Çubuk Cankut, Lau Rachel, Cutillas Pedro, Rajeeve Vinothini, John Christopher R, Surace Anna E A, Hands Rebecca, Fossati-Jimack Liliane, Lewis Myles J, Pitzalis Costantino
Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts NIHR BRC & NHS Trust, Charterhouse Square, London, EC1M 6BQ, UK.
Cell Signalling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
Arthritis Res Ther. 2024 Jun 12;26(1):120. doi: 10.1186/s13075-024-03351-4.
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.
激酶是细胞内信号传导介质，也是类风湿关节炎（RA）中维持炎症过程的关键因素。Janus激酶家族（JAKs）的口服抑制剂在RA中广泛使用，而其他激酶家族的抑制剂，如磷酸肌醇3激酶（PI3K），仍在研发中。目前大多数生物标志物平台可量化mRNA/蛋白质水平，但无法直接提供蛋白质是否处于活性/非活性状态的信息。磷酸化蛋白质组分析有潜力在组织水平测量特定酶的激活状态。
我们使用无标记质谱法验证了对8例未经治疗的RA患者的治疗前滑膜活检样本进行磷酸化蛋白质组和总蛋白质组分析的可行性，以识别滑膜组织中可能解释对RA治疗无反应的活跃细胞信号通路。
差异表达分析和功能富集显示，淋巴样和髓样RA病理类型之间的磷酸化蛋白质组和蛋白质组谱有明显区分。特定磷酸化位点的丰度与炎症状态程度相关。淋巴样病理类型富含淋巴增殖信号磷酸化位点，包括雷帕霉素哺乳动物靶标（MTOR）信号传导，而髓样病理类型与丝裂原活化蛋白激酶（MAPK）和细胞周期蛋白依赖性激酶（CDK）介导的信号传导相关。该分析还突出了以前未与RA相关联的新型激酶，如髓样病理类型中的DNA激活蛋白激酶催化亚基（PRKDC）。几个磷酸化位点与临床特征相关，如疾病活动评分（DAS）-28，这表明磷酸化位点分析在识别疾病严重程度和预后的组织水平新型生物标志物方面具有潜力。
特定的磷酸化蛋白质组/蛋白质组特征描绘了RA病理类型，可能对RA患者分层以实现个性化医疗具有临床应用价值。
