Identification of Pivotal Genes and Pathways in Osteoarthritic Degenerative Meniscal Lesions via Bioinformatics Analysis of the GSE52042 Dataset

Gene expression analyses in mouse sensory ganglia determine a crucial role of NGF/TrkA in knee osteoarthritis chronification

OBJECTIVE

Osteoarthritis (OA) can be experimentally induced by injecting mono-iodoacetate (MIA) in the knee capsule of mice. Our aim was to assess the role of NGF/TrkA axis in OA identifying differentially expressed genes (DEGs) and functional pathways in knee-innervating dorsal root ganglia (DRG) from WT and hypersensitive TrkAP782S (KI) mice after MIA injection.

METHOD

We performed saline or MIA-injection in knee joints of WT and KI mice and harvested L3-L5 DRGs at 5 and 21 days after injection, pooling males and females (n = 4/group). RNA was extracted and microarray analysis was performed. Upon comparisons between different groups, identification of DEGs was defined as adjusted P < 0.01. Gene ontology, pathway analysis and protein interactions were conducted using Gene Set Enrichment Analysis over Gene Ontology and REACTOME databases, and STRING database.

RESULTS

For each comparison regarding genotype (WT vs KI), numerous DEGs were identified but with limited overlap, being Lingo1, Socs2, and Slc4a4 already related to pain, OA and/or NGF/TrkA axis. Regarding comparisons of early vs late OA (D5 vs D21), many more DEGs were revealed including genes previously implicated in OA such as Gal, Gja1, and Lep. Moreover, we found enriched pathways in the KI_MIA group such as gene expression, neuronal system and signal transduction, in which NTRK1 and MAPK pathways indicate specificity in the NGF/TrkA axis and in the transition from early to late OA pain.

CONCLUSIONS

Our results identify new mouse DEGs and pathways that demonstrate the relevance of the NGF/TrkA system in the chronification of OA pain.

Impact of LITAF on Mitophagy and Neuronal Damage in Epilepsy via MCL-1 Ubiquitination

OBJECTIVE

This study aims to investigate how the E3 ubiquitin ligase LITAF influences mitochondrial autophagy by modulating MCL-1 ubiquitination, and its role in the development of epilepsy.

METHODS

Employing single-cell RNA sequencing (scRNA-seq) to analyze brain tissue from epilepsy patients, along with high-throughput transcriptomics, we identified changes in gene expression. This was complemented by in vivo and in vitro experiments, including protein-protein interaction (PPI) network analysis, western blotting, and behavioral assessments in mouse models.

RESULTS

Neuronal cells in epilepsy patients exhibited significant gene expression alterations, with increased activity in apoptosis-related pathways and decreased activity in neurotransmitter-related pathways. LITAF was identified as a key upregulated factor, inhibiting mitochondrial autophagy by promoting MCL-1 ubiquitination, leading to increased neuronal damage. Knockdown experiments in mouse models further confirmed that LITAF facilitates MCL-1 ubiquitination, aggravating neuronal injury.

CONCLUSION

Our findings demonstrate that LITAF regulates MCL-1 ubiquitination, significantly impacting mitochondrial autophagy and contributing to neuronal damage in epilepsy. Targeting LITAF and its downstream mechanisms may offer a promising therapeutic strategy for managing epilepsy.

Short-term response of primary human meniscus cells to simulated microgravity

BACKGROUND

Mechanical unloading of the knee articular cartilage results in cartilage matrix atrophy, signifying the osteoarthritic-inductive potential of mechanical unloading. In contrast, mechanical loading stimulates cartilage matrix production. However, little is known about the response of meniscal fibrocartilage, a major mechanical load-bearing tissue of the knee joint, and its functional matrix-forming fibrochondrocytes to mechanical unloading events.

METHODS

In this study, primary meniscus fibrochondrocytes isolated from the inner avascular region of human menisci from both male and female donors were seeded into porous collagen scaffolds to generate 3D meniscus models. These models were subjected to both normal gravity and mechanical unloading via simulated microgravity (SMG) for 7 days, with samples collected at various time points during the culture.

RESULTS

RNA sequencing unveiled significant transcriptome changes during the 7-day SMG culture, including the notable upregulation of key osteoarthritis markers such as COL10A1, MMP13, and SPP1, along with pathways related to inflammation and calcification. Crucially, sex-specific variations in transcriptional responses were observed. Meniscus models derived from female donors exhibited heightened cell proliferation activities, with the JUN protein involved in several potentially osteoarthritis-related signaling pathways. In contrast, meniscus models from male donors primarily regulated extracellular matrix components and matrix remodeling enzymes.

CONCLUSION

These findings advance our understanding of sex disparities in knee osteoarthritis by developing a novel in vitro model using cell-seeded meniscus constructs and simulated microgravity, revealing significant sex-specific molecular mechanisms and therapeutic targets.

TPX2 upregulates MMP13 to promote the progression of lipopolysaccharide-induced osteoarthritis

Purpose

This study seeks to identify potential clinical biomarkers for osteoarthritis (OA) using bioinformatics and investigate OA mechanisms through cellular assays.

Methods

Differentially Expressed Genes (DEGs) from GSE52042 (four OA samples, four control samples) were screened and analyzed with protein-protein interaction (PPI) analysis. Overlapping genes in GSE52042 and GSE206848 (seven OA samples, and seven control samples) were identified and evaluated using Gene Set Enrichment Analysis (GSEA) and clinical diagnostic value analysis to determine the hub gene. Finally, whether and how the hub gene impacts LPS-induced OA progression was explored by in vitro experiments, including Western blotting (WB), co-immunoprecipitation (Co-IP), flow cytometry, etc.

Result

Bioinformatics analysis of DEGs (142 up-regulated and 171 down-regulated) in GSE52042 identified two overlapping genes (U2AF2, TPX2) that exhibit significant clinical diagnostic value. These genes are up-regulated in OA samples from both GSE52042 and GSE206848 datasets. Notably, TPX2, which AUC = 0.873 was identified as the hub gene. In vitro experiments have demonstrated that silencing TPX2 can alleviate damage to chondrocytes induced by lipopolysaccharide (LPS). Furthermore, there is a protein interaction between TPX2 and MMP13 in OA. Excessive MMP13 can attenuate the effects of TPX2 knockdown on LPS-induced changes in OA protein expression, cell growth, and apoptosis.

Conclusion

In conclusion, our findings shed light on the molecular mechanisms of OA and suggested TPX2 as a potential therapeutic target. TPX2 could promote the progression of LPS-induced OA by up-regulating the expression of MMP13, which provides some implications for clinical research.

Paeoniflorin, the Main Monomer Component of Paeonia lactiflora, Exhibits Anti-inflammatory Properties in Osteoarthritis Synovial Inflammation

OBJECTIVE

To explore the mechanism of paeoniflorin (PF) on osteoarthritis (OA) synovial inflammation from network pharmacology to experimental pharmacology.

METHODS

Targets of OA were constructed by detecting the database of network database platforms (Therapeutic Target database, DrugBank and GeneCards), and the targets of PF were constructed by PubChem and Herbal Ingredients' Targets database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these co-targeted genes were conducted via Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, and protein-protein interaction (PPI) networks were conducted via the search tool for the retrieval of interacting genes (STRING) database. Cell counting kit-8 (CCK-8) assay was performed to assess the potential toxicity of PF on human OA fibroblast-like synoviocytes (FLS), quantitative real-time polymerase chain reaction (qPCR), enzyme-linked immunosorbent assay (ELISA) and Western blot were used to verify the potential mechanism of PF in synovial inflammation.

RESULTS

Twenty-six co-targeted genes were identified. GO enrichment results showed that these co-targeted genes were most likely localized in the cytoplasm, and the biological processes mainly involved 'cellular response to hypoxia' 'lipopolysaccharide (LPS)-mediated signaling pathway' and 'positive regulation of gene expression'. KEGG pathway analysis indicated that these co-targeted genes may function through pathways associated with 'hypoxia-inducible factor-1 (HIF-1) signaling pathway' and 'tumor-necrosis factor (TNF) signaling pathway'. The PPI network showed that the top 3 hub genes were TP53, TNF, and CASP3. Molecular docking results showed that PF was well docking with TNF. CCK-8 showed no potential toxicity of 10, 20 and 50 µmol/L PF on human OA FLS. And PF significantly decreased the expression levels of interleukin-1 β, interleukin-6, TNF-α matrix metalloproteinase 13 (MMP13), and a disintegrin and metalloproteinase with thrombospondin motifs 5 (ADAMTS5) and TNF-α in LPS-induced OA FLS.

CONCLUSION

PF exhibited potent anti-inflammatory effect in OA synovial inflammation.

Screening crucial lncRNAs and genes in osteoarthritis by integrated analysis

BACKGROUND

Osteoarthritis (OA) is one of the most frequent chronic diseases with high morbidity worldwide, marked by degradation of the cartilage and bone, joint instability, stiffness, joint space stenosis and subchondral sclerosis. Due to the elusive mechanism of osteoarthritis (OA), we aimed to identify potential markers for OA and explore the molecular mechanisms underlying OA.

METHODS

Expression profiles data of OA were collected from the Gene Expression Omnibus database to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in OA. Functional annotation and protein-protein interaction (PPI) networks were performed. Then, nearby DEmRNAs of DElncRNAs was obtained. Moreover, GO and KEGG pathway enrichment analysis of nearby DEmRNAs of DElncRNAs was performed. Finally, expression validation of selected mRNAs and lncRNAs was performed by quantitative reverse transcriptase-polymerase chain reaction.

RESULTS

In total, 2080 DEmRNAs and 664 DElncRNAs were determined in OA. PI3K-Akt signaling pathway, Endocytosis and Rap1 signaling pathway were significantly enriched KEGG pathways in OA. YWHAB, HSPA8, NEDD4L and SH3KBP1 were four hub proteins in PPI network. The AC093484.4/TRPV2 interact pair may be involved in the occurrence and development of OA.

CONCLUSION

Our study identified several DEmRNAs and DElncRNAs associated with OA. The molecular characters could provide more information for further study on OA.

A Study on the Potential Mechanism of Shujin Dingtong Recipe against Osteoarthritis Based on Network Pharmacology and Molecular Docking

Background. With the aging of the social population, Osteoarthritis (OA) has already become a vital health and economic problem globally. Shujin Dingtong recipe (SJDTR) is an effective formula to treat OA in China. Although studies have shown that SJDTR can significantly alleviate OA symptoms, its mechanism still remains unclear. Purpose. This study is aimed at investigating the potential mechanism of SJDTR for the treatment of OA based on network pharmacology and molecular docking. Methods. Main ingredients of SJDTR were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. OA disease targets were obtained from the Gene Expression Omnibus (GEO) database. The overlapped targets and signaling pathways were explored using Protein-Protein Interaction (PPI) network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). Following this, the core targets were employed to dock with corresponding components via molecular docking in order to further explore the mechanism of SJDTR in the treatment of OA. Results. From network pharmacology, we found 100 active components of SJDTR, 31 drug and OA-related targets, 1161 GO items, and 91 signaling pathways. Based on the analysis with PPI network and molecular docking, TP53, CCNB1, and MMP-2 were selected for the core targets of SJDTR against OA. Molecular docking demonstrated that Quercetin, Baicalein, and Luteolin, had good binding with the TP53, CCNB1, and MMP-2 protein, respectively. Conclusion. To conclude, our study suggested the main ingredients of SJDTR might alleviate the progression of OA through multiple targets and pathways. Additionally, network pharmacology and molecular docking, as new approaches, were adopted for systematically exploring the potential mechanism of SJDTR for the treatment of OA.

The molecular characteristics in different procedures of spermatogenesis

Spermatogenesis is a multistep biological process. In addition to somatic cells, it involves the orderly differentiation of dozens of spermatogenic cells. In this process, the regulatory networks between different spermatogenic cell populations are significantly different. RNA m6A regulators and miRNAs have been found to be closely related to spermatogenesis in recent years, and they are an important part of the above regulatory networks. Understanding gene expression and its rules in different spermatogenic cell populations will help in the in-depth exploration of their detailed roles in spermatogenesis. This study collected a public dataset of nonobstructive azoospermia (NOA). Based on the Johnson score, the testicular samples of NOA were divided into three types, Sertoli-cell only syndrome, meiotic arrest and postmeiotic arrest, which represented the loss of three germ cell populations, including whole spermatogenic cells, postmeiotic spermatogenic cells, and a mixture of late spermatids and spermatozoa, respectively. The aforementioned three types of testis data were compared with normal testis data, and the molecular expression characteristics of the abovementioned three germ cell populations were obtained. Our study showed that different germ cell populations have different active molecules and their pathways. In addition, RNA m6A regulators, including METTL3, IGF2BP2 and PRRC2A, and miRNAs, including hsa-let-7a-2, hsa-let-7f-1, hsa-let-7g, hsa-miR-15a, hsa-miR-197, hsa-miR-21, hsa-miR-30e, hsa-miR-32, hsa-miR-503 and hsa-miR-99a, also presented regulatory roles in almost all germ cells.

Long-term dynamic compression enhancement TGF-β3-induced chondrogenesis in bovine stem cells: a gene expression analysis

Background

Bioengineering has demonstrated the potential of utilising mesenchymal stem cells (MSCs), growth factors, and mechanical stimuli to treat cartilage defects. However, the underlying genes and pathways are largely unclear. This is the first study on screening and identifying the hub genes involved in mechanically enhanced chondrogenesis and their potential molecular mechanisms.

Methods

The datasets were downloaded from the Gene Expression Omnibus (GEO) database and contain six transforming growth factor-beta-3 (TGF-β3) induced bovine bone marrow-derived MSCs specimens and six TGF-β3/dynamic-compression-induced specimens at day 42. Screening differentially expressed genes (DEGs) was performed and then analysed via bioinformatics methods. The Database for Annotation, Visualisation, and Integrated Discovery (DAVID) online analysis was utilised to obtain the Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment. The protein-protein interaction (PPI) network of the DEGs was constructed based on data from the STRING database and visualised through the Cytoscape software. The functional modules were extracted from the PPI network for further analysis.

Results

The top 10 hub genes ranked by their connection degrees were IL6, UBE2C, TOP2A, MCM4, PLK2, SMC2, BMP2, LMO7, TRIM36, and MAPK8. Multiple signalling pathways (including the PI3K-Akt signalling pathway, the toll-like receptor signalling pathway, the TNF signalling pathway, and the MAPK pathway) may impact the sensation, transduction, and reaction of external mechanical stimuli.

Conclusions

This study provides a theoretical finding showing that gene UBE2C, IL6, and MAPK8, and multiple signalling pathways may play pivotal roles in dynamic compression-enhanced chondrogenesis.

Identification of Novel Targets of Knee Osteoarthritis Shared by Cartilage and Synovial Tissue

Arthritis is the leading cause of disability among adults, while osteoarthritis (OA) is the most common form of arthritis that results in cartilage loss. However, accumulating evidence suggests that the protective hyaline cartilage should not be the sole focus of OA treatment. Particularly, synovium also plays essential roles in OA's initiation and progression and warrants serious consideration when battling against OA. Thus, biomarkers with similar OA-responsive expressions in cartilage and synovium should be the potential targets for OA treatment. On the other hand, molecules with a distinguished response during OA in cartilage and synovium should be ruled out as OA therapeutic(s) to avoid controversial effects in different tissues. Here, to pave the path for developing a new generation of OA therapeutics, two published transcriptome datasets of knee articular cartilage and synovium were analyzed in-depth. Genes with statistically significantly different expression in OA and healthy cartilage were compared with those in the synovium. Thirty-five genes with similar OA-responsive expression in both tissues were identified while recognizing three genes with opposite OA-responsive alteration trends in cartilage and synovium. These genes were clustered based on the currently available knowledge, and the potential impacts of these clusters in OA were explored.

New insights into the potential mechanisms of spermatogenic failure in patients with idiopathic azoospermia

Idiopathic azoospermia (IA) refers to azoospermia without a clear aetiology. Due to the unclear aetiology and pathological mechanism of IA, there is no effective treatment for IA. The development of assisted reproductive and microsperm extraction technologies has brought hope to patients with IA with fertility problems. However, there are still many patients with IA whose testes lack healthy sperm, causing infertility. Therefore, it is key to identify how testicular spermatogenic failure can be reversed to promote spermatogenesis in patients with IA to resolve fertility problems; these goals are a great challenge in reproductive medicine. The underlying genetic factors seem to be important pathological factors of IA. Understanding the role of genetic factors in the pathological mechanism of spermatogenic failure in patients with IA is of great value for future studies and treatments and is also an important reference for the reproductive health of males and their offspring. A method combining sequencing technology and bioinformatics analysis is an important means to understand the genetic pathological mechanisms. We used bioinformatics analysis to study the public human IA dataset. We found that the pathogenic mechanism of IA may be related to abnormal ciliary structure and function and disrupted RNA metabolism in spermatogenic cells. Disrupted m6A regulation of spermatogenesis may be an important pathological mechanism of IA and warrants attention. Finally, we screened for key genes and potential therapeutic drugs to determine future research directions.