Fig. 1

Overview of colon protein expression in a chemically induced and SIV rhesus macaque model of ulcerative colitis. a Subject PCA plots demonstrating the effect of (i) DSS treatment and (ii) SIV infection on protein expression. PCA plots show two separate clusters for untreated and DSS-treated RMs. RMs with acute DSS treatment are distributed between untreated and treated clusters. SIV+ RMs tended to cluster with RMs not treated with DSS. RMs treated with both SIV and DSS tended to cluster with RMs without DSS treatment. b (i) Heatmap of 425 differentially expressed proteins between DSS-untreated (n = 6), and DSS chronic RMs (n = 12, adjusted p value<0.05, BH correction). Protein expression is also shown for RMs with acute DSS treatments (n = 5). Main functions based on DAVID analysis (adjusted p value <0.05, BH correction) are listed to the right of each cluster. Major downregulated pathways included oxidative phosphorylation, fatty acid metabolism, and butanoate metabolism. Upregulated pathways included complement and coagulation cascades, ribosomal pathways, and regulation of the actin cytoskeleton. (ii) Heatmap of 37 upregulated proteins in SIV+ RMs against DSS-untreated RMs. DAVID analysis of two clusters (adjusted p value <0.05, BH correction) revealed upregulation of defense response to virus and proteasome complex proteins. (c) Biological pathways were analyzed for their ability to classify DSS-untreated RMs (DSS untreated, SIV+ RMs, n = 10) from DSS-treated RMs (DSS acute, DSS chronic, DSS SIV+ n = 20). (i) Thirteen complement components were detected in the dataset and were able to classify DSS-treated RMs (red) from non-treated RMs (blue) with 90.2% calibration (Cal) accuracy and 67.4% cross-validation (CV) accuracy. (ii) One hundred and twenty eight proteins involved in cytoskeletal processes showed a 97.2% Cal accuracy and 76.9% CV accuracy. (iii) Seventeen proteins involved in β-oxidization of fatty acids were also able to distinguish DSS-treated RMs with 80.7% Cal accuracy and 60.3% CV accuracy