目的:粘膜细胞类型之间的相互作用,环境压力源,和肠道微生物群有助于炎症性肠病(IBD)的发病机理。这里,我们应用粘膜-腔界面的元蛋白质组学研究人类结肠粘膜的疾病相关生物学。
方法:我们招募了51名IBD和非IBD受试者的发现队列,通过粘膜灌洗在6个结肠区域进行内窥镜采样,和38名非IBD受试者的验证队列。为每个样品产生元蛋白质组数据集,并使用一套生物信息学方法分析与结肠位点和疾病状态的关联。通过人内窥镜活检样品的免疫印迹分析和免疫组织化学确定选择的蛋白质的定位。
结果:发现队列元蛋白质组的共现分析表明,粘膜表面的蛋白质聚集成模块,具有差异功能特化的证据(例如,铁调节,微生物防御)和细胞起源(例如,上皮或造血)。这些模块,在独立队列中验证,沿着胃肠道在空间上差异相关,和7个模块有选择地与非IBD相关联,溃疡性结肠炎,和/或克罗恩病状态。此外,某些模块的详细组成在疾病和健康状态下发生了变化。我们通过免疫印迹和免疫组织化学可视化证实了代表4种不同疾病相关模块的28种蛋白质的预测空间和疾病相关定位,有证据表明它们的分布是毫米尺度的微地理马赛克。
结论:这些发现表明,粘膜表面是反映局部粘膜生态学的功能网络的微观地理马赛克,其在疾病和健康样本中的组成差异可以提供生理和病理粘膜状态的独特读数。
OBJECTIVE: Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal-luminal interface to study the disease-related biology of the human colonic mucosa.
METHODS: We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects. Metaproteome data sets were produced for each sample and analyzed for association with colonic site and disease state using a suite of bioinformatic approaches. Localization of select proteins was determined by immunoblot analysis and immunohistochemistry of human endoscopic biopsy samples.
RESULTS: Co-occurrence analysis of the discovery cohort metaproteome showed that proteins at the mucosal surface clustered into modules with evidence of differential functional specialization (eg, iron regulation, microbial defense) and cellular origin (eg, epithelial or hemopoietic). These modules, validated in an independent cohort, were differentially associated spatially along the gastrointestinal tract, and 7 modules were associated selectively with non-IBD, ulcerative colitis, and/or Crohn\'s disease states. In addition, the detailed composition of certain modules was altered in disease vs healthy states. We confirmed the predicted spatial and disease-associated localization of 28 proteins representing 4 different disease-related modules by immunoblot and immunohistochemistry visualization, with evidence for their distribution as millimeter-scale microgeographic mosaic.
CONCLUSIONS: These findings suggest that the mucosal surface is a microgeographic mosaic of functional networks reflecting the local mucosal ecology, whose compositional differences in disease and healthy samples may provide a unique readout of physiologic and pathologic mucosal states.