Identification of Novel Genes in Osteoarthritic Fibroblast-Like Synoviocytes Using Next-Generation Sequencing and Bioinformatics Approaches

MicroRNA signature for early prediction of knee osteoarthritis structural progression using integrated machine and deep learning approaches

OBJECTIVE

Conventional methodologies are ineffective in predicting the rapid progression of knee osteoarthritis (OA). MicroRNAs (miRNAs) show promise as biomarkers for patient stratification. We aimed to develop a miRNA prognosis model for identifying knee OA structural progressors/non-progressors using integrated machine/deep learning tools.

METHODS

Baseline serum miRNAs from Osteoarthritis Initiative (OAI) participants were isolated and sequenced. Participants were categorized based on their likelihood of knee structural progression/non-progression using magnetic resonance imaging and X-ray data. For prediction model development, 152 OAI participants (91 progressors, 61 non-progressors) were used. MiRNA features were reduced through VarClusHi clustering. Key miRNAs and OA determinants (age, sex, body mass index, race) were identified using seven machine learning tools. The final prediction model was developed using advanced machine/deep learning techniques. Model performance was assessed with area under the curve (AUC) (95% confidence intervals) and accuracy. Monte Carlo cross-validation ensured robustness. Model validation used 30 OAI baseline plasma samples from an independent set of participants (14 progressors, 16 non-progressors).

RESULTS

Feature clustering selected 107 miRNAs. Elastic Net was chosen for feature selection. An optimized prediction model based on an Artificial Neural Network comprising age and four miRNAs (hsa-miR-556-3p, hsa-miR-3157-5p, hsa-miR-200a-5p, hsa-miR-141-3p) exhibited excellent performance (AUC, 0.94 [0.89, 0.97]; accuracy, 0.84 [0.77, 0.89]). Model validation performance (AUC, 0.81 [0.63, 0.92]; accuracy, 0.83 [0.66, 0.93]) demonstrated the potential for generalization.

CONCLUSION

This study introduces a novel miRNA prognosis model for knee OA patients at risk of structural progression. It requires five baseline features, demonstrates excellent performance, is validated with an independent set, and holds promise for future personalized therapeutic monitoring.

MiR203a-3p as a potential biomarker for synovial pathology associated with osteoarthritis: a pilot study

BACKGROUND

Osteoarthritis (OA) is a degenerative musculoskeletal disease that significantly impacts the quality of life. Currently, no validated biomarkers for early detection of OA are defined. The possibility of discovering OA biomarkers is the focus of this study.

METHODS

Human primary OA synovial cells (SVs), isolated from discarded joint tissue of patients with Kellgren & Lawrence score (KL) < 3, (mild/moderate) and KL ≥ 3 (severe), were characterized by FACS analysis. Through qRT-PCR and ELISA assays the inflammation, fibrosis status and the different miRNAs expression has been investigated. The role of miR-203a-3p and its precursors were evaluated through gain and loss of function study, IL-1β synoviocytes treatments and methylation analysis of miR203a promoter. The qRT-PCR analysis of miR203a-3p and pre-miR203a on plasma (isolated 24 h before surgery, 3 days and 1 month after surgery) and synovial fluid (recovered during the surgery) were done to support our in vitro data.

RESULTS

MiR203a-3p expression is inversely correlated with the aggressiveness of OA, modulating the expression of epithelial to mesenchymal transition (EMT) and pro-inflammatory factors, as well as regulating the expression of secreted protein acidic and rich in cysteine (SPARC) mRNA. Methylation analysis of the miR203a promoter and SVs IL-1β treatment's highlighted the impact of inflammation on miR203a-3p and pre-miR203a expression; as confirmed by both miRNAs detection in biological fluids derived from patients with severe OA.

CONCLUSION

Our preliminary results suggest that miR-203a-3p might be a potential candidate for staging OA progression and a new protective/predictive biomarker for synovial OA degeneration. Further studies are needed to validate its potential impact on OA.

Osteoarthritis versus psoriasis arthritis: Physiopathology, cellular signaling, and therapeutic strategies

Osteoarthritis and psoriasis arthritis are two degenerative forms of arthritis that share similar yet also different manifestations at the histological, cellular, and clinical levels. Rheumatologists have marked them as two entirely distinct arthropathies. Given recent discoveries in disease initiation and progression, potential mechanisms, cellular signaling pathways, and ongoing clinical therapeutics, there are now more opportunities for discovering osteoarthritis drugs. This review summarized the osteoarthritis and psoriasis arthritis signaling pathways, crosstalk between BMP, WNT, TGF-β, VEGF, TLR, and FGF signaling pathways, biomarkers, and anatomical pathologies. Through bench research, we demonstrated that regenerative medicine is a promising alternative for treating osteoarthritis by highlighting significant scientific discoveries on entheses, multiple signaling blockers, and novel molecules such as immunoglobulin new antigen receptors targeted for potential drug evaluation. Furthermore, we offered valuable therapeutic approaches with a multidisciplinary strategy to treat patients with osteoarthritis or psoriasis arthritis in the coming future in the clinic.

Polymorphic transposable elements provide new insights on high-altitude adaptation in the Tibetan Plateau

Several studies demonstrated that populations living in the Tibetan plateau are genetically and physiologically adapted to high-altitude conditions, showing genomic signatures ascribable to the action of natural selection. However, so far most of them relied solely on inferences drawn from the analysis of coding variants and point mutations. To fill this gap, we focused on the possible role of polymorphic transposable elements in influencing the adaptation of Tibetan and Sherpa highlanders. To do so, we compared high-altitude and middle/low-lander individuals of East Asian ancestry by performing in silico analyses and differentiation tests on 118 modern and ancient samples. We detected several transposable elements associated with high altitude, which map genes involved in cardiovascular, hematological, chem-dependent and respiratory conditions, suggesting that metabolic and signaling pathways taking part in these functions are disproportionately impacted by the effect of environmental stressors in high-altitude individuals. To our knowledge, our study is the first hinting to a possible role of transposable elements in the adaptation of Tibetan and Sherpa highlanders.

Downregulation of Gadd45β alleviates osteoarthritis by repressing lipopolysaccharide-induced fibroblast-like synoviocyte inflammation, proliferation and migration

OBJECTIVE

Gadd45β have a regulatory role in cellular inflammation, proliferation and migration. However, the role of Gadd45β in synovial inflammation in osteoarthritis (OA) remains to be explored. This study aimed to ascertain whether Gadd45β is involved in OA synovial inflammation.

METHODS

The rat model was induced by sodium iodoacetate and the cellular model was constructed with lipopolysaccharide (LPS)-induced fibroblast-like synoviocytes (FLSs). siRNA was applied to interfere with the expression of intracellular Gadd45β. Real-time quantitative polymerase chain reaction (RT-qPCR) and western blotting were used to detect the expression of Gadd45β mRNA and protein. The inflammation, proliferation, and migration of OA-FLSs were detected by enzyme-linked immunosorbent assay, cell scratch assay, 5-ethynyl-2'-deoxyuridine assay, etc. The effect of downregulation of Gadd45β on the nuclear factor-κB (NF-κB) pathway was investigated.

RESULTS

Expression of Gadd45β in OA rat synovial tissues and OA-FLSs was increased, and LPS treatment promoted cell proliferation and enhanced cell migration. Gadd45β interference inhibited the inflammation, proliferation and migration of cells induced by LPS. LPS promoted P65 expression in the nucleus and activated the NF-κB signaling pathway, whereas si-Gadd45β reversed this situation.

CONCLUSIONS

si-Gadd45β inhibited the inflammatory response, proliferation and migration of FLSs, and activation of the NF-κB signaling pathway, which could delay the progression of OA. Hence, it may become a potential therapeutic target for OA.

Hyaluronic Acid-Based Injective Medical Devices: In Vitro Characterization of Novel Formulations Containing Biofermentative Unsulfated Chondroitin or Extractive Sulfated One with Cyclodextrins

Currently, chondroitin sulfate (CS) and hyaluronic acid (HA) pharma-grade forms are used for osteoarthritis (OA) management, CS as an oral formulations component, and HA as intra-articular injective medical devices. Recently, unsulfated chondroitin, obtained through biofermentative (BC) manufacturing, has been proposed for thermally stabilized injective preparation with HA. This study aimed to highlight the specific properties of two commercial injective medical devices, one based on HA/BC complexes and the other containing HA, extractive CS, and cyclodextrins, in order to provide valuable information for joint disease treatments. Their biophysical and biomechanical features were assayed; in addition, biological tests were performed on human pathological chondrocytes. Rheological measurements displayed similar behavior, with a slightly higher G' for HA/BC, which also proved superior stability to the hyaluronidase attack. Both samples reduced the expression of specific OA-related biomarkers such as NF-kB, interleukin 6 (IL-6), and metalloprotease-13 (MMP-13). Moreover, HA/BC better ensured chondrocyte phenotype maintenance by up-regulating collagen type 2A1 (COLII) and aggrecan (AGN). Notwithstanding, the similarity of biomolecule components, the manufacturing process, raw materials characteristics, and specific concentration resulted in affecting the biomechanical and, more interestingly, the biochemical properties, suggesting potential better performances of HA/BC in joint disease treatment.

Molecular Fingerprint of Human Pathological Synoviocytes in Response to Extractive Sulfated and Biofermentative Unsulfated Chondroitins

Pharma-grade extractive chondroitin sulfate (CS) is widely used for osteoarthritis (OA) treatment. Recently, unsulfated biofermentative chondroitin (BC) proved positive effects in OA in vitro model. This study, based on primary pathological human synoviocytes, aimed to analyze, by a multiplex assay, a panel of OA-related biomarkers in response to short-term treatments with bovine (CS_b), pig (CS_p) and fish (CS_f) chondroitins, in comparison to BC. As expected, all samples had anti-inflammatory properties, however CS_b, CS_f and especially BC affected more cytokines and chemokines. Based on these results and molecular weight similarity, CS_f and BC were selected to further explore the synoviocytes' response. In fact, Western blot analyses showed CS_f and BC were comparable, downregulating OA-related biomarkers such as the proteins mTOR, NF-kB, PTX-3 and COMP-2. Proteomic analyses, performed by applying a nano-LC-MS/MS TMT isobaric labelling-based approach, displayed the modulation of both common and distinct molecules to chondroitin treatments. Thus, CS_f and BC modulated the biological mediators involved in the inflammation cascade, matrix degradation/remodeling, glycosaminoglycans' synthesis and cellular homeostasis. This study helps in shedding light on different molecular mechanisms related to OA disease that may be potentially affected not only by animal-source chondroitin sulfate but also by unsulfated biofermentative chondroitin.

LncRNA TM1-3P Regulates Proliferation, Apoptosis and Inflammation of Fibroblasts in Osteoarthritis through miR-144-3p/ONECUT2 Axis

OBJECTIVE

This study explores LncRNA TM1-3P effects on the proliferation, apoptosis, and inflammatory response of fibroblasts in osteoarthritis (OA) and its underlying mechanism.

METHODS

Bioinformatics was performed to analyze OA disease-related genes, miRNA profiles, and function. The targeted regulation of LncRNA TM1-3P and miR-144-3p, ONECUT2 and miR-144-3p were analyzed by dual luciferase reporter gene assay, RNA Binding Protein Immunoprecipitation (RIP), and RNA pull down. Histopathological morphology of the knee joint was observed by hematoxylin-eosin (HE) and Annona Red O/Fast Green. The expressions of mRNAs and proteins were detected by RT-qPCR, Western blot, and immunohistochemistry. Unpaired T test was used between groups, and the one-way analysis of variance of repeated measurement data was applied for multi-group comparison, following Tukey's post-test.

RESULTS

ONECUT2 and Smurf2 genes were significantly elevated in the osteoarthritis group compared with the normal group (P < 0.001, P < 0.001). Expressions of ONECUT2 and LncRNA TM1-3P were increased, and expression of miR-144-3p was decreased in interleukin (IL)-1β-induced human fibroblast synovial cells (hFSCs) (mRNA: 1.06 ± 0.24 vs. 3.29 ± 0.73, proteins: 0.22 ± 0.03 vs. 0.46 ± 0.22, 1.23 ± 0.22 vs. 3.76 ± 0.73, 1.06 ± 0.25 vs. 0.37 ± 0.13, P < 0.01, P < 0.001, P < 0.01, P < 0.05). Overexpression of miR-144-3p down-regulated the ONECUT2 expression, reduced cell proliferation, promoted apoptosis in hFSCs induced by IL-1β (mRNA: 0.89 ± 0.14 vs. 0.15 ± 0.01, P < 0.05; proteins: 0.46 ± 0.01 vs. 0.23 ± 0.01, P < 0.001; CCK8: 1.88 ± 0.07 vs. 1.65 ± 0.07; P < 0.05; EDU: 55.82 ± 1.44 vs 40.57 ± 2.24, P < 0.05; apoptosis: 10.57 ± 0.79 vs 16.36 ± 0.35, P < 0.0001). Overexpression of LncRNA TM1-3P up-regulated the expression of ONECUT2, promoted cell proliferation, and inhibited apoptosis (mRNA: 0.9 ± 0.09 vs 1.94 ± 0.12, P < 0.05; proteins: 0.61 ± 0.05 vs 0.76 ± 0.03, P > 0.05; CCK8: 2.07 ± 0.05 vs 2.47 ± 0.06; P < 0.01; EDU: 52.67 ± 1.17 vs 60.06 ± 3.24, P < 0.05; apoptosis: 10.57 ± 0.79 vs 16.36 ± 0.35, P < 0.001), which were reversed by the overexpression of miR-144-3p treatment (mRNA: 1.82 ± 0.07 vs 0.31 ± 0.07, P < 0.0001; proteins: 0.74 ± 0.02 vs 0.35 ± 0.01, P < 0.01; CCK8: 2.41 ± 0.01 vs 1.67 ± 0.02; P < 0.0001; EDU: 66.85 ± 2.86 vs 44.68 ± 1.97, P < 0.0001; apoptosis: 7.19 ± 0.19 vs 13.36 ± 0.53, P < 0.0001). Silencing LncRNA TM1-3P attenuated the injury of knee joint tissue, down-regulated the expression of ONECUT2, Smurf2, IL-1β, IL-6, TNF-α, and improved the expression of Rap1 in rats (0.71 ± 0.04 vs 0.48 ± 0.02, 0.68 ± 0.06 vs 0.36 ± 0.02, 0.74 ± 0.03 vs 0.49 ± 0.04, 0.78 ± 0.01 vs 0.54 ± 0.03, 0.68 ± 0.02 vs 0.4 ± 0.04, 0.24 ± 0.01 vs 0.4 ± 0.03, P < 0.05, P < 0.05, P < 0.05, P < 0.01, P < 0.01, P < 0.05).

CONCLUSION

LncRNA TM1-3P improved inflammation and damage of knee joints in OA rats through miR-144-3p/ONECUT2 axis, providing a new theoretical basis for gene therapy of OA.

Multi-omics molecular biomarkers and database of osteoarthritis

Osteoarthritis (OA) is the most common form of arthritis in the adult population and is a leading cause of disability. OA-related genetic loci may play an important role in clinical diagnosis and disease progression. With the rapid development of diverse technologies and omics methods, many OA-related public data sets have been accumulated. Here, we retrieved a diverse set of omics experimental results from 159 publications, including genome-wide association study, differentially expressed genes and differential methylation regions, and 2405 classified OA-related gene markers. Meanwhile, based on recent single-cell RNA-seq data from different joints, 5459 cell-type gene markers of joints were collected. The information has been integrated into an online database named OAomics and molecular biomarkers (OAOB). The database (http://ibi.zju.edu.cn/oaobdb/) provides a web server for OA marker genes, omics features and so on. To our knowledge, this is the first database of molecular biomarkers for OA.

A Novel Intercellular Communication-Associated Gene Signature for Prognostic Prediction and Clinical Value in Patients With Lung Adenocarcinoma

Background

Lung cancer remains the leading cause of cancer death globally, with lung adenocarcinoma (LUAD) being its most prevalent subtype. This study aimed to identify the key intercellular communication-associated genes (ICAGs) in LUAD.

Methods

Eight publicly available datasets were downloaded from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The prognosis-related ICAGs were identified and a risk score was developed by using survival analysis. Machine learning models were trained to predict LUAD recurrence based on the selected ICAGs and clinical information. Comprehensive analyses on ICAGs and tumor microenvironment were performed. A single-cell RNA-sequencing dataset was assessed to further elucidate aberrant changes in intercellular communication.

Results

Eight ICAGs with prognostic potential were identified in the present study, and a risk score was derived accordingly. The best machine-learning model to predict relapse was developed based on clinical information and the expression levels of these eight ICAGs. This model achieved a remarkable area under receiver operator characteristic curves of 0.841. Patients were divided into high- and low-risk groups according to their risk scores. DNA replication and cell cycle were significantly enriched by the differentially expressed genes between the high- and the low-risk groups. Infiltrating immune cells, immune functions were significantly related to ICAGs expressions and risk scores. Additionally, the changes of intercellular communication were modeled by analyzing the single-cell sequencing dataset.

Conclusion

The present study identified eight key ICAGs in LUAD, which could contribute to patient stratification and act as novel therapeutic targets.

MicroRNAs in Synovial Pathology Associated With Osteoarthritis

Osteoarthritis (OA) is the most common type of arthritis, a disease that affects the entire joint. The relative involvement of each tissue, and their interactions, add to the complexity of OA, hampering our understanding of the underlying molecular mechanisms, and the generation of a disease modifying therapy. The synovium is essential in maintaining joint homeostasis, and pathologies associated with the synovium contribute to joint destruction, pain and stiffness in OA. MicroRNAs (miRNAs) are post-transcriptional regulators dysregulated in OA tissues including the synovium. MiRNAs are important contributors to OA synovial changes that have the potential to improve our understanding of OA and to act as novel therapeutic targets. The purpose of this review is to summarize and integrate current published literature investigating the roles that miRNAs play in OA-related synovial pathologies including inflammation, matrix deposition and cell proliferation.

Investigating lubricin and known cartilage-based biomarkers of osteoarthritis

Introduction: Osteoarthritis (OA) is a degenerative disease which primarily affects hyaline cartilage, leading to pain, stiffness and loss of mobility of the entire articulation. Diagnosis is commonly based on symptoms and radiographs, but there is a growing interest in detecting novel biomarkers, in serum, urine and synovial fluid, which can be predictors of disease onset and progression.Areas covered: This review provides an overview of the main biomarkers currently used in OA clinical practice, with a focus on lubricin, a surface glycoprotein secreted in the synovial fluid that lubricates the cartilage and reduces the coefficient of friction within the joint. Key findings of the last years are presented throughout the article.Expert opinion: Analysis of biomarkers might suggest personalized protocols of treatment, guide the classification of OA phenotypes, contribute to precision medicine, avoid further unnecessary exams, facilitate drug discovery or refine treatment guidelines. For all these reasons, the investigation of novel cartilage-based biomarker of osteoarthritis needs to be promoted and improved.