Sen Luo , Zeyu Liu , Jiewen Zhang , Yuanyuan Chen , Yutian Lei , Xu Gao , ChengYan Liu , Yutao Chen , Chenkun Liu , Peng Yan , Yang Chen , Heng Li , Chuanchuan Zhao , Haifan Wang , Kunzheng Wang , Chunsheng Wang , Run Tian , Pei Yang
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At the meanwhile, differentially expressed genes (DEGs) were identified in the same dataset and intersected with IRGs to find IR-DEGs. Protein-protein interaction network and enrichment analyses and further gene filtering using LASSO regression led to the discovery of potential biomarkers, which were then validated by ROC curve analysis, single-cell RNA sequencing, qRT-PCR, western blot and immunofluorescence. ScRNA-seq analysis using GSE196678, qRT-PCR, western blot and immunofluorescence results confirmed the upregulation of their expression levels in early-stage OA SCB samples. Our comprehensive analysis revealed lymphocytes infiltration as a major feature in early OA SCB. A total of 13 IR-DEGs were identified, showing significant enrichment in T- or B-cell activation pathways. Three of them (CD247, POU2AF1, and TNFRSF13B) were selected via the LASSO regression analysis, and results from the ROC curve analyses indicated the diagnostic efficacy of these 3 genes as biomarkers. 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引用次数: 0
摘要
骨关节炎(OA)是一种退行性关节疾病,软骨下骨(SCB)的免疫浸润机制尚不清楚。因此,本研究旨在发现骨关节炎早期和晚期阶段软骨下骨中免疫浸润的变化,并确定相关的生物标记物。利用基因表达总库数据库中的 GSE515188 批量序列图谱,我们在进行加权基因共表达网络分析的同时,还进行了单样本基因组富集分析,以确定参与这两个阶段 SCB 的关键细胞和免疫相关基因(IRGs)。同时,在同一数据集中鉴定差异表达基因(DEGs),并与IRGs交叉以发现IR-DEGs。蛋白质-蛋白质相互作用网络和富集分析以及使用LASSO回归进一步筛选基因,发现了潜在的生物标记物,然后通过ROC曲线分析、单细胞RNA测序、qRT-PCR、Western印迹和免疫荧光进行了验证。利用GSE196678进行的ScRNA-seq分析、qRT-PCR、Western印迹和免疫荧光结果都证实了它们在早期OA SCB样本中表达水平的上调。我们的综合分析表明,淋巴细胞浸润是早期 OA SCB 的主要特征。共鉴定出 13 个 IR-DEG,它们在 T 细胞或 B 细胞活化途径中表现出明显的富集。其中三个基因(CD247、POU2AF1 和 TNFRSF13B)是通过 LASSO 回归分析选出的,ROC 曲线分析结果表明这三个基因作为生物标记物具有诊断功效。这些发现有助于研究OA中SCB免疫浸润的机制、对OA进展进行分层以及确定相关的治疗靶点。
Three-gene signature revealing the dynamics of lymphocyte infiltration in subchondral bone during osteoarthritis progression
Osteoarthritis (OA), a degenerative joint disorder, has an unclear immune infiltration mechanism in subchondral bone (SCB). Thus, this study aims to discern immune infiltration variations in SCB between early- and late-stages of OA and identify pertinent biomarkers. Utilizing the GSE515188 bulk-seq profile from the Gene Expression Omnibus database, we performed single-sample gene-set enrichment analysis alongside weighted gene co-expression network analysis to identify key cells and immune-related genes (IRGs) involved in SCB at both stages. At the meanwhile, differentially expressed genes (DEGs) were identified in the same dataset and intersected with IRGs to find IR-DEGs. Protein-protein interaction network and enrichment analyses and further gene filtering using LASSO regression led to the discovery of potential biomarkers, which were then validated by ROC curve analysis, single-cell RNA sequencing, qRT-PCR, western blot and immunofluorescence. ScRNA-seq analysis using GSE196678, qRT-PCR, western blot and immunofluorescence results confirmed the upregulation of their expression levels in early-stage OA SCB samples. Our comprehensive analysis revealed lymphocytes infiltration as a major feature in early OA SCB. A total of 13 IR-DEGs were identified, showing significant enrichment in T- or B-cell activation pathways. Three of them (CD247, POU2AF1, and TNFRSF13B) were selected via the LASSO regression analysis, and results from the ROC curve analyses indicated the diagnostic efficacy of these 3 genes as biomarkers. These findings may aid in investigating the mechanisms of SCB immune infiltration in OA, stratifying OA progression, and identifying relevant therapeutic targets.
期刊介绍:
International Immunopharmacology is the primary vehicle for the publication of original research papers pertinent to the overlapping areas of immunology, pharmacology, cytokine biology, immunotherapy, immunopathology and immunotoxicology. Review articles that encompass these subjects are also welcome.
The subject material appropriate for submission includes:
• Clinical studies employing immunotherapy of any type including the use of: bacterial and chemical agents; thymic hormones, interferon, lymphokines, etc., in transplantation and diseases such as cancer, immunodeficiency, chronic infection and allergic, inflammatory or autoimmune disorders.
• Studies on the mechanisms of action of these agents for specific parameters of immune competence as well as the overall clinical state.
• Pre-clinical animal studies and in vitro studies on mechanisms of action with immunopotentiators, immunomodulators, immunoadjuvants and other pharmacological agents active on cells participating in immune or allergic responses.
• Pharmacological compounds, microbial products and toxicological agents that affect the lymphoid system, and their mechanisms of action.
• Agents that activate genes or modify transcription and translation within the immune response.
• Substances activated, generated, or released through immunologic or related pathways that are pharmacologically active.
• Production, function and regulation of cytokines and their receptors.
• Classical pharmacological studies on the effects of chemokines and bioactive factors released during immunological reactions.