Data-independent acquisition-based quantitative proteomic analysis reveals differences in host immune response of peripheral blood mononuclear cells to sepsis

Human peripheral blood mononuclear cells as a valuable source of disease-related biomarkers: Evidence from comparative proteomics studies

PURPOSE

The discovery of specific and sensitive disease-associated biomarkers for early diagnostic purposes of many diseases is still highly challenging due to various complex molecular mechanisms triggered, high variability of disease-related interactions, and an overlap of manifestations among diseases. Human peripheral blood mononuclear cells (PBMCs) contain protein signatures corresponding to essential immunological interplay. Certain diseases stimulate PBMCs and contribute towards modulation of their proteome which can be effectively identified and evaluated via the comparative proteomics approach.

EXPERIMENTAL DESIGN

In this review, we made a detailed survey of the PBMCS-derived protein biomarker candidates for a variety of diseases, published in the last 15 years. Articles were preselected to include only comparative proteomics studies.

RESULTS

PBMC-derived biomarkers were investigated for cancer, glomerular, neurodegenerative/neurodevelopmental, psychiatric, chronic inflammatory, autoimmune, endocrinal, infectious, and other diseases. A detailed review of these studies encompassed the proteomics platforms, proposed candidate biomarkers, their immune cell type specificity, and potential clinical application.

CONCLUSIONS

Overall, PBMCs have shown a solid potential in giving early diagnostic and prognostic biomarkers for many diseases. The future of PBMC biomarker research should reveal its full potential through well-designed comparative studies and extensive testing of the most promising protein biomarkers identified so far.

Proteomic Profiling of Early Secreted Proteins in Response to Lipopolysaccharide-Induced Vascular Endothelial Cell EA.hy926 Injury

Sepsis is a crucial public health problem with a high mortality rate caused by a dysregulated host immune response to infection. Vascular endothelial cell injury is an important hallmark of sepsis, which leads to multiple organ failure and death. Early biomarkers to diagnose sepsis may provide early intervention and reduce risk of death. Damage-associated molecular patterns (DAMPs) are host nuclear or cytoplasmic molecules released from cells following tissue damage. We postulated that DAMPs could potentially be a novel sepsis biomarker. We used an in vitro model to determine suitable protein-DAMPs biomarkers for early sepsis diagnosis. Low and high lipopolysaccharide (LPS) doses were used to stimulate the human umbilical vein endothelial cell line EA.hy926 for 24, 48, and 72 h. Results showed that cell viability was reduced in both dose-dependent and time-dependent manners. Cell injury was corroborated by a significant increase in lactate dehydrogenase (LDH) activity within 24 h in cell-conditioned medium. Secreted protein-DAMPs in the supernatant, collected at different time points within 24 h, were characterized using shotgun proteomics LC-MS/MS analysis. Results showed that there were 2233 proteins. Among these, 181 proteins from the LPS-stimulated EA.hy926 at 1, 12, and 24 h were significantly different from those of the control. Twelve proteins were up-regulated at all three time points. Furthermore, a potential interaction analysis of predominant DAMPs-related proteins using STITCH 5.0 revealed the following associations with pathways: response to stress; bacterium; and LPS (GO:0080134; 0009617; 0032496). Markedly, alpha-2-HS-glycoprotein (AHSG or fetuin-A) and lactotransferrin (LTF) potentially presented since the first hour of LPS stimulation, and were highly up-regulated at 24 h. Taken together, we reported proteomic profiling of vascular endothelial cell-specific DAMPs in response to early an in vitro LPS stimulation, suggesting that these early damage-response protein candidates could be novel early biomarkers associated with sepsis.

A complementary approach for genetic diagnosis of inborn errors of immunity using proteogenomic analysis

Advances in next-generation sequencing technology have identified many genes responsible for inborn errors of immunity (IEI). However, there is still room for improvement in the efficiency of genetic diagnosis. Recently, RNA sequencing and proteomics using peripheral blood mononuclear cells (PBMCs) have gained attention, but only some studies have integrated these analyses in IEI. Moreover, previous proteomic studies for PBMCs have achieved limited coverage (approximately 3000 proteins). More comprehensive data are needed to gain valuable insights into the molecular mechanisms underlying IEI. Here, we propose a state-of-the-art method for diagnosing IEI using PBMCs proteomics integrated with targeted RNA sequencing (T-RNA-seq), providing unique insights into the pathogenesis of IEI. This study analyzed 70 IEI patients whose genetic etiology had not been identified by genetic analysis. In-depth proteomics identified 6498 proteins, which covered 63% of 527 genes identified in T-RNA-seq, allowing us to examine the molecular cause of IEI and immune cell defects. This integrated analysis identified the disease-causing genes in four cases undiagnosed in previous genetic studies. Three of them could be diagnosed by T-RNA-seq, while the other could only be diagnosed by proteomics. Moreover, this integrated analysis showed high protein-mRNA correlations in B- and T-cell-specific genes, and their expression profiles identified patients with immune cell dysfunction. These results indicate that integrated analysis improves the efficiency of genetic diagnosis and provides a deep understanding of the immune cell dysfunction underlying the etiology of IEI. Our novel approach demonstrates the complementary role of proteogenomic analysis in the genetic diagnosis and characterization of IEI.

Abnormal Proteomics Profile of Plasma Reveals the Immunological Pathogenesis of Severe Aplastic Anemia

Severe aplastic anemia (SAA) is an immune-mediated bone marrow failure characterized by pancytopenia. This study was aimed at uncovering proteins of plasma that were differentially expressed in SAA patients. 8 SAA patients and 8 health controls were enrolled and detected by data independent acquisition (DIA) technology. 154 differential expression proteins (DEPs) in plasma of SAA patients were identified. GO and KEGG analyses indicated DEPs were mainly involved in the immune system process. Specifically, C-C motif chemokine 18 (CCL18), matrix metalloproteinase-3 (MMP3), histidine-rich glycoprotein (HRG), and lactotransferrin (lactoferrin (Lf)) may play an important role in the immune pathogenesis of SAA. CCL18, MMP3, HRG, and Lf might be potential biomarkers for SAA.

Human peripheral blood mononuclear cells: A review of recent proteomic applications

Human peripheral blood mononuclear cells (PBMCs) represent a sentinel blood sample which reacts to different pathophysiological stimuli in the form of immunological responses/immunophenotypic changes. The study of molecular content of PBMCs can provide better understanding of immune processes giving the possibility of monitoring the health conditions of the host organism. Proteomic analysis of PBMCs can achieve mentioned goal as important immune-related biomarkers are easily accessible for analysis. PBMCs have been gaining attention in different research areas including preclinical or clinical investigations. In this review, recent applications of proteomic analysis of PBMCs are described and discussed. Approaches are divided based on different proteomic workflows such as in-gel, in-solution and on-filter modes. The effect of various diseases such as autoimmune, cancer, neurodegenerative, viral, metabolic, and various immune stimulations such as radiation, vaccine, corticosteroids over PBMCs proteome, are described with emphasis on promising protein biomarker candidates. This article is protected by copyright. All rights reserved.

Nephrotoxicity evaluation of 3-monochloropropane-1,2-diol exposure in Sprague-Dawley rats using data-independent acquisition-based quantitative proteomics analysis

3-Monochloropropane-1,2-diol (3-MCPD), as a heat-induced food process contaminant, possesses strongly toxic effect on kidney. The present study focuses on characterizing the proteome and clarifying the underlying molecular regulatory mechanisms in a model of kidney injury in rats treated with 3-MCPD. Data-independent acquisition (DIA)-mass spectrometry (MS) based proteomics was used to identify dysregulated proteins in kidney tissues of Sprague-Dawley (SD) rats treated with 30 mg/kg/day 3-MCPD by gavage for 28 days. It was found that a total of 975 proteins were deregulated after 3-MCPD treatment. Bioinformatic analyses revealed that several enzymes related to the metabolisms of amino acid, lipid and carbohydrate in endogenous metabolism were altered in response to 3-MCPD treatment. Moreover, some proteins involved in these pathways were also changed, mainly including oxidative stress, oxidative phosphorylation, apoptosis and autophagy. Our study unravels the vital roles of loss of mitochondrial homeostasis and function and cell death pathways in the development of renal damage induced by 3-MCPD, which provides further valuable insights into the initiation and resolution of 3-MCPD nephrotoxicity. The proposed DIA-MS workflow not only provides a choice for proteomic analysis in toxicological research, but also provides a more comprehensive understanding of the molecular mechanisms of nephrotoxicity induced by toxins.

Low-Density Granulocyte Contamination From Peripheral Blood Mononuclear Cells of Patients With Sepsis and How to Remove It - A Technical Report

Elucidating the mechanisms contributing to the dysregulated host response to infection as part of the syndrome is a current challenge in sepsis research. Peripheral blood mononuclear cells are widely used in immunological studies. Density gradient centrifugation, a common method, is of limited use for blood drawn from patients with sepsis. A significant number of low-density granulocytes co-purify contributing to low purity of isolated peripheral blood mononuclear cells. Whole blood anticoagulated with lithium heparin was drawn from patients with sepsis (n=14) and healthy volunteers (n=11). Immediately after drawing, the plasma fraction was removed and PBMC were isolated from the cellular fraction by density gradient centrifugation. Samples derived from patients with sepsis were subsequently incubated with cluster of differentiation 15 MicroBeads and granulocytes were depleted using magnetic-activated cell sorting. Core cellular functions as antigen presentation and cytokine secretion were analyzed in cells isolated from healthy volunteers (n=3) before and after depletion to confirm consistent functionality. We report here that depleting CD15⁺ cells after density gradient centrifugation is a feasible way to get rid of the low-density granulocyte contamination. Afterwards, the purity of isolated, functionally intact peripheral blood mononuclear cells is comparable to healthy volunteers. Information on the isolation purity and identification of the containing cell types are necessary for good comparability between different studies. Depletion of CD15⁺ cells after density gradient centrifugation is an easy but highly efficient way to gain a higher quality and more reliability in studies using peripheral blood mononuclear cells from septic patients without affecting the functionality of the cells.

LGALS3BP: A Potential Plasma Biomarker Associated with Diagnosis and Prognosis in Patients with Sepsis

Purpose

This study aimed to screen differentially expressed proteins (DEPs) in plasma of patients with sepsis through data-independent acquisition (DIA) and enzyme-linked immunosorbent assays (ELISAs), and provide convenient and accurate serum markers for determining the condition of septic patients.

Methods

A total of 53 septic patients and 16 normal controls who were admitted to the Affiliated Hospital of Southwest Medical University between January 2019 and December 2020 were enrolled in this study; 6 specimens from the normal group and 15 from the sepsis group were randomly selected for DIA-based quantitative proteomic analysis. The acquired data were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and a protein-protein interaction (PPI) network was constructed to screen potential markers. The selected proteins were further verified through ELISAs. The differences between control and sepsis groups and between survivors and non-survivors were analysed. Receiver operating characteristic (ROC) curves were drawn to explore their diagnostic value and prognostic efficacy.

Results

A total of 149 DEPs were identified by bioinformatics methods. The analyses showed that these proteins are mainly involved in biological processes such as cell movement, stress response, cell proliferation, and immune response. Functional pathway analysis showed that they are mainly involved in leukocyte transendothelial migration, protein synthesis and processing, and various bacterial infections. LGALS3BP was selected as a potential plasma biomarker and further verified through an ELISA. Its level in septic patients was significantly higher than that in normal controls, and its level in non-survivors was also higher than that in survivors. The ROC curves suggested its great diagnostic efficacy and prognostic ability in sepsis.

Conclusion

LGALS3BP levels were significantly different between the normal and sepsis groups; it has good diagnostic value in sepsis, and is related to patient prognosis; thus, it might be a biomarker for sepsis.

Development of Prediction Models for New Integrated Models and a Bioscore System to Identify Bacterial Infections in Systemic Lupus Erythematosus

Objectives

Distinguishing flares from bacterial infections in systemic lupus erythematosus (SLE) patients remains a challenge. This study aimed to build a model, using multiple blood cells and plasma indicators, to improve the identification of bacterial infections in SLE.

Design

Building PLS-DA/OPLS-DA models and a bioscore system to distinguish bacterial infections from lupus flares in SLE.

Setting

Department of Rheumatology of the Second Hospital of Shanxi Medical University.

Participants

SLE patients with flares (n = 142) or bacterial infections (n = 106) were recruited in this retrospective study.

Outcome

The peripheral blood of these patients was collected by the experimenter to measure the levels of routine examination indicators, immune cells, and cytokines. PLS-DA/OPLS-DA models and a bioscore system were established.

Results

Both PLS-DA (R2Y = 0.953, Q2 = 0.931) and OPLS-DA (R2Y = 0.953, Q2 = 0.942) models could clearly identify bacterial infections in SLE. The white blood cell (WBC), neutrophile granulocyte (NEUT), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6), IL-10, interferon-γ (IFN-γ), and tumor necrosis factor α (TNF-α) levels were significantly higher in bacteria-infected patients, while regulatory T (Treg) cells obviously decreased. A multivariate analysis using the above 10 dichotomized indicators, based on the cut-off value of their respective ROC curve, was established to screen out the independent predictors and calculate their weights to build a bioscore system, which exhibited a strong diagnosis ability (AUC = 0.842, 95% CI 0.794–0.891). The bioscore system showed that 0 and 100% of SLE patients with scores of 0 and 8–10, respectively, were infected with bacteria. The higher the score, the greater the likelihood of bacterial infections in SLE.

Conclusions

The PLS-DA/OPLS-DA models, including the above biomarkers, showed a strong predictive ability for bacterial infections in SLE. Combining WBC, NEUT, CRP, PCT, IL-6, and IFN-γ in a bioscore system may result in faster prediction of bacterial infections in SLE and may guide toward a more appropriate, timely treatment for SLE.

Proteomic alterations in the plasma of Beagle dogs induced by Toxocara canis infection

Toxocara canis causes ocular larva migrans and visceral larva migrans in humans. Knowledge about the molecular mechanism of T. canis-hosts interaction is limited. The proteomic alterations in the plasma of Beagle dogs induced by T. canis infection were studied by the quantitative mass spectrometry-based data-independent acquisition (DIA). 418, 414 and 411 plasma proteins were identified at 24 h post-infection (hpi), 96 hpi and 36 days post-infection (dpi), including 6, 5 and 23 proteins with differential abundance, respectively. At 24 hpi, the altered proteins, retinoic acid receptor responder protein 2 (RARRES2), WD repeat-containing protein 1 (WDR1), moesin and filamin-A, may participate in pro-inflammatory reaction or promote larvae migration. At 96 hpi, the altered protein C and fibroleukin may maintain the stability of the coagulation system to protect the lung. At 36 dpi, the alterations of C-reactive protein (CRP), ficolin (FCN), complement factor H-related protein 5 (CFHR5) and other complements can affect the three traditional complement system, including the classic pathway, lectin pathway and alternative pathway. These proteins may play important roles in the interaction between T. canis and its definitive hosts. Further study on these altered proteins triggered by T. canis infection may discovery novel therapeutic or diagnostic targets for toxocariasis. SIGNIFICANCE OF THE STUDY: Toxocara canis is one of the globally distributed soil-transmitted helminths, which causes ocular larva migrans and visceral larva migrans in humans and a wide range of warm-blooded animals. T. canis adapts to different microenvironments by resisting and adjusting various biological processes of the hosts. Knowledge about the molecular mechanism of T. canis-hosts interaction is limited. Plasma proteins are good marker for monitoring the occurrence and development of diseases. The proteomic alterations in the plasma of Beagle dogs induced by T. canis infection were studied by the quantitative mass spectrometry-based data-independent acquisition (DIA) in this study. A total of 418, 414 and 411 plasma proteins were identified at 24 h post-infection (hpi), 96 hpi and 36 days post-infection, respectively. Ten protein with differential abundances were validated by using parallel reaction monitoring (PRM). Collectively, our deep proteomic analysis of plasma revealed that proteins alterations were affected by disease development, and proteomic analysis is an ideal method for quantifying changes in circulating factors on a global scale in response to pathophysiological perturbations such as T. canis infection.

Endothelial dysfunction is an early indicator of sepsis and neutrophil degranulation of septic shock in surgical patients

Background

Stratification of the severity of infection is currently based on the Sequential Organ Failure Assessment (SOFA) score, which is difficult to calculate outside the ICU. Biomarkers could help to stratify the severity of infection in surgical patients.

Methods

Levels of ten biomarkers indicating endothelial dysfunction, 22 indicating emergency granulopoiesis, and six denoting neutrophil degranulation were compared in three groups of patients in the first 12 h after diagnosis at three Spanish hospitals.

Results

There were 100 patients with infection, 95 with sepsis and 57 with septic shock. Seven biomarkers indicating endothelial dysfunction (mid‐regional proadrenomedullin (MR‐ProADM), syndecan 1, thrombomodulin, angiopoietin 2, endothelial cell‐specific molecule 1, vascular cell adhesion molecule 1 and E‐selectin) had stronger associations with sepsis than infection alone. MR‐ProADM had the highest odds ratio (OR) in multivariable analysis (OR 11·53, 95 per cent c.i. 4·15 to 32·08; P = 0·006) and the best area under the curve (AUC) for detecting sepsis (0·86, 95 per cent c.i. 0·80 to 0·91; P < 0·001). In a comparison of sepsis with septic shock, two biomarkers of neutrophil degranulation, proteinase 3 (OR 8·09, 1·34 to 48·91; P = 0·028) and lipocalin 2 (OR 6·62, 2·47 to 17·77; P = 0·002), had the strongest association with septic shock, but lipocalin 2 exhibited the highest AUC (0·81, 0·73 to 0·90; P < 0·001).

Conclusion

MR‐ProADM and lipocalin 2 could be alternatives to the SOFA score in the detection of sepsis and septic shock respectively in surgical patients with infection.