Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning
Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning
复制标题
DOI：
10.1021/acs.jproteome.1c00028
复制
发表时间：
2021-05-19
影响因子：
4.4
通讯作者：
Hess, Sonja
中科院分区：
文献类型：
--
作者：
Chaerkady, Raghothama;Zhou, Yebin;Hess, Sonja
瓜氨酸是一种重要的翻译后修饰，涉及许多疾病，包括类风湿性关节炎（RA），阿尔茨海默病和癌症。神经细胞和肥大细胞具有不同的蛋白质精氨酸脱亚胺酶（PAD）表达谱，离子霉素诱导的活化使其成为研究瓜氨酸敏感蛋白质的理想细胞模型。我们进行了高分辨率质谱分析和严格的数据过滤，以确定在中性粒细胞和肥大细胞中的瓜氨酸位点，用和不用离子霉素。我们在395种蛋白质上共鉴定了833个经验证的瓜氨酸位点。这些瓜氨酸化蛋白质中有几种是参与先天免疫应答的途径的重要组成部分。使用这个基准一级序列数据集，我们开发了机器学习模型来预测中性粒细胞和肥大细胞蛋白中的瓜氨酸。我们表明，我们的模型预测瓜氨酸的可能性分别为0.735和0.766 AUC（受试者工作特征曲线下的面积），在独立的验证集。总之，本研究提供了中性粒细胞和肥大细胞蛋白中最大数量的经验证瓜氨酸位点。使用我们的新的基序分析方法来预测瓜氨酸位点将有助于发现蛋白质精氨酸脱亚胺酶（PAD）的新蛋白质底物，这可能是理解各种疾病的免疫病理学的关键。
Citrullination is an important post-translational modification implicated in many diseases including rheumatoid arthritis (RA), Alzheimer's disease, and cancer. Neutrophil and mast cells have different expression profiles for protein-arginine deiminases (PADs), and ionomycin-induced activation makes them an ideal cellular model to study proteins susceptible to citrullination. We performed high-resolution mass spectrometry and stringent data filtration to identify citrullination sites in neutrophil and mast cells treated with and without ionomycin. We identified a total of 833 validated citrullination sites on 395 proteins. Several of these citrullinated proteins are important components of pathways involved in innate immune responses. Using this benchmark primary sequence data set, we developed machine learning models to predict citrullination in neutrophil and mast cell proteins. We show that our models predict citrullination likelihood with 0.735 and 0.766 AUCs (area under the receiver operating characteristic curves), respectively, on independent validation sets. In summary, this study provides the largest number of validated citrullination sites in neutrophil and mast cell proteins. The use of our novel motif analysis approach to predict citrullination sites will facilitate the discovery of novel protein substrates of protein-arginine deiminases (PADs), which may be key to understanding immunopathologies of various diseases.