Proteomic study provides new clues for complications of hemodialysis caused by dialysis membrane

In-Depth Analysis of the Extracorporeal Proteome Adsorbed to Dialysis Membranes during Hemodialysis

Used hemodialysis membranes (HD-M) are a valuable reservoir of biological information. Proteins bind to HD-M, but whether this process depends on the type of membrane or patient factors or selectively affects specific protein classes has not been adequately elucidated. State-of-the-art proteomics techniques are capable of identifying and quantifying this therapy-specific subproteome to enable the analysis of disease- or membrane-induced pathophysiologies. We demonstrate the feasibility of the deep proteomic characterization of the extracorporeal proteome adsorbed to HD-M. A shotgun proteomics approach using nano-flow liquid chromatography coupled to mass-spectrometry identified 1648 unique proteins eluted by a chaotropic buffer from the HD-M of eight patients. In total, 995 proteins were present in all eluates; a more stringent approach showed that a core proteome of 310 proteins could be identified independently in all samples. Stability of the dialyzer proteome was demonstrated by a >90% re-identification rate on longitudinal samples of a single patient. The core proteome showed an overrepresentation of pathways of hemostasis and the immune system, and showed differences in membrane materials (polysulfone vs. helixone). This study demonstrates that optimized conditions combined with high-performance proteomics enable the in-depth exploration of the subproteome bound to HD-M, yielding a stable core proteome that can be exploited to study patient-specific factors and improve hemodialysis therapy.

Ionic Liquid-Based Extraction System for In-Depth Analysis of Membrane Protein Complexes

Limited by the rare efficient extraction system in extracting hydrophobic membrane protein complexes (MPCs) without compromising the stability of protein-protein interactions (PPIs), the in-depth functional study of MPCs has lagged far behind. In this study, the first systematic screening of ionic liquids (ILs) was performed and showed that triethylammonium acetate (TEAA) IL exhibited excellent performance in stabilizing PPIs, which was further confirmed by molecular docking simulations. By combining TEAA with the conventional detergent Nonidet P-40 (NP-40), a novel IL-based extraction system, i-TAN (TEAA IL with 1% NP-40), was proposed, which demonstrated superior performance in extracting and stabilizing MPCs, attributed to its larger size, more uniform distribution, and closer-to-neutral microenvironment of micelles. Extraction of MPCs with i-TAN allowed the confident identification of more hydrophobic EGFR-interacting proteins that are easily dissociated during the extraction process. Quantitative analysis of the difference in EGFR complexes between trastuzumab-sensitive and trastuzumab-resistant breast cancer cells provided comprehensive insights to understand the drug resistance mechanism, suggesting that i-TAN has great potential in interactomics and functional analysis of MPCs. This study provides a novel strategy for MPC extraction and downstream processing.

Molecularly imprinted monoliths: Recent advances in the selective recognition of biomacromolecules related biomarkers

Biomarkers are significant indicators to assist the early diagnosis of diseases and assess the therapeutic response. However, due to the low-abundance of biomarkers in complex biological fluids, it is highly desirable to explore efficient techniques to attain their selective recognition and capture before the detection. Molecularly imprinted monoliths integrate the high selectivity of imprinted polymers and the rapid convective mass transport of monoliths, and as a result are promising candidates to achieve the specific enrichment of biomarkers from complex samples. This review summarizes the various imprinting approaches for the preparation of molecularly imprinted monoliths. The state-of-art advances as an effective platform for applications in the selective capture of biomacromolecules related biomarkers were also outlined. This article is protected by copyright. All rights reserved.

An integrated model using the Taguchi method and artificial neural network to improve artificial kidney solidification parameters

BACKGROUND

Hemodialysis mainly relies on the "artificial kidney," which plays a very important role in temporarily or permanently substituting for the kidney to carry out the exchange of waste and discharge of water. Nevertheless, a previous study on the artificial kidney has paid little attention to the optimization of factors and levels for reducing the solidification of the artificial kidney during the hemodialysis procedure. Thus, this study proposes an integrated model that uses the Taguchi method, omega formula, and back-propagation network to determine the optimal factors and levels for addressing this issue.

METHODS

First, we collected the recommendations of medical doctors and nursing staff through a small group discussion, and used the Taguchi method to analyze the key factors at different levels. Next, the omega formula was used to convert the analysis results from the Taguchi method to assess the defect rate. Finally, we utilized back-propagation network algorithms to predict the optimal factors and levels for artificial kidney solidification, in order to confirm that the key factors and levels identified can effectively improve the solidification rate of the artificial kidney and thereby enhance the effect of hemodialysis.

RESULTS

The research finding proposes the following as the optimal factors and levels for artificial kidney solidification: the amount of anticoagulation should be set at 500 units, the velocity of blood flow at 300 ml/min, the dehydration volume at 2.5 kg, and the vascular access type as autologous blood vessels. We obtained 270 sets of data from the patients of End Stage Renal Disease (ESRD) under the setting of the optimal combination of the factors at different levels; the defect rate of artificial kidney solidification is 12.9%, which is better than the defect rate of 32% in the original experiment. Meanwhile, the patient characteristics for physiological status in BMI, serum calcium, hematocrit, ferritin, and transferrin saturation percentage are improved by this study.

CONCLUSION

This conclusion validates the ability of the proposed model in this study to improve the solidification rate of the artificial kidney, thereby confirming the model's use as a standard operation procedure in the hemodialysis experiment. The ideas behind and the implications of the proposed model are further discussed in this study.

A Multiplex Fragment-Ion-Based Method for Accurate Proteome Quantification

Multiplex proteome quantification with high accuracy is urgently required to achieve a comprehensive understanding of dynamic cellular and physiological processes. Among the existing quantification strategies, fragment-ion-based methods can provide highly accurate results, but the multiplex capacity is limited to 3-plex. Herein, we developed a multiplex pseudo-isobaric dimethyl labeling (m-pIDL) method to extend the capacity of the fragment-ion-based method to 6-plex by one-step dimethyl labeling with several millidalton and dalton mass differences between precursor ions and enlarging the isolation window of precursor ions to 10 m/ z during data acquisition. m-pIDL showed high quantification accuracy within the 20-fold dynamic range. Notably, the ratio compression was 1.13-fold in a benchmark two-proteome model (5:1 mixed E. coli proteins with HeLa proteins as interference), indicating that by m-pIDL, the ratio distortion of isobaric labeling approaches and the approximate 40% ratio shift of the label-free quantification strategy could be effectively eliminated. Additionally, m-pIDL did not show ratio variation among post-translational modifications (CV = 6.66%), which could benefit the measurement of universal protein properties for proteomic atlases. We further employed m-pIDL to monitor the time-resolved responses of the TGF-β-induced epithelial-mesenchymal transition (EMT) in lung adenocarcinoma A549 cell lines, which facilitated the finding of new potential regulatory proteins. Therefore, the 6-plex quantification of m-pIDL with the remarkably high accuracy might create new prospects for comprehensive proteome analysis.

Proteomics investigation of the changes in serum proteins after high- and low-flux hemodialysis

PURPOSE

This study aimed to use proteomics methods to investigate the changes in serum protein levels after high- and low-flux hemodialysis (HD).

METHODS

Before and after HD, serum samples were obtained from two selected patients who were treated with a Polyflux 140 H high-flux dialyzer and a Polyflux 14 L low-flux dialyzer during two continuous therapy sessions. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to identify the proteins.

RESULTS

A total of 212 and 203 serum proteins were identified after high-flux and low-flux HD, respectively. After high-flux HD, 21 proteins increased, and 132 proteins decreased. After low-flux HD, 87 proteins increased, and 45 proteins decreased. High-flux HD led to a significantly greater reduction in protein levels than low-flux HD (0.73 ± 0.13 vs. 0.84 ± 0.18, p = .00). Among the increased and decreased proteins, the isoelectric point (pI) values mainly ranged from 5 to 7, and the molecular weights (Mws) were mostly smaller than 30 kDa. The serum proteins showed no difference in pI or Mw for high- and low-flux HD. Gene ontology (GO) analysis showed that the detected proteins were related to immune system processes and complement activation.

CONCLUSIONS

Serum protein levels differentially changed after high- and low-flux HD. Long-term effects should be observed in future studies.