Prediction of a Potential Mechanism of Intervertebral Disc Degeneration Based on a Novel Competitive Endogenous RNA Network

microRNA-9a-5p disrupts the ELAVL1/VEGF axis to alleviate traumatic brain injury

Plasma microRNA (miR)-9 has been identified as a promising diagnostic biomarker for traumatic brain injury (TBI). This study aims to investigate the possible role and mechanisms of miR-9a-5p affecting TBI. Microarray-based gene expression profiling of TBI was used for screening differentially expressed miRNAs and genes. TBI rat models were established. miR-9a-5p, ELAVL1 and VEGF expression in the brain tissue of TBI rats was detected. The relationship among miR-9a-5p, ELAVL1 and VEGF was tested. TBI modeled rats were injected with miR-9a-5p-, ELAVL1 or VEGF-related sequences to identify their effects on TBI. miR-9a-5p was poorly expressed in the brain tissue of rats with TBI. ELAVL1 was a downstream target gene of miR-9a-5p, which could negatively regulate its expression. Enforced miR-9a-5p expression prevented brain tissue damage in TBI rats by targeting ELAVL1. Meanwhile, ELAVL1 could increase the expression of VEGF, which was highly expressed in the brain tissue of rats with TBI. In addition, ectopically expressed miR-9a-5p alleviated brain tissue damage in TBI rats by downregulating the ELAVL1/VEGF axis. Overall, miR-9a-5p can potentially reduce brain tissue damage in TBI rats by targeting ELAVL1 and down-regulating VEGF expression.

GAS5, a long noncoding RNA, contributes to annulus fibroblast osteogenic differentiation and apoptosis in intervertebral disk degeneration via the miR-221-3p/SOX11 axis

miR-221-3p has been reported to attenuate the osteogenic differentiation of annulus fibrosus cells (AFs), which has been implicated in intervertebral disk degeneration (IVDD) development. This study aimed to elucidate miR-221-3p's role in osteogenic differentiation and apoptosis of AFs in an IVDD model. After successfully establishing an IVDD rat model by annulus fibrosus needle puncture, AFs were isolated. Bioinformatics, dual-luciferase reporter, and AGO2-RNA immunoprecipitation (RIP) assays predicted and confirmed the potential miR-221-3p lncRNA and gene target. Functional analyses were performed after AF transfection to explore the roles of the identified lncRNA and gene. Western blotting, Alkaline phosphatase (ALP), and Alizarin red and TUNEL staining were performed to investigate AF apoptosis and osteogenic differentiation with different transfections. Compared with AFs isolated from sham rats, IVDD-isolated Afs exhibited stronger osteogenic potential and higher apoptosis rates accompanied by miR-221-3p downregulation. The growth arrest-specific transcript 5 (GAS5) was identified as miR-221-3p's target lncRNA, which was highly expressed in IVDD. GAS5 overexpression facilitated AF apoptosis and osteogenic differentiation, whereas silencing GAS5 had the opposite effect. SRY box-related11 (SOX11) was identified as a downstream miR-221-3p target gene in IVDD. GASS silencing-induced suppression of AF apoptosis and osteogenic differentiation could be reversed by SOX11 overexpression. Our findings uncovered a lncRNA GAS5/miR-221-3p/SOX11 axis in Afs under IVDD, which may help implement novel IVDD therapeutic strategies.

Identification of novel gene signatures and immune cell infiltration in intervertebral disc degeneration using bioinformatics analysis

Background: Intervertebral disc degeneration (IDD) is the leading cause of lower back pain, and an overall understanding of the molecular mechanisms related to IDD is still lacking. The purpose of this study was to explore gene signatures and immune cell infiltration related to IDD via bioinformatics analysis. Methods: A total of five expression profiles of mRNA and non-coding RNA were downloaded from the Gene Expression Omnibus (GEO) database. The potentially involved lncRNA/circRNA-miRNA-mRNA networks and protein-protein interaction networks were constructed by miRNet, circBank, STRING, and the Cytoscape database. Gene ontology, Kyoto Encyclopaedia of Genes and Genomes Analysis, Gene Set Enrichment Analysis, Gene Set Variation Analysis, Immune Infiltration Analysis, and Drug-Gene Interaction were used to analyse the top 20 hub genes. RT-qPCR was conducted to confirm the 12 differential expressions of genes both in the nucleus pulposus and annulus fibrosus tissues Results: There were 346 differentially expressed mRNAs, 12 differentially expressed miRNAs, 883 differentially expressed lncRNAs, and 916 differentially expressed circRNAs in the GEO database. Functional and enrichment analyses revealed hub genes associated with platelet activation, immune responses, focal adhesion, and PI3K-Akt signalling. The apoptotic pathway, the reactive oxygen species pathway, and oxidative phosphorylation play an essential role in IDD. Immune infiltration analysis demonstrated that the Treg cells had significant infiltration, and three levels of immune cells, including dendritic cells, Th2 cells, and tumour-infiltrating lymphocytes, were inhibited in IDD. Drug-gene interaction analysis showed that COL1A1 and COL1A2 were targeted by collagenase clostridium histolyticum, ocriplasmin, and PDGFRA was targeted by 66 drugs or molecular compounds. Finally, 24 cases of IDD tissues and 12 cases of normal disc tissues were collected, and the results of RT-qPCR were consistent with the bioinformatics results. Conclusion: Our data indicated that the 20 hub genes and immune cell infiltration were involved in the pathological process of IDD. In addition, the PDGFRA and two potential drugs were found to be significant in IDD development.

LncRNA miR663AHG represses the development of colon cancer in a miR663a-dependent manner

The MIR663AHG gene encodes both miR663AHG and miR663a. While miR663a contributes to the defense of host cells against inflammation and inhibits colon cancer development, the biological function of lncRNA miR663AHG has not been previously reported. In this study, the subcellular localization of lncRNA miR663AHG was determined by RNA-FISH. miR663AHG and miR663a were measured by qRT-PCR. The effects of miR663AHG on the growth and metastasis of colon cancer cells were investigated in vitro and in vivo. CRISPR/Cas9, RNA pulldown, and other biological assays were used to explore the underlying mechanism of miR663AHG. We found that miR663AHG was mainly distributed in the nucleus of Caco2 and HCT116 cells and the cytoplasm of SW480 cells. The expression level of miR663AHG was positively correlated with the level of miR663a (r = 0.179, P = 0.015) and significantly downregulated in colon cancer tissues relative to paired normal tissues from 119 patients (P < 0.008). Colon cancers with low miR663AHG expression were associated with advanced pTNM stage (P = 0.021), lymph metastasis (P = 0.041), and shorter overall survival (hazard ratio = 2.026; P = 0.021). Experimentally, miR663AHG inhibited colon cancer cell proliferation, migration, and invasion. The growth of xenografts from RKO cells overexpressing miR663AHG was slower than that of xenografts from vector control cells in BALB/c nude mice (P = 0.007). Interestingly, either RNA-interfering or resveratrol-inducing expression changes of miR663AHG or miR663a can trigger negative feedback regulation of transcription of the MIR663AHG gene. Mechanistically, miR663AHG could bind to miR663a and its precursor pre-miR663a, and prevent the degradation of miR663a target mRNAs. Disruption of the negative feedback by knockout of the MIR663AHG promoter, exon-1, and pri-miR663A-coding sequence entirely blocked these effects of miR663AHG, which was restored in cells transfected with miR663a expression vector in rescue experiment. In conclusion, miR663AHG functions as a tumor suppressor that inhibits the development of colon cancer through its cis-binding to miR663a/pre-miR663a. The cross talk between miR663AHG and miR663a expression may play dominant roles in maintaining the functions of miR663AHG in colon cancer development.

Method for the Isolation of "RNA-seq-Quality" RNA from Human Intervertebral Discs after Mortar and Pestle Homogenization

The problem of isolating high-quality total RNA from intervertebral discs has no recognized solution yet. This is due to the extremely low content of live cells in the samples and the voluminous intercellular matrix. A variety of published protocols focused on isolating RNA from articular cartilage have recommended the use of expensive equipment, enzymatic matrix cleavage, or cell culture. In our study, we used a combination of the traditional QIAzol protocol (Qiagen, Germany) and RNEasy column purification (Qiagen, Germany) to obtain high-quality RNA from post-surgical intervertebral disc fragments. Only a mortar and a pestle were used for grinding, making our method particularly accessible. The isolated RNA with a RIN of ~7 is suitable for studying the expression profile of chondrocytes in situ. RNA-seq analysis of three samples demonstrated cell type ratios to be mostly relevant to intervertebral disc tissues, with over 70% of the chondrocytes of the three subtypes having an admixture of blood-related cells.

Comprehensive analysis of potential ceRNA network and immune cell infiltration in intervertebral disc degeneration

Background

Intervertebral disc degeneration (IDD) has become a serious public health problem, the mechanism of which is complex and still unclear. We aimed to construct a ceRNA network related to IDD to explore its pathogenesis.

Methods

We downloaded the GSE67566, GSE63492, GSE116726 and GSE124272 datasets from GEO database, and obtained the differentially expressed RNAs. Then, we constructed a ceRNA network and the KEGG and GO enrichment analysis were performed. Finally, we performed immune cell infiltration analysis on the GSE124272 dataset and analysed the correlation between immune cell abundance and hub genes expression levels.

Results

The ceRNA network included three down-regulated circRNAs: hsa_circ_0074817, hsa_circ_0002702, hsa_circ_0003600, three up-regulated miRNAs: hsa-miR-4741, hsa-miR-3158-5p, hsa-miR-508-5p, and 57 down-regulated mRNAs, including six hub genes: IGF1, CHEK1, CCNB1, OIP5, BIRC5, AR. GO and KEGG analysis revealed that the network is involved in various biological functions. Immune infiltration analysis showed that IDD was closely related to immune cell infiltration, and hub genes could further affect the development of IDD by affecting immune cell infiltration.

Conclusion

This study identified the hsa_circ_0074817-hsa-miR-508-5p-IGF1/CHEK1/CCNB1, the hsa_circ_0003600-hsa-miR-4741-BIRC5/OIP5/AR and the hsa_circ_0002702-hsa-miR-3158-5p-IGF1/AR as important regulatory axis of IDD, which will help us gain further insight into the pathogenesis of IDD and determine potential therapeutic targets.

Long Non-Coding RNAs Might Regulate Phenotypic Switch of Vascular Smooth Muscle Cells Acting as ceRNA: Implications for In-Stent Restenosis

Coronary in-stent restenosis is a late complication of angioplasty. It is a multifactorial process that involves vascular smooth muscle cells (VSMCs), endothelial cells, and inflammatory and genetic factors. In this study, the transcriptomic landscape of VSMCs’ phenotypic switch process was assessed under stimuli resembling stent injury. Co-cultured contractile VSMCs and endothelial cells were exposed to a bare metal stent and platelet-derived growth factor (PDGF-BB) 20 ng/mL. Migratory capacity (wound healing assay), proliferative capacity, and cell cycle analysis of the VSMCs were performed. RNAseq analysis of contractile vs. proliferative VSMCs was performed. Gene differential expression (DE), identification of new long non-coding RNA candidates (lncRNAs), gene ontology (GO), and pathway enrichment (KEGG) were analyzed. A competing endogenous RNA network was constructed, and significant lncRNA–miRNA–mRNA axes were selected. VSMCs exposed to “stent injury” conditions showed morphologic changes, with proliferative and migratory capacities progressing from G0-G1 cell cycle phase to S and G2-M. RNAseq analysis showed DE of 1099, 509 and 64 differentially expressed mRNAs, lncRNAs, and miRNAs, respectively. GO analysis of DE genes showed significant enrichment in collagen and extracellular matrix organization, regulation of smooth muscle cell proliferation, and collagen biosynthetic process. The main upregulated nodes in the lncRNA-mediated ceRNA network were PVT1 and HIF1-AS2, with downregulation of ACTA2-AS1 and MIR663AHG. The PVT1 ceRNA axis appears to be an attractive target for in-stent restenosis diagnosis and treatment.

Long non-coding RNA RP11-342L8.2, derived from RNA sequencing and validated via RT-qPCR, is upregulated and correlates with disease severity in psoriasis patients

OBJECTIVE

This study aimed to explore the dysregulated long non-coding RNA (lncRNA) expression profile in psoriatic tissue vs. normal skin tissue via RNA sequencing (RNA-seq), then further sort candidate lncRNAs to be validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR), in order to investigate the comprehensive linkage of lncRNA with psoriasis.

METHODS

Twenty-five psoriasis patients were consecutively enrolled, with their psoriatic and surrounding normal skin tissues obtained. Ten pairs of psoriatic and normal tissues were proposed to RNA-seq. Then, top 6 differentially expressed lncRNAs (DElncRNA) were sorted as candidate lncRNAs for validation by RT-qPCR in 25 pairs of samples.

RESULTS

Principal component analysis (PCA) exhibited that lncRNA profile clearly distinguished psoriatic tissue from normal tissue, so did heatmap. Volcano plot disclosed 412 upregulated and 625 downregulated DElncRNAs in psoriatic tissue vs. normal tissue. Gene Ontology (GO) and Kyoko Encyclopedia of Genes and Genomes (KEGG) enrichment analyses exhibited that these DElncRNAs were mainly enriched in immune, inflammation, or proliferation-related biological processes and pathways such as neutrophil degranulation, regulation of immune response, positive regulation of cell proliferation, and MAPK signaling pathway. By RT-qPCR validation, lncRNAs RP11-22A3.2, RP11-342L8.2, and CTD-2006H14.2 were increased (all P < 0.001), while lncRNAs AP000442.4, CCDC144NL-AS1, and MIR663AHG were decreased (all P < 0.01) in psoriatic tissue vs. normal tissue. Interestingly, psoriatic lncRNA RP11-342L8.2 was also observed to positively correlated with psoriasis area and severity index (PASI) (r = 0.405, P = 0.045).

CONCLUSION

Our present study exhibits some evidence for the landscape of lncRNAs implicated in psoriasis.