressed RNAs were constructed. Real-time polymerase chain reactions (RT-PCR) were performed to validate the expression levels of selected candidates.Results: The serum lipid levels of the experimental group were significant higher than those of the control group (p < 0.05). In total, 389 mRNAs, 73 miRNAs, 770 lncRNAs and 7 circRNAs were shown to be differentially expressed (p < 0.05, fold change > 2). GO analysis found that regulation of bone mineralization, negative regulation of chondrocyte differentiation and bone development changed significantly. The network that maybe related to osteogenesis included 6 mRNAs, 8 miRNAs, 6 circRNAs, 119 lncRNAs and 362 associations. Expression level of most RNAs detected by RT-PCR was consistent with that by RNA sequencing. Conclusion: Functional analysis predicted a panel of differentially expressed mRNAs and ncRNAs associated with osteogenesis. The results of the current study will greatly contribute to the elucidation of the mechanism for implant osseointegration under hyperlipidemia.
2021-04-01 | GSE113520 | GEO
Project description:Purpose: Hyperlipidemia has been shown to contribute to reduced implant osseointegration, but the underlying mechanism remains poorly understood. Recently, non-coding RNAs (ncRNAs) have been established as key regulators of various pathophysiological processes. Therefore, the current study aims to examine the expression profiles of mRNAs and ncRNAs in femoral tissues around surgical implants in a murine hyperlipidemia model via RNA sequencing.Materials and method: Twenty adult male Wistar rats were equally divided between an experimental group and a control group, which were fed a high-fat diet and a normal diet, respectively. Titanium root-form implants was inserted into both femoral shafts of each rat in eight weeks. Bone tissues were collected at day 10 after the insertion of the implants and subsequently used for RNA extraction and sequencing. The sequenced reads were refined, assembled and annotated to obtain mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) transcripts. The levels of all types of RNA molecules in both animal groups were quantified and differentially expressed candidates were identified. The function of the identified RNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. LncRNA-miRNA-mRNA and circRNA-miRNA-mRNA co-expression network of differentially expressed RNAs were constructed. Real-time polymerase chain reactions (RT-PCR) were performed to validate the expression levels of selected candidates.Results: The serum lipid levels of the experimental group were significant higher than those of the control group (p < 0.05). In total, 389 mRNAs, 73 miRNAs, 770 lncRNAs and 7 circRNAs were shown to be differentially expressed (p < 0.05, fold change > 2). GO analysis found that regulation of bone mineralization, negative regulation of chondrocyte differentiation and bone development changed significantly. The network that maybe related to osteogenesis included 6 mRNAs, 8 miRNAs, 6 circRNAs, 119 lncRNAs and 362 associations. Expression level of most RNAs detected by RT-PCR was consistent with that by RNA sequencing. Conclusion: Functional analysis predicted a panel of differentially expressed mRNAs and ncRNAs associated with osteogenesis. The results of the current study will greatly contribute to the elucidation of the mechanism for implant osseointegration under hyperlipidemia.
2021-04-01 | GSE113521 | GEO
Project description:Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats
| PRJNA451430 | ENA
Project description:Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (miRNA-seq data sets)
| PRJNA451435 | ENA
Project description:Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (RNA-seq data sets)
| PRJNA451434 | ENA
Project description:BackgroundWater stress seriously constrains plant growth and yield. Long non-coding RNAs (lncRNAs) serve as versatile regulators in various biological regulatory processes. To date, the systematic screening and potential functions of lncRNA have not yet been characterized in Cleistogenes songorica, especially under water stress conditions.ResultsIn this study, we obtained the root and shoot transcriptomes of young C. songorica plants subjected to different degrees of water stress and recovery treatments by Illumina-based RNA-seq. A total of 3397 lncRNAs were identified through bioinformatics analysis. LncRNA differential expression analysis indicated that the higher response of roots compared to shoots during water stress and recovery. We further identified the 1644 transcription factors, 189 of which were corresponded to 163 lncRNAs in C. songorica. Though comparative analyses with major Poaceae species based on blast, 81 water stress-related orthologues regulated to lncRNAs were identified as a core of evolutionary conserved genes important to regulate water stress responses in the family. Among these target genes, two genes were found to be involved in the abscisic acid (ABA) signalling pathway, and four genes were enriched for starch and sucrose metabolism. Additionally, the 52 lncRNAs were predicted as target mimics for microRNAs (miRNAs) in C. songorica. RT-qPCR results suggested that MSTRG.43964.1 and MSTRG.4400.2 may regulate the expression of miRNA397 and miRNA166, respectively, as target mimics under water stress and during recovery. Finally, a co-expression network was constructed based on the lncRNAs, miRNAs, protein-coding genes (PCgenes) and transcription factors under water stress and during recovery in C. songorica.ConclusionsIn C. songorica, lncRNAs, miRNAs, PCgenes and transcription factors constitute a complex transcriptional regulatory network which lncRNAs can regulate PCgenes and miRNAs under water stress and recovery. This study provides fundamental resources to deepen our knowledge on lncRNAs during ubiquitous water stress.
| S-EPMC6330494 | biostudies-literature
Project description:BackgroundTo explore long non-coding RNA (lncRNA), mRNA and circular RNA (circRNA) expression profiles and their biological functions in the pathogenesis of kidney stones in ethylene glycol-induced urolithiasis rats.ResultsThe expression of 1440 lncRNAs, 2455 mRNAs and 145 circRNAs was altered in the kidneys of urolithiasis rats. GO and KEGG biological pathway analysis were performed to predict the functions of differentially expressed lncRNAs, circRNAs and co-expressed potential targeting genes. Co-expression networks of lncRNA-mRNA and circRNA-miRNA were constructed based on correlation analysis between differentially expressed RNAs. mRNAs coexpressed with lncRNAs were involved in many kidney diseases, e.g., Ephb6 was associated with the reabsorption ability of the kidney. Arl5b was associated with the dynamic changes in the podocyte foot process in podocyte injury. miRNAs co-expressed with circRNAs, such as rno-miR-138-5p and rno-miR-672-5p, have been proven to be functional in hypercalciuria urolithiasis.ConclusionThe expression profile provided a systematic perspective on the potential functions of lncRNAs and circRNAs in the pathogenesis of kidney stones. Differentially expressed lncRNAs and circRNAs might serve as treatment targets for kidney stones.
| S-EPMC6131827 | biostudies-literature
Project description:BackgroundCadmium (Cd) exposure has been found to have detrimental effects on the development of the central nervous system and cognitive ability in children. However, there is ongoing debate regarding the impact of maternal Cd exposure on the cognitive ability of offspring. In this study, we aimed to investigate the mechanisms underlying the influence of maternal Cd exposure on the cognitive ability of offspring rats.MethodsHere, we constructed a model of cadmium poisoning in first-generation rats through gavage. The cognitive and memory abilities of its offspring were evaluated by water maze experiment. Then, we used the gene chip to find out the key genes, and we performed qRT-PCR detection of these genes. Subsequently, enrichment analysis was employed to identify pathways. Finally, we constructed a co-expression network consisting of LncRNAs and mRNAs to elucidate the biological functions and regulatory mechanisms of LncRNAs.ResultsThe results of the water maze trial demonstrated that the offspring of rats exposed to cadmium in the first generation had reduced cognitive and memory abilities. Through an analysis of gene expression in the hippocampus of the cadmium-treated rats' offspring and the control group, we identified a correlation between the islet secretion pathway and the cognitive impairment observed in the offspring. Utilizing various algorithms, we identified Cpa1 and Prss1 as potential key genes associated with the cognitive impairment caused by cadmium. The results of qRT-PCR demonstrated a decrease in the expression levels of these genes in the hippocampus of the cadmium-treated rats' offspring. In addition, in the co-expression network, we observed that Cpa1 was co-expressed with 11 LncRNAs, while Prss1 was associated with 4 unexplored LncRNAs. Furthermore, we conducted an analysis to examine the relationship between Cpa1, Prss1-related transcription factors, and LncRNAs.ConclusionOverall, this study provides novel insights into the molecular effects of first generation Cd exposure on the cognitive ability of offspring. The target genes and signaling pathways investigated in this study could serve as potential targets for improving neurodevelopment and cognitive ability in children.
| S-EPMC10823636 | biostudies-literature
Project description:Circular RNAs (circRNAs) are a recently identified class of non-coding RNAs that participate in multiple biological processes and tumour progression. However, circRNA expression pattern in parathyroid neoplasms remains unknown. The circRNA profile of 6 parathyroid carcinomas (PCs), 6 parathyroid adenomas (PAs) and 4 normal parathyroid tissues was assessed by a microarray. Bioinformatic analyses were performed to investigate potential core circRNAs via co-expression network. CircRNA and corresponding mRNA expression were validated in a cohort of parathyroid neoplasms by RT-qPCR and fluorescence in situ hybridization (FISH). Compared to normal parathyroid, 5310 and 1055 circRNAs were differentially expressed in PC and PA tissues, respectively. The differential expression of 4 circRNAs (hsa_circRNA_0035563 (p = 0.006), hsa_circRNA_0017545 (p = 0.009), hsa_circRNA_0001687 (p = 0.005) and hsa_circRNA_0075005 (p = 0.001)) and 4 mRNAs (MYC, FSCN1, ANXA2 and AKR1C3) between PC and PA tissues were confirmed by RT-qPCR. In addition, high expression of hsa_circ_0035563 was related to CDC73 mutations (p = 0.022) and recurrence in PC patients (p = 0.042). Furthermore, hsa_circ_0075005 helped distinguish PCs from benign lesions using FISH, and the area under the curve was 0.779 (p = 0.013). Our findings describe the circRNA profile of PC for the first time and suggest that circRNAs and mRNAs interact in parathyroid tumourigenesis. This study demonstrates that hsa_circ_0075005 and MYC mRNA may be used for the differential diagnosis of PC and PA. The expression levels of hsa_circ_0035563 are related to CDC73 mutations and recurrence in malignancy, highlighting the significance of this parameter in prognosis of PC patients.
| S-EPMC6693544 | biostudies-literature
Project description:AbstractPre-eclampsia (PE) is a common complication of pregnancy, associated with maternal and fetal morbidity and mortality. In this study, we aimed to explore important long non-coding RNAs (lncRNAs) and their possible mechanisms in PE.GSE60438 expression profile including 25 PE samples and 23 normal samples were obtained from gene expression omnibus (GEO) database. After normalization with betaqn package in R, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified using the limma package. Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway were analyzed using DAVID 6.7 and GSEA 3.0. LncRNAs-mRNAs coexpression was implemented using weighted gene co-expression network analysis (WGCNA). MicroRNAs linked with these DElncRNAs and DEmRNAs were predicted and a competitive endogenous RNA (ceRNA) network was built.A total of 53 DElncRNAs and 301 DEmRNAs were identified between control and PE samples. These DEmRNAs were enriched into pathways such as protein digestion and absorption, osteoclast differentiation. WGCNA constructed a lncRNA-mRNA coexpression network, among which SUMO1P3, NACAP1, NCF1C, ANXA2P1, GTF2IP1, NAPSB, OR7E37P were hub genes. ceRNA network was constructed together with microRNAs (miRNAs), and functional analysis indicated cellular membrane and sugar binding were involved in PE progression. Five lncRNAsANXA2P1, GTF2IP1, NACAP1, NCF1C and OR7E37P were successfully validated in our clinical specimens.The DElncRNAs, including ANXA2P1, GTF2IP1, NACAP1, NCF1C and OR7E37P might play important roles in PE. However, the exact mechanism of these lncRNAs in prediction and diagnosis of PE should be further explored.
| S-EPMC8036074 | biostudies-literature