bims-prodis 2018-07-01 papers

Issue of 2018‒07‒01
six papers selected by
Nancy Gough
Bioserendipity

J Proteomics. 2018 Jun 20. pii: S1874-3919(18)30253-7. [Epub ahead of print]

Proteomic study of endothelial dysfunction induced by AGEs and its possible role in diabetic cardiovascular complications.

Reema Banarjee, Akshay Sharma, Shakuntala Bai, Arati Deshmukh, Mahesh Kulkarni.

Endothelial dysfunction is one of the primary steps in the development of diabetes associated cardiovascular diseases. Hyperglycemic condition in diabetes promotes accumulation of advanced glycation end products (AGEs) in the plasma, that interact with the receptor for AGEs (RAGE) present on the endothelial cells and negatively affect their function. Using Human umbilical vascular endothelial cells (HUVECs) in culture, the effect of glycated human serum albumin on global proteomic changes was studied by SWATH-MS, a label free quantitative proteomic approach. Out of the 1860 proteins identified, 161 showed higher abundance while 123 showed lesser abundance in cells treated with glycated HSA. Bioinformatic analysis revealed that the differentially regulated proteins were involved in various processes such as apoptosis, oxidative stress etc. that are associated with endothelial dysfunction. Furthermore, the iRegulon analysis and immunofuorescence studies indicated that several of the differentially regulated proteins were transcriptionally regulated by NF-κB, that is downstream to AGE-RAGE axis. Some of the important differentially regulated proteins include ICAM1, vWF, PAI-1that affect important endothelial functions like cell adhesion and blood coagulation. qPCR analysis showed an increase in expression of the AGE receptor RAGE along with other genes involved in endothelial function. AGE treatment to HUVEC cells led to increased oxidative stress and apoptosis. This is the first proteomics study that provides insight into proteomic changes downstream to AGE-RAGE axis leading to endothelial dysfunction and predisposing to cardiovascular complications.SIGNIFICANCE: Cardiovascular disease (CVD) is a major pathological outcome in diabetic patients and it is important to address ways that target its development before the onset. Elevated plasma AGEs in diabetes can affect endothelial function and can continue to show their effects even after blood glucose levels are back to normal. Since endothelial dysfunction acts as one of the initiating factors for the development of CVD, understanding how AGEs affect the endothelial cell proteome to cause dysfunction will provide insight into the mechanisms involved and aid designing new therapeutic approaches.

Keywords: Atherosclerosis; Diabetes; Endothelial dysfunction; Glycation; Mass spectrometry; SWATH

DOI: https://doi.org/10.1016/j.jprot.2018.06.009

In Vivo. 2018 Jul-Aug;32(4):32(4): 871-878

Novel Potential Biomarkers for Opisthorchis viverrini Infection and Associated Cholangiocarcinoma.

Nithikoon Aksorn, Sittiruk Roytrakul, Suthathip Kittisenachai, Kawin Leelawat, Pithi Chanvorachote, Supachai Topanurak, Shinjiro Hamano, Usa Lek-Uthai.

BACKGROUND/AIM: Early detection of disease is a pivotal factor for determining prognosis and clinical outcome of patients with cancer. As cholangiocarcinoma (CCA) is currently difficult to detect and most cases of such cancer present with late-stage disease at the time of initial diagnosis, we employed proteomic analysis of the bile to identify potential candidate biomarkers for Opisthorchis viverrini (OV)-associated CCA.MATERIALS AND METHODS: Proteins in pooled bile samples from patients with CCA and OV infection, with CCA without OV infection, with OV infection but no CCA, and with neither OV infection nor CCA were separated by 15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, in-gel trypsin digestion and analyzed by liquid chromatography-tandem mass spectrometry.
RESULTS: According to our analysis, three proteins, namely aristaless-like homeobox1 isoform X1 (ALX1), major histocompatibility complex polypeptide-related sequence A (MICA), and uncharacterized protein C14orf105 isoform X12 were found to be potential markers for OV infection, as they were predominantly found in all OV-infected groups. Although these proteins were detected in both OV-infected patients with and without CCA, their abundance was 2.90-, 7.06-and 3.65-fold higher, respectively, in those with CCA. In patients with CCA, potential novel biomarkers wre immunoglobulin heavy chain, translocated in liposarcoma (TLS), visual system homeobox 2 (VSX2) and an unnamed protein product.
CONCLUSION: We provided novel information regarding potential biomarkers for OV infection and CCA. These two protein profiles could benefit diagnosis as well as monitoring of CCA.

Keywords: Opisthorchis viverrini; bile; biomarkers; cholangiocarcinoma; proteomics

DOI: https://doi.org/10.21873/invivo.11321

J Chromatogr A. 2018 Jun 09. pii: S0021-9673(18)30763-5. [Epub ahead of print]

Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling.

Lu Xue, Lin Lin, Wenbin Zhou, Wendong Chen, Jun Tang, Xiujie Sun, Peiwu Huang, Ruijun Tian.

Plasma proteome profiling by LC-MS based proteomics has drawn great attention recently for biomarker discovery from blood liquid biopsy. Due to standard multi-step sample preparation could potentially cause plasma protein degradation and analysis variation, integrated proteomics sample preparation technologies became promising solution towards this end. Here, we developed a fully integrated proteomics sample preparation technology for both fast and deep plasma proteome profiling under its native pH. All the sample preparation steps, including protein digestion and two-dimensional fractionation by both mixed-mode ion exchange and high-pH reversed phase mechanism were integrated into one spintip device for the first time. The mixed-mode ion exchange beads design achieved the sample loading at neutral pH and protein digestion within 30 min. Potential sample loss and protein degradation by pH changing could be voided. 1 μL of plasma sample with depletion of high abundant proteins was processed by the developed technology with 12 equally distributed fractions and analyzed with 12 h of LC-MS gradient time, resulting in the identification of 862 proteins. The combination of the Mixed-mode-SISPROT and data-independent MS method achieved fast plasma proteome profiling in 2 h with high identification overlap and quantification precision for a proof-of-concept study of plasma samples from 5 healthy donors. We expect that the Mixed-mode-SISPROT become a generally applicable sample preparation technology for clinical oriented plasma proteome profiling.

Keywords: Biomarker; Integrated sample preparation; Multi-dimensional fractionation; Plasma proteomics

DOI: https://doi.org/10.1016/j.chroma.2018.06.020

Zhonghua Zhong Liu Za Zhi. 2018 Jun 23. 40(6): 418-421

[Diagnostic value of protein markers in plasma exosomes of lung squamous cell carcinoma].

N Sun, S G Sun, Z L Lu, J He.

Objective: To investigate the tumor-associated protein molecules carried by plasma exosomes of patients with lung squamous cell carcinoma before treatment and analyze their value as clinical markers. Methods: Exosomes from 2 patients with lung squamous cell carcinoma before treatment and 2 healthy controls were collected by ultracentrifugation. Proteomics was applied to analyze the protein expression profiles of exosomes. Candidate molecules were verified in another 30 exosomes samples from lung squamous cell carcinoma and healthy controls using enzyme-linked immunosorbent assay (ELISA). Results: Electron microscopy and particle-counting assay showed that high-quality exosomes were collected. The number of exosomes distributed from 45 to 135 nm in 2 cases of lung cancer patients were 7.89×10(11)/ml and 9.71×10(11)/ml, respectively, significantly higher than 2.76×10(11)/ml and 1.41×10(11)/ml in healthy controls. Proteomic analysis showed that proteins of exosomes in lung squamous cell carcinoma patients were very different from those of healthy controls, and some proteins are related to important functions in tumor progression. 14-3-3ζ from exosomes was selected and further verified as a marker, and the area under the receiver operating characteristic curve (ROC) was 0.68. The sensitivity and specificity of 14-3-3 ζ from exosomes were 60.0% and 80.0%, respectively, suggested that it could be used as a diagnostic marker for lung squamous cell carcinoma. Conclusion: The exosome counts in plasma and the protein molecules from exosomes, such as 14-3-3ζ, are closely related to the tumorigenesis, which can be used to assist clinical diagnosis of lung squamous cell carcinoma patients.

Keywords: 14-3-3ζ; Diagnosis; Exosomes; Lung neoplasms, squamous cell carcinoma; Proteomics

DOI: https://doi.org/10.3760/cma.j.issn.0253-3766.2018.06.004

Fertil Steril. 2018 Jun;pii: S0015-0282(18)30407-2. [Epub ahead of print]109(6): 952-963

Personalized medicine: motivation, challenges, and progress.

Laura H Goetz, Nicholas J Schork.

There is a great deal of hype surrounding the concept of personalized medicine. Personalized medicine is rooted in the belief that since individuals possess nuanced and unique characteristics at the molecular, physiological, environmental exposure, and behavioral levels, they may need to have interventions provided to them for diseases they possess that are tailored to these nuanced and unique characteristics. This belief has been verified to some degree through the application of emerging technologies such as DNA sequencing, proteomics, imaging protocols, and wireless health monitoring devices, which have revealed great inter-individual variation in disease processes. In this review, we consider the motivation for personalized medicine, its historical precedents, the emerging technologies that are enabling it, some recent experiences including successes and setbacks, ways of vetting and deploying personalized medicines, and future directions, including potential ways of treating individuals with fertility and sterility issues. We also consider current limitations of personalized medicine. We ultimately argue that since aspects of personalized medicine are rooted in biological realities, personalized medicine practices in certain contexts are likely to be inevitable, especially as relevant assays and deployment strategies become more efficient and cost-effective.

Keywords: Precision medicine; biomarkers; genomics; patient monitoring

DOI: https://doi.org/10.1016/j.fertnstert.2018.05.006

Microb Pathog. 2018 Jun 21. pii: S0882-4010(18)30066-4. [Epub ahead of print]123 9-17

Proteomic changes in EHEC O157:H7 under catechin intervention.

Zongjun Li, Jiaqi Xie, Xing Tian, Ke Li, Aixiang Hou, Yuanliang Wang.

Catechin exhibits antimicrobial activity against various microorganisms, such as EHEC O157:H7. This study reports the bactericidal effect of catechin on EHEC O157:H7 in simulated human gastrointestinal environment and the underlying antibacterial mechanism. Bacteriostasis test results showed that the minimum bactericidal concentration of catechin for EHEC O157:H7 was 5 g/L. The bactericidal effect of catechin in the gastrointestinal juice became more significant with increased culture time, and catechin exhibited a synergistic effect with bile salt in inhibiting EHEC O157:H7. Changes in the profile of protein expression in EHEC O157:H7 in response to catechin intervention were investigated. Two-dimensional electrophoresis identified 34 proteins with significantly altered expression. A total of 2 and 12 proteins were upregulated and downregulated, respectively. However, 20 proteins disappeared. No new protein was expressed compared with the control. Hence, catechin intervention resulted in diverse changes in the expression of proteins associated with cell structure and genetic information processing. Catechin could cause the disappearance of certain proteins or the destruction of certain peptides. These processes lead to the inhibition of EHEC O157: H7 cells.

Keywords: Bacterial proteome; Bactericidal effect; Catechin; EHEC O157:H7; Two-dimensional electrophoresis