SPPUSM: An MS/MS spectra merging strategy for improved low-input and single-cell proteome identification.

Single and rare cell analysis provides unique insights into the investigation of biological processes and disease progress by resolving the cellular heterogeneity that is masked by bulk measurements. Although many efforts have been made, the techniques used to measure the proteome in trace amounts of samples or in single cells still lag behind those for DNA and RNA due to the inherent non-amplifiable nature of proteins and the sensitivity limitation of current mass spectrometry. Here, we report an MS/MS spectra merging strategy termed SPPUSM (same precursor-produced unidentified spectra merging) for improved low-input and single-cell proteome data analysis. In this method, all the unidentified MS/MS spectra from multiple test files are first extracted. Then, the corresponding MS/MS spectra produced by the same precursor ion from different files are matched according to their precursor mass and retention time (RT) and are merged into one new spectrum. The newly merged spectra with more fragment ions are next searched against the database to increase the MS/MS spectra identification and proteome coverage. Further improvement can be achieved by increasing the number of test files and spectra to be merged. Up to 18.2% improvement in protein identification was achieved for 1 ng HeLa peptides by SPPUSM. Reliability evaluation by the "entrapment database" strategy using merged spectra from human and E. coli revealed a marginal error rate for the proposed method. For application in single cell proteome (SCP) study, identification enhancement of 28%-61% was achieved for proteins for different SCP data. Furthermore, a lower abundance was found for the SPPUSM-identified peptides, indicating its potential for more sensitive low sample input and SCP studies.

An angled-shape tip-based strategy for highly sensitive proteomic profiling of a low number of cells.

Profiling proteins plays an essential role in understanding the functions and dynamic networks in biological systems. Mass spectrometry-based proteomic analysis commonly requires multistep sample processing, which results in severe sample loss. Although the recently developed microproteomic strategies have substantially reduced sample loss via droplet microfluidic technology, specialized equipment and well-trained personnel are needed, which may limit their wide adoption. Here, we report an angled-shape tip-based strategy for rapid sample preparation and sensitive proteomic profiling of small cell populations (<1000 cells). The angled-shape tip provided a 'reactor' for the entire proteomic sample processing workflow, from cell capture and lysis to protein digestion, eliminating the sample transfer-induced protein loss. The angled-shape tip was surface-treated for anti-protein adsorption which further reduced the sample loss. Using this strategy, 1241 ± 38-4110 ± 37 protein groups and 4010 ± 700-34 879 ± 575 peptides were identified from 10-1000 HeLa cells with high quantification reproducibility in only 4.5 h sample processing time, which was superior to the reported methods and commercial kits, especially for <100 cells. This approach was easily accessible, straightforward to operate, and compatible with flow cytometry-based cell sorting. It showed great potential for in-depth proteomic profiling of rare cells (<1000 cells) in both basic biological research and clinical application.

A New Strategy for High-Efficient Tandem Enrichment and Simultaneous Profiling of N-Glycopeptides and Phosphopeptides in Lung Cancer Tissue.

N-glycosylation and phosphorylation, two common posttranslational modifications, play important roles in various biological processes and are extensively studied for biomarker and drug target screening. Because of their low abundance, enrichment of N-glycopeptides and phosphopeptides prior to LC-MS/MS analysis is essential. However, simultaneous characterization of these two types of posttranslational modifications in complex biological samples is still challenging, especially for tiny amount of samples obtained in tissue biopsy. Here, we introduced a new strategy for the highly efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO2 microparticles. The N-glycopeptides and phosphosites obtained by tandem enrichment were 21%-377% and 22%-263% higher than those obtained by enriching the two PTM peptides separately, respectively, using 160-20 µg tryptic digested peptides as the starting material. Under the optimized conditions, 2798 N-glycopeptides from 434 N-glycoproteins and 5130 phosphosites from 1986 phosphoproteins were confidently identified from three technical replicates of HeLa cells by mass spectrometry analysis. Application of this tandem enrichment strategy in a lung cancer study led to simultaneous characterization of the two PTM peptides and discovery of hundreds of differentially expressed N-glycosylated and phosphorylated proteins between cancer and normal tissues, demonstrating the high sensitivity of this strategy for investigation of dysregulated PTMs using very limited clinical samples.

Suboptimal management of hypertriglyceridemia in the outpatient setting is associated with the recurrent pancreatitis: A retrospective cohort study.

Hyperlipemia is a well-established etiology of acute pancreatitis. However, few data are available in the medical literature about the management of triglyceride levels in the outpatient setting in patients with hypertriglyceridemic acute pancreatitis (HTG-AP). We evaluated the blood triglyceride levels and followed the triglyceride management of patients with HTG-AP.This retrospective study enrolled patients with HTG-AP from January 2013 to March 2019 in the Affiliated Hospital of Southwest Medical of University. By reviewing the hospitalization records and the follow-up data, the clinical features, blood triglyceride levels, use of lipid-lowering medications and rate of blood triglyceride levels monitoring after hospital discharge were analyzed.A total of 133 patients (46 women, 87 men; median age at presentation 37.4 years) diagnosed with HTG-AP were enrolled in the study. Thirty-two patients (24.1%) presented with recurrent acute pancreatitis (RAP). Patients who had RAP were younger and had higher blood triglyceride levels than those with a single attack (P < .05). No difference in serum amylase levels, hospitalization duration or mortality rate were observed between non-recurrent acute pancreatitis and RAP patients. Lipid monitoring was only observed in 12.8% of patients and 10 patients (7.5%) took medications to control their blood triglyceride levels after hospital discharge. The follow-up of triglyceride levels in the outpatient setting were higher in RAP patients than in patients with non-recurrent acute pancreatitis (P < .05). Among the patients who measured their triglyceride levels after discharge, 83.3% of patients with RAP had at least 1 follow-up triglyceride level that was higher than 500 mg/dL, while no patients had an HTG-AP attack with a triglyceride level higher than 500 mg/dL.Triglyceride levels after hospital discharge higher than 500 mg/dL may be associated with an increased risk of relapse of clinical acute pancreatitis events. Inappropriate management for triglyceride control in the outpatient setting may be associated with an increased risk of relapse of clinical HTG-AP events.

Blockade of high-mobility group box 1 attenuates intestinal mucosal barrier dysfunction in experimental acute pancreatitis.

The release of inflammatory cytokines, that plays a dominant role in local pancreatic inflammation and systemic complications in severe acute pancreatitis (SAP). High-mobility group box 1 (HMGB1) is implicated in the mechanism of organ dysfunction and bacterial translocation in SAP. This current study aims to investigate possible role of HMGB1 in the intestinal mucosal barrier dysfunction of SAP, and the effect of anti-HMGB1 antibody treatment in intestinal mucosal injury in SAP. Our data revealed that the HMGB1 expression was significantly increased in AP mice induced by caerulein and LPS, and the inhibition of HMGB1 played a protective role in intestinal mucosal barrier dysfunction, reduced the serum level of other proinflammatory cytokines include IL-1ß, IL-6, TNF-α. Next we investigated the downstream receptors involving in HMGB1 signaling. We found that the expressions of toll-like receptor (TLR) 4 and TLR9 were elevated in ileum of AP mice, the administration of HMGB1 neutralizing antibody significantly reduced the TLR4 and TLR9 expression. It was concluded that HMGB1 contributed the mechanism to the intestinal mucosal barrier dysfunction during AP. Blockade of HMGB1 by administration of HMGB1 neutralizing antibody may be a beneficial therapeutic strategy in improving intestinal mucosal barrier dysfunction in SAP.

Endoplasmic reticulum stress may not be involved in intestinal epithelial cell apoptosis in experimental acute pancreatitis.

OBJECTIVES: To investigate whether endoplasmic reticulum (ER) stress is activated in the intestinal epithelium of acute pancreatitis (AP), and whether it is one of the inducing factors of the intestinal epithelial cell apoptosis in AP. METHODS: Twenty-four rats were randomly divided into two groups. AP was induced via retrograde injection of 3 % sodium taurocholate into the pancreatic duct. As a control group, rats received a sham operation. Forty-eight hours after the operation, the ultrastructural changes of ileal epithelial cells were investigated by transmission electron microscope. The protein expressions of GRP78, CHOP, caspase-12, and JNK in the ileal epithelium were determined by immunohistochemistry, and apoptosis was determined by TdT-mediated dUTP nick end labeling. The mRNA expressions of GRP78, CHOP, caspase-12, and JNK in the ileal epithelium were determined using quantitative RT-PCR. RESULTS: The ileal epithelium in rats with AP had significantly higher apoptotic cells compared with that of the control rats (P < 0.05). ER stress was activated in the ileal epithelium, which was characterized by dilated, irregular ER and upregulated expressions of GRP78 mRNA and protein. The mRNA and protein expressions of CHOP, caspase-12, and JNK in rats with AP were similar to that in the control rats (P > 0.05). CONCLUSIONS: ER stress is induced in intestinal epithelium during AP; however, ER stress is not likely to be involved in the apoptosis of the intestinal epithelium during AP.

ER stress and ER stress-induced apoptosis are activated in gastric SMCs in diabetic rats.

AIM: To investigate the gastric muscle injury caused by endoplasmic reticulum (ER) stress in rats with diabetic gastroparesis. METHODS: Forty rats were randomly divided into two groups: a control group and a diabetic group. Diabetes was induced by intraperitoneal injection of 60 mg/kg of streptozotocin. Gastric emptying was determined at the 4(th) and 12(th) week. The ultrastructural changes in gastric smooth muscle cells (SMCs) were investigated by transmission electron microscopy. TdT-mediated dUTP nick end labeling (TUNEL) assay was performed to assess apoptosis of SMCs. Expression of the ER stress marker, glucose-regulated protein 78 (GRP78), and the ER-specific apoptosis mediator, caspase-12 protein, was determined by immunohistochemistry. RESULTS: Gastric emptying was significantly lower in the diabetic rats than in the control rats at the 12(th) wk (40.71% ± 2.50%, control rats vs 54.65% ± 5.22%, diabetic rats; P < 0.05). Swollen and distended ER with an irregular shape was observed in gastric SMCs in diabetic rats. Apoptosis of gastric SMCs increased in the diabetic rats in addition to increased expression of GRP78 and caspase-12 proteins. CONCLUSION: ER stress and ER stress-mediated apoptosis are activated in gastric SMCs in diabetic rats with gastroparesis.

Glucagonlike peptide 2 protects intestinal barrier in severe acute pancreatitis through regulating intestinal epithelial cell proliferation and apoptosis.

OBJECTIVE: To investigate the protective effect of glucagon-like peptide 2 (GLP-2) on intestinal barrier dysfunction in severe acute pancreatitis and to explore the putative mechanism of this effect. METHODS: Thirty rats were randomly divided into 3 groups. Group 1 received sham operation. Severe acute pancreatitis was induced in group 2 and group 3 via retrograde injection of 3% sodium taurocholate to the pancreatic duct. Rats in group 3 were peritoneally injected with GLP-2. Intestinal barrier dysfunction was characterized by the histological measurements and concentration of plasma diamine oxidase. The tissue sections of ileum were collected for the detection of proliferating cell nuclear antigen protein and apoptosis. RESULTS: Glucagon-like peptide 2 administration improved the ileal mucosal injury, which was also demonstrated by the histological score of ileal mucosa. The concentration of diamine oxidase was decreased in rats with acute pancreatitis treated with GLP-2. Acute pancreatitis-induced epithelial cell apoptosis was partly prevented by GLP-2. Immunohistochemical staining of proliferating cell nuclear antigen protein was increased in group 3 compared with that in group 2. CONCLUSIONS: Results from this study suggest that GLP-2 has a protective effect on intestinal barrier dysfunction in rats with severe acute pancreatitis via mechanisms closely involving promotion of cell growth and inhibition of intestinal epithelial cell apoptosis.