Long non‑coding RNA TUG1 knockdown repressed the viability, migration and differentiation of osteoblasts by sponging miR‑214

Sequence pre-training-based graph neural network for predicting lncRNA-miRNA associations

MicroRNAs (miRNAs) silence genes by binding to messenger RNAs, whereas long non-coding RNAs (lncRNAs) act as competitive endogenous RNAs (ceRNAs) that can relieve miRNA silencing effects and upregulate target gene expression. The ceRNA association between lncRNAs and miRNAs has been a research hotspot due to its medical importance, but it is challenging to verify experimentally. In this paper, we propose a novel deep learning scheme, i.e. sequence pre-training-based graph neural network (SPGNN), that combines pre-training and fine-tuning stages to predict lncRNA-miRNA associations from RNA sequences and the existing interactions represented as a graph. First, we utilize a sequence-to-vector technique to generate pre-trained embeddings based on the sequences of all RNAs during the pre-training stage. In the fine-tuning stage, we use Graph Neural Network to learn node representations from the heterogeneous graph constructed using lncRNA-miRNA association information. We evaluate our proposed scheme SPGNN on our newly collected animal lncRNA-miRNA association dataset and demonstrate that combining the $k$-mer technique and Doc2vec model for pre-training with the Simple Graph Convolution Network for fine-tuning is effective in predicting lncRNA-miRNA associations. Our approach outperforms state-of-the-art baselines across various evaluation metrics. We also conduct an ablation study and hyperparameter analysis to verify the effectiveness of each component and parameter of our scheme. The complete code and dataset are available on GitHub: https://github.com/zixwang/SPGNN.

LncRNA TUG1 relieves renal mesangial cell injury by modulating the miR-153-3p/Bcl-2 axis in lupus nephritis

BACKGROUND

Lupus nephritis (LN) is one of the most common and serious complications of systemic lupus erythematosus. Our experiments aimed to evaluate the molecular mechanisms of long noncoding RNA (lncRNA) TUG1 in a human renal mesangial cell (HRMC) model of LN.

METHODS

Cells were treated with lipopolysaccharide (LPS) to induce inflammatory damage. StarBase, TargetScan, and a luciferase reporter assay were used to predict and confirm the interactions between lncRNA TUG1, miR-153-3p, and Bcl-2. We determined the lncRNA TUG1 and miR-153-3p levels in LPS-induced HRMCs using quantitative reverse transcription PCR (RT-qPCR). MTT and flow cytometry analyses were used to detect HRMC proliferation and apoptosis, respectively. In addition, the expression of the apoptosis-related proteins Bax and Bcl-2 was evaluated using western blot analysis and RT-qPCR. Lastly, the secretion of inflammatory cytokines (IL-1β, IL-6, and TNF-α) was assessed using ELISA.

RESULTS

miR-153-3p directly targeted lncRNA TUG1. The level of lncRNA TUG1 was remarkably lower and miR-153-3p expression was markedly higher in LPS-treated HRMCs than in untreated cells. Transfection with TUG1-plasmid relieved LPS-induced HRMC injury, as evidenced by increased cell viability, inhibited apoptotic cells, reduced Bax expression, increased Bcl-2 level, and reduced secretion of inflammatory cytokines. Importantly, these findings were reversed by miR-153-3p mimic. We also found that miR-153-3p directly targeted Bcl-2 and negatively regulated Bcl-2 expression in HRMCs. In addition, our findings suggest that miR-153-3p inhibitor relieved LPS-induced HRMC injury via the upregulation of Bcl-2.

CONCLUSION

lncRNA TUG1 alleviated LPS-induced HRMC injury through regulation of the miR-153-3p/Bcl-2 axis in LN.

Functions of the bone morphogenetic protein signaling pathway through non-coding RNAs

Bone morphogenetic proteins (BMPs) are proteins of the transforming growth factor-β (TGF-β) family, which plays an important role in the formation of skeletal and cartilage tissue and their regeneration. BMPs play a key role in the formation of new blood vessels and promote the migration, proliferation, and differentiation of mesenchymal stem cells (MSCs) into chondroblasts and osteoblasts. It is known that malfunction of BMPs signaling can cause a disease state. Epigenetic regulation of expression plays a key role in the control of many cellular processes. Important participants in this regulation are non-coding RNAs (ncRNAs), which are RNA molecules that are not translated into proteins. The best known of these are microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). In addition, the results of many studies make it possible to establish an unambiguous functional relationship between these ncRNAs. Being involved in the regulation of a large number of target genes responsible for the life of the cell, miRNAs, lncRNAs, and circRNAs are essential for the normal development and functioning of the body, and the violation of their functions accompanies the development of many pathophysiological processes including oncogenesis. In the present review, we discuss different insights into the regulation of BMPs signaling pathway by miRNAs, lncRNAs and circRNAs governed.

Downregulation of miR-221-3p by LncRNA TUG1 Promoting the Healing of Closed Tibial Fractures in Mice

Objective

To probe into the effect of LncRNA TUG1 on the healing of closed tibial fracture in mice.

Methods

The closed tibial fracture model of mice was established, selecting the mouse osteoblast line MC3T3-E1, with the cells separated into four groups. The expression levels of TUG1 and miR-221-3p were determined by RT-qPCR analysis, with the targeting relationship between TUG1 and miR-221-3p authenticated by dual luciferase reporter (DLR) assay, detection of cell migration (CM) ability based on Transwell cell migration (TCM) assay, and cell proliferation (CP) acquired by cell counting kit-8 (CCK-8).

Results

Prediction results of the target gene by bioinformatics software showed that miR-221-3p had binding sites with the 3'-UTR of TUG1, and DLR assay authenticated the targeting relationship between LncRNA TUG1 and miR-221-3p. Downregulation of TUG1 inhibited osteoblast CP and CM and promoted osteoblast cell apoptosis (CA). Cell cycle analysis indicated that miR-221-3p provoked cell cycle arrest in G1 stage of MC3T3-E1 cells. The siLncRNA-NC group had higher anticyclin D1 and D3 levels than the siLncRNA TUG1 group, with a lower CA rate in the former, implying that miR-221-3p overexpression inhibited osteoblast CP and CM and LncRNA TUG1 inhibited CA. Downregulation of miR-221-3p partly reversed the retardation out of downregulating TUG1 on osteoblast CP and CM. Bcl-2 level was higher in the LncRNA TUG1 group compared to the siLncRNA TUG1 and miR-221-3p overexpression groups, with remarkably lower SDF-1 level in the miR-221-3p overexpression group than those in the control, miRNA-NC, and LncRNA TUG1 groups.

Conclusion

The downregulation of miR-221-3p by LncRNA TUG1 can promote the healing of closed tibial fractures in mice.