Proteomic analysis of biopsied human colonic mucosa

iTRAQ-based pharmacoproteomics reveals potential targets of berberine, a promising therapy for ulcerative colitis

Previous studies by us and others have indicated that berberine is a promising therapy for ulcerative colitis (UC). However, the mechanisms of UC and the therapeutic targets of berberine are poorly understood. iTRAQ-based proteomics was utilized to characterize the proteins and pathways associated with the development of colitis and its improvement after berberine treatment. By using a modified dextran sodium sulfate (DSS) colitis as the UC model, confirmed that berberine significantly attenuated clinical symptoms and colon shorting of the colitis mice. Proteomics identified 140 and 391 proteins that were differentially expressed in the colons of DSS- or DSS plus berberine-treated mice, respectively. Subsequent verification of 15 selected differentially expressed proteins (DEPs) by multiple reaction monitoring confirmed the reliability of the iTRAQ data. Further comparisons and bioinformatics analysis demonstrated that among the identified DEPs, 26, including Hist2h2be, Tubb3, and five immunoglobulins, were oppositely regulated by DSS and DSS plus berberine treatments. In addition, five commonly dysregulated pathways, including natural killer cell-mediated cytotoxicity and RRAR signaling were identified. Network analysis revealed that proteins involved in 7 and 11 pathways in DSS and DSS plus berberine treated mice, respectively, engaged in protein-protein interactions. Our study provides the first pharmacoproteomics profiling of colitis and its recovery after berberine treatment. The proteins, pathways and networks identified provide novel insights into the pathogenesis of colitis and the action mechanism of berberine, demonstrating their values for validation in human UC which could serve as targets for the development of novel therapies for UC.

Murine colon proteome and characterization of the protein pathways

Background

Most of the current proteomic researches focus on proteome alteration due to pathological disorders (i.e.: colorectal cancer) rather than normal healthy state when mentioning colon. As a result, there are lacks of information regarding normal whole tissue- colon proteome.

Results

We report here a detailed murine (mouse) whole tissue- colon protein reference dataset composed of 1237 confident protein (FDR < 2) with comprehensive insight on its peptide properties, cellular and subcellular localization, functional network GO annotation analysis, and its relative abundances. The presented dataset includes wide spectra of pI and Mw ranged from 3–12 and 4–600 KDa, respectively. Gravy index scoring predicted 19.5% membranous and 80.5% globularly located proteins. GO hierarchies and functional network analysis illustrated proteins function together with their relevance and implication of several candidates in malignancy such as Mitogen- activated protein kinase (Mapk8, 9) in colorectal cancer, Fibroblast growth factor receptor (Fgfr 2), Glutathione S-transferase (Gstp1) in prostate cancer, and Cell division control protein (Cdc42), Ras-related protein (Rac1,2) in pancreatic cancer. Protein abundances calculated with 3 different algorithms (NSAF, PAF and emPAI) provide a relative quantification under normal condition as guidance.

Conclusions

This highly confidence colon proteome catalogue will not only serve as a useful reference for further experiments characterizing differentially expressed proteins induced from diseased conditions, but also will aid in better understanding the ontology and functional absorptive mechanism of the colon as well.

Janice Drew’s work on diet and cancer

Obesity and associated reduced consumption of plant derived foods are linked to increased risk of colon cancer as well as a number of other organ specific cancers. Inflammatory processes are a contributing factor but the precise mechanisms remain elusive. Obesity and cancer incidence are increasing worldwide, presenting bleak prospects for reducing, or preventing, obesity related cancers. The incidence of these preventable cancers can be achieved with greater understanding of the molecular mechanisms linking diet and carcinogenesis. Janice Drew has developed a research program over recent years to investigate molecular mechanisms related to consumption of anti-inflammatory metabolites generated from consumption of plant based diets, the impact of high fat diets and associated altered metabolism and obesity on regulation of colon inflammatory responses and processes regulating the colon epithelium. Comprehensive strategies have been developed incorporating transcriptomics, including the novel gene expression technology, the GenomeLab System and proteomics, together with biochemical analyses of plasma and tissue samples to assess correlated changes in oxidative stress, inflammation and pathology. The approaches developed have achieved success in establishing antioxidant and anti-inflammatory activity of dietary antioxidants and associated genes and pathways that interact to modulate redox status in the colon. Cellular processes and genes altered in response to obesity and high fat diets have provided evidence of molecular mechanisms that are implicated in obesity related cancer.

Global expression study in colorectal cancer on proteins with alkaline isoelectric point by two-dimensional difference gel electrophoresis

Colorectal cancer is one of the leading causes of cancer death worldwide. To identify candidates for biomarkers and therapeutic targets, we investigated the proteome of colorectal cancer tissues. Using 2D-DIGE in combination with our original large format electrophoresis apparatus, we compared surgically resected normal and tumor tissues from 53 patients with colorectal cancer. We focused on proteins with an alkaline pI using IPG gels for the alkaline range. We observed 1687 protein spots, and found 100 spots with statistical (p<0.01) and significant (>2-fold) differences between the normal and the tumor tissue groups. Among these 100 protein spots, five showed a different intensity between tumor tissues from the stage-II and the stage-III patients. MS experiments revealed that these 100 protein spots corresponded to 58 unique proteins. These included six proteins which had not been previously reported to be associated with colorectal cancer. Among these proteins, five were not reported in any type of malignancy. IEF/western blotting confirmed the differences in protein expression between the normal and the tumor tissues. These results may provide an insight for biomarker development and drug target discovery in colorectal cancer.