Proteomics Highlights Common and Distinct Pathophysiological Processes Associated with Ileal and Colonic Ulcers in Crohn’s Disease

Abstract

Background and Aims Based on genetics and natural history, Crohn’s disease can be separated into two entities, an ileal and a colonic disease. Protein-based approaches are needed to elucidate whether such subphenotypes are related to distinct pathophysiological processes. Methods The proteome of ulcer edges was compared with that of paired control tissue samples [n = 32 biopsies] by differential proteomics in the ileum and the colon of Crohn’s disease patients [n = 16]. The results were analysed using a hypothesis-driven approach [based on the literature] and a hypothesis-free approach [pathway enrichment analyses] to determine common and segment-specific pathophysiological processes associated with ileal and colonic CD ulcer edges. To confirm the involvement of a key pathway highlighted by proteomics, two proteins were also studied by immunochemistry. Results In the ileum and the colon, 4428 and 5204 proteins, respectively, were identified and quantified. Ileal and colonic ulcer edges differed in having a distinct distribution of proteins associated with epithelial–mesenchymal transition, neutrophil degranulation, and ribosomes. Ileal and colonic ulcer edges were similarly characterized by an increase in the proteins implicated in the endoplasmic reticulum protein-processing pathway and a decrease in mitochondrial proteins. Immunochemistry confirmed the presence of endoplasmic reticulum stress in the mucosa of ileal and colonic ulcer edges. Conclusion This study provides protein-based evidence for partially distinct pathophysiological processes being associated with ileal and colonic ulcer edges in Crohn’s disease patients. This could constitute a first step toward the development of gut segment–specific diagnostic markers and therapeutics.

Review article: distinctions between ileal and colonic Crohn's disease: from physiology to pathology

“…In a proteomic study, we found evidence well supporting a higher level of neutrophil activity in colonic than ileal ulcer edge of CD patients 63 . When compared to paired control mucosa, ulcer edge mucosa presented a much higher increase in neutrophils markers (including calprotectin and lactotransferrin) in the colon than the ileum 63 . Thus, the measure of neutrophil markers in stools seems not only to reflect the extent and the severity of the affected surface but it could also testify from the localisation of the lesions (ileum vs colon).…”

“…However, these proposition are only speculative and they did not consider the possibility that neutrophils could show different activity according to disease location. In a proteomic study, we found evidence well supporting a higher level of neutrophil activity in colonic than ileal ulcer edge of CD patients 63 . When compared to paired control mucosa, ulcer edge mucosa presented a much higher increase in neutrophils markers (including calprotectin and lactotransferrin) in the colon than the ileum 63 .…”

“…When injured, IECs can contribute to the fibrotic process by acquiring mesenchymal features and this phenomenon of cellular plasticity is called epithelial‐to‐mesenchymal transition (EMT) 61 . Intriguingly, we reported evidence (via the measure of 30 markers) supporting the presence of EMT in the ileal ulcer edge of CD patients while this phenomenon was barely detectable in the colon 63 . Thus, in case of lesional process affecting the epithelium, ileum could be more prone to EMT than colon.…”

Endoplasmic Reticulum Stress of Gut Enterocyte and Intestinal Diseases

“…First of all, various physiological and pathological situations produce alterations in the ER in the animal model of DSS-induced colitis IBD ( Yin et al, 2021 ). This theory was further confirmed in the cells and organoids from human specimens, even the tissue directly derived from IBD patients ( Pierre et al, 2020 ; Rees et al, 2020 ). Enteroid-derived primary cell monolayers generated from IBD subjects exhibited significantly lower basal expression of GRP78 and higher basal CHOP expression and XBP1s/XBP1u ratios compared to the healthy control subjects.…”

Marked Increased Production of Acute Phase Reactants by Skeletal Muscle during Cancer Cachexia

“…Purified and reconditioned protein digests were analyzed as described previously [51] on an instrumental system composed of a nanoACQUITY two-dimensional UPLC (Waters) coupled to a Q Exactive Quadrupole-Orbitrap hybrid mass spectrometer (Thermo Fisher Scientific). The 2D-UPLC separation of the peptides (2.0 µg) was obtained using a reversed-phase pH 10/reversed-phase pH 3-based separation.…”