Department of Translational Medicine, South San Francisco, California, USA.
Proteomics Clin Appl. 2024 Sep;18(5):e2300075. doi: 10.1002/prca.202300075. Epub 2024 Mar 29.
Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), is characterized by chronic gastrointestinal inflammation. A high unmet need exists for noninvasive biomarkers in IBD to monitor changes in disease activity and guide treatment decisions. Stool is an easily accessed, disease proximal matrix in IBD, however the composition of the IBD fecal proteome remains poorly characterized.
A data-independent acquisition LC-MS/MS approach was used to profile the human fecal proteome in two independent cohorts (Cohort 1: healthy n = 5, UC n = 5, CD n = 5, Cohort 2: healthy n = 20, UC n = 10, and CD n = 10) to identify noninvasive biomarkers reflective of disease activity.
688 human proteins were quantified, with 523 measured in both cohorts. In UC stool 96 proteins were differentially abundant and in CD stool 126 proteins were differentially abundant compared to healthy stool (absolute log2 fold change > 1, p-value < 0.05). Many of these fecal proteins are associated with infiltrating immune cells and ulceration/rectal bleeding, which are hallmarks of IBD pathobiology. Mapping the identified fecal proteins to a whole blood single-cell RNA sequencing data set revealed the involvement of various immune cell subsets to the IBD fecal proteome.
Findings from this study not only confirmed the presence of established fecal biomarkers for IBD, such as calprotectin and lactoferrin, but also revealed new fecal proteins from multiple pathways known to be dysregulated in IBD. These novel proteins could serve as potential noninvasive biomarkers to monitor specific aspects of IBD disease activity which could expedite clinical development of novel therapeutic targets.
炎症性肠病（IBD）包括溃疡性结肠炎（UC）和克罗恩病（CD），其特征为慢性胃肠道炎症。IBD 患者存在对非侵入性生物标志物的高度未满足需求，这些生物标志物可用于监测疾病活动的变化并指导治疗决策。粪便作为一种易于获取的、接近疾病发生部位的 IBD 基质，但 IBD 粪便蛋白质组的组成仍未得到充分描述。
使用数据非依赖性采集 LC-MS/MS 方法对两个独立队列（队列 1：健康对照 n=5，UC n=5，CD n=5；队列 2：健康对照 n=20，UC n=10，CD n=10）的人类粪便蛋白质组进行分析，以鉴定反映疾病活动的非侵入性生物标志物。
共定量了 688 个人类蛋白质，其中两个队列均测量到 523 个蛋白质。与健康粪便相比，UC 粪便中有 96 个蛋白质丰度差异，CD 粪便中有 126 个蛋白质丰度差异（绝对对数 2 倍变化>1，p 值<0.05）。这些粪便蛋白中的许多与浸润免疫细胞和溃疡/直肠出血有关，这是 IBD 病理生物学的标志。将鉴定出的粪便蛋白映射到全血单细胞 RNA 测序数据集，揭示了各种免疫细胞亚群对 IBD 粪便蛋白质组的参与。
本研究的结果不仅证实了 calprotectin 和乳铁蛋白等已建立的 IBD 粪便生物标志物的存在，还揭示了来自多个已知在 IBD 中失调的途径的新的粪便蛋白。这些新的蛋白质可以作为潜在的非侵入性生物标志物，用于监测 IBD 疾病活动的特定方面，从而加速新型治疗靶点的临床开发。
