Table_1_Expression patterns of eight RNA-modified regulators correlating with immune infiltrates during the progression of osteoarthritis.pdf

BackgroundRNA modifications in eukaryotic cells have emerged as an exciting but under-explored area in recent years and are considered to be associated with many human diseases. While several studies have been published relating to m6A in osteoarthritis (OA), we only have limited knowledge of other kinds of RNA modifications. Our study investigated eight RNA modifiers’ specific roles in OA including A-to-I, APA, m5C, m6A, m7G, mcm5s2U, Nm and Ψ together with their relationship with immune infiltration.
MethodsRNA modification patterns in OA samples were identified based on eight-type RNA modifiers and their correlation with the degree of immune infiltration was also methodically investigated. Receiver operating characteristic curves (ROC) and qRT-PCR was performed to confirm the abnormal expression of hub genes. The RNA modification score (Rmscore) was generated by the applications of principal component analysis (PCA) algorithm in order to quantify RNA modification modes in individual OA patients.
ResultsWe identified 21 differentially-expressed RNA modification related genes between OA and healthy samples. For example, CFI, CBLL1 and ALKBH8 were expressed at high levels in OA (P<0.001), while RPUSD4, PUS1, NUDT21, FBL and WDR4 were expressed at low levels (P<0.001). Two candidate RNA modification regulators (WDR4 and CFI) were screened out utilizing a random forest machine learning model. We then identified two distinctive RNA modification modes in OA which were found to display distinctive biological features. High Rmscore, characterized by increased immune cell infiltration, indicated an inflamed phenotype.
ConclusionsOur study was the first to systematically reveal the crosstalk and dysregulations eight-type of RNA modifications in OA. Assessing individuals’ RNA modification patterns will be conductive to enhance our understanding of the properties of immune infiltration, provide novel diagnostic and prognostic biomarkers, and guide more effective immunotherapy strategies in the future.

背景
近年来，真核细胞内的RNA修饰已成为一个令人振奋但仍未得到充分探索的研究领域，且被认为与多种人类疾病密切相关。目前已有多项研究探讨了N6-甲基腺嘌呤（m6A）与骨关节炎（OA）的关联，但我们对其他类型RNA修饰的认知仍十分有限。本研究针对8种RNA修饰调控因子在OA中的特异性作用展开探究，涵盖A-to-I编辑、多聚腺苷酸化位点（APA）、5-甲基胞嘧啶（m5C）、N6-甲基腺嘌呤（m6A）、7-甲基鸟苷（m7G）、5-羧甲基氨基甲基-2-硫尿嘧啶（mcm5s2U）、核糖甲基化（Nm）以及假尿嘧啶（Ψ），同时分析了这些修饰与免疫浸润的关联。

方法
本研究基于8类RNA修饰调控因子，对OA样本中的RNA修饰模式进行鉴定，并系统分析了其与免疫浸润程度的相关性。通过受试者工作特征曲线（ROC）与实时荧光定量聚合酶链反应（qRT-PCR）验证核心差异基因的异常表达情况。利用主成分分析（PCA）算法构建RNA修饰评分（Rmscore），以量化单个OA患者的RNA修饰模式。

结果
本研究在OA样本与健康对照样本之间鉴定出21个与RNA修饰相关的差异表达基因。例如，CFI、CBLL1与ALKBH8在OA样本中呈高表达（P<0.001），而RPUSD4、PUS1、NUDT21、FBL及WDR4则呈低表达（P<0.001）。通过随机森林机器学习模型筛选出2个候选RNA修饰调控因子（WDR4与CFI）。本研究进一步在OA中鉴定出两种具有独特生物学特征的RNA修饰模式。高Rmscore以免疫细胞浸润增加为特征，提示炎症表型。

结论
本研究首次系统揭示了OA中8类RNA修饰之间的串扰与表达失调情况。对个体RNA修饰模式进行评估，有助于加深我们对免疫浸润特性的理解，为临床提供新型诊断与预后生物标志物，并为未来更有效的免疫治疗策略提供指导。