Table 3_Combination of single-cell and bulk RNA-seq reveals changes in the immune landscape in osteomyelitis.xlsx

ObjectiveThis study presented a comprehensive characterization of the osteomyelitis immune microenvironment, identified driver genes and pathogenic cell populations underlying disease progression, and uncovered potential therapeutic targets through single-cell and bulk transcriptomic analysis.
MethodsWe analyzed time-series transcriptomic sequencing data from mouse osteomyelitis samples in the dataset GSE168896. Fuzzy c-means clustering was applied to reveal gene sets linked to disease progression. Immune cell infiltration analysis was conducted through the online tool ImmuCellAI-mouse. Furthermore, by leveraging single-cell sequencing data, we characterized immune cell subpopulations and pinpointed the key cell subtypes that were present in the osteomyelitis mice.
ResultsWe identified six gene clusters exhibiting distinct temporal expression patterns and functional roles in osteomyelitis, such as leukocyte and lymphocyte activation and ossification. Single-cell sequencing analysis further showed seven distinct cellular subpopulations. Among these, macrophages demonstrated a significant increase following osteomyelitis, and the infiltration of Mif+Cd63+, Arg1+Sdc4+, and Cxcl1+Ccl4+ macrophages significantly increased. Moreover, Ccl3–Ccr1 and Cxcl2–Cxcr2 ligand–receptors contributed mostly in immune cells.
ConclusionOur findings tracked the transcriptional dynamics and evolving immune landscape of osteomyelitis, highlighting macrophages as central regulators of disease progression. We identified that significant infiltration of Arg1+Sdc4+, Cxcl1+Ccl4+, and Mif+Cd63+ macrophages may affect osteomyelitis through the Ccl3–Ccr1 and Cxcl2–Cxcr2 signaling pathways. These findings offer a new perspective on immune regulation in osteomyelitis.

研究目的 本研究对骨髓炎（osteomyelitis）的免疫微环境进行了全面表征，明确了疾病进展背后的驱动基因与致病细胞群，并通过单细胞与批量转录组（bulk transcriptomic）分析揭示了潜在治疗靶点。
研究方法 本研究分析了数据集GSE168896中小鼠骨髓炎样本的时序转录组测序数据。采用模糊C均值聚类（Fuzzy c-means clustering）揭示与疾病进展相关的基因集；通过在线工具ImmuCellAI-mouse开展免疫细胞浸润分析。此外，本研究借助单细胞测序（single-cell sequencing）数据对免疫细胞亚群进行表征，并精准定位了骨髓炎小鼠体内的关键细胞亚型。
研究结果 本研究鉴定出6个在骨髓炎中具有独特时序表达模式与功能的基因簇，其功能涉及白细胞与淋巴细胞活化、骨化等过程。单细胞测序分析进一步揭示了7种不同的细胞亚群。其中，巨噬细胞（macrophages）在骨髓炎发生后显著增多，而Mif+Cd63+、Arg1+Sdc4+及Cxcl1+Ccl4+巨噬细胞的浸润水平显著升高。此外，Ccl3–Ccr1与Cxcl2–Cxcr2配体-受体轴在免疫细胞互作中发挥主要调控作用。
研究结论 本研究阐明了骨髓炎的转录动态变化与免疫微环境演化过程，明确巨噬细胞是疾病进展的核心调控因子。本研究发现，Arg1+Sdc4+、Cxcl1+Ccl4+及Mif+Cd63+巨噬细胞的显著浸润可通过Ccl3–Ccr1与Cxcl2–Cxcr2信号通路影响骨髓炎的发生发展。本研究结果为骨髓炎的免疫调控研究提供了全新视角。