Improved Integrated Whole Proteomic and Phosphoproteomic Profiles of Severe Acute Pancreatitis

Abstract

Severe acute pancreatitis (SAP) is caused by complicated biological factors, and revealing its complex pathogenesis by single-target analysis is difficult. Systematic studies have developed slowly because extraction of degradable pancreatic proteins exposed to multiple proteases is challenging. We present integrated whole proteomic and phosphoproteomic profiles of SAP rats based on a modified protein extraction strategy with less protein degradation. Data-dependent acquisition (DDA) and data-independent acquisition (DIA) strategies were applied to select an appropriate method. Total 275 differentially expressed proteins and 757 differentially expressed phosphorylated proteins were identified by DIA-based quantitative proteomics. Several signal transduction pathways, including the AMPK, MAPK, and PI3K-Akt pathways, were enriched in SAP. Up-regulation of phosphorylated proteins involved in the process of TNFA signaling and inflammatory response was also detected in SAP. Our results improve the understanding of SAP development and progression.

Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in Arabidopsis Seedlings upon Cold Exposure

“…Ga 3+ -based immobilized metal affinity chromatography (Ga-IMAC) was used to enrich phosphopeptides in this study since it was shown to be reproducible and specific in purifying phosphoproteins in Arabidopsis seedlings [ 26 ] and efficient in enriching phosphopeptides in Arabidopsis inflorescence tissues [ 27 ] and in rat pancreas [ 28 ]. A spectral library for phosphoproteome was constructed using Ga-IMAC enrichment followed by high-pH reversed-phase fractionation, LC-MS/MS analysis and identification by Proteome Discoverer ( Figure 1 and Table S1 , FDR < 1% for PSMs and peptide groups).…”

Transcriptome and proteome analysis of the antitumor activity of maslinic acid against pancreatic cancer cells

“…Housekeeping genes for basic cell maintenance are also suggested to maintain constant expression levels in all cells, under all conditions [ 14 ]. Our analysis revealed that housekeeping proteins, including ACTB, PGK1, RPS18, RPS27A, RPL11, RPL19, RPL32, NONO, ARHGDIA, TUBA1B, TUBA1C, TUBB4B, and HSP90B1 were stably expressed in both the control and MA groups ( Supplementary Figure 2C ), demonstrating the reliability of the proteomic sequencing results [ 15 ].…”

Temporal Proteomic and Lipidomic Profiles of Cerulein-Induced Acute Pancreatitis Reveal Novel Insights for Metabolic Alterations in the Disease Pathogenesis

“…Additionally, it was surprisingly that the majority of altered proteins revealed by KEGG that are involved in energy metabolism and amino acid metabolism showed a pattern of pullback after growing at the inflammatory peak, which was different from the prior proteomics findings. ,, For example, prior proteomics studies on the CER-induced AP rat model found that important enzymes involved in the TCA cycle, glycolysis, or BCAA metabolism were reduced . Based on a rat model of SAP, decreased oxidative phosphorylation, carbon metabolism, and degradation of valine, leucine, and isoleucine were also observed . This heterogeneity needed to be further demonstrated and compared.…”

“…Severity indices of CER-induced AP in mice; upset plot showing overlapping proteins in 30 GO terms; relationships between AP dysregulated proteins and KEGG pathways (top 10); relative expressions of SPIs, filaments, and HSP 70s; enrichment analysis of 306 proteins that were screened by time-course analysis after the removal of greater abundances proteins; mass list of DIA windows; and list of 25…”

“…Systematic proteomic studies have considerably accelerated the hunt for biomarkers and revealed disease mechanisms in earlier pancreatic disease research. − Particularly, the advent of high-throughput proteomics based on LC–MS/MS has elucidated hundreds of divergent proteins and effectively addressed the workflow issue of pancreatic protein degradation . Numerous important up- and down-regulated proteins associated with inflammation, digestive enzymes, metabolism, signal transduction, and other processes were identified by these quantitative proteomic analyses in conjunction with functional annotations. − However, we were unable to fully comprehend the pathophysiology of AP due to the inconsistent protein changes obtained from CER − , or sodium taurocholate (NaT)-induced AP rats at a single time point.…”