Kinases are intracellular signalling mediators and key to sustaining the inflammatory process in rheumatoid arthritis (RA). Oral inhibitors of Janus Kinase family (JAKs) are widely used in RA, while inhibitors of other kinase families e.g. phosphoinositide 3-kinase (PI3K) are under development. Most current biomarker platforms quantify mRNA/protein levels, but give no direct information on whether proteins are active/inactive. Phosphoproteome analysis has the potential to measure specific enzyme activation status at tissue level. We validated the feasibility of phosphoproteome and total proteome analysis on 8 pre-treatment synovial biopsies from treatment-naive RA patients using label-free mass spectrometry, to identify active cell signalling pathways in synovial tissue which might explain failure to respond to RA therapeutics. Differential expression analysis and functional enrichment revealed clear separation of phosphoproteome and proteome profiles between lymphoid and myeloid RA pathotypes. Abundance of specific phosphosites was associated with the degree of inflammatory state. The lymphoid pathotype was enriched with lymphoproliferative signalling phosphosites, including Mammalian Target Of Rapamycin (MTOR) signalling, whereas the myeloid pathotype was associated with Mitogen-Activated Protein Kinase (MAPK) and CDK mediated signalling. This analysis also highlighted novel kinases not previously linked to RA, such as Protein Kinase, DNA-Activated, Catalytic Subunit (PRKDC) in the myeloid pathotype. Several phosphosites correlated with clinical features, such as Disease-Activity-Score (DAS)-28, suggesting that phosphosite analysis has potential for identifying novel biomarkers at tissue-level of disease severity and prognosis. Specific phosphoproteome/proteome signatures delineate RA pathotypes and may have clinical utility for stratifying patients for personalised medicine in RA.

中文翻译：

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早期类风湿性关节炎滑膜的磷酸化蛋白质组学分析揭示了活跃的信号通路并区分炎症病理类型


激酶是细胞内信号传导介质，是维持类风湿性关节炎 (RA) 炎症过程的关键。 Janus 激酶家族 (JAK) 的口服抑制剂广泛用于 RA，而其他激酶家族的抑制剂例如磷酸肌醇 3-激酶 (PI3K) 正在开发中。目前大多数生物标志物平台都会量化 mRNA/蛋白质水平，但没有提供有关蛋白质是否活性/非活性的直接信息。磷酸化蛋白质组分析有可能在组织水平上测量特定酶的激活状态。我们使用无标记质谱法验证了对来自未接受治疗的 RA 患者的 8 例治疗前滑膜活检进行磷酸化蛋白质组和总蛋白质组分析的可行性，以确定滑膜组织中的活跃细胞信号传导途径，这可能解释对 RA 治疗失败的原因。差异表达分析和功能富集揭示了淋巴和骨髓 RA 病理型之间磷酸化蛋白质组和蛋白质组谱的清晰分离。特定磷酸位点的丰度与炎症状态的程度相关。淋巴病理型富含淋巴增殖信号磷酸位点，包括哺乳动物雷帕霉素靶点 (MTOR) 信号传导，而骨髓病理型则与丝裂原激活蛋白激酶 (MAPK) 和 CDK 介导的信号传导相关。该分析还强调了以前与 RA 无关的新型激酶，例如骨髓病理型中的蛋白激酶、DNA 激活催化亚基 (PRKDC)。一些磷酸位点与临床特征相关，例如疾病活动评分（DAS）-28，表明磷酸位点分析有可能在组织水平上识别疾病严重程度和预后的新型生物标志物。 特定的磷酸化蛋白质组/蛋白质组特征描绘了 RA 病理型，并且可能具有临床实用性，可用于对 RA 患者进行个性化医疗分层。