Plasma proteomics in pediatric patients with sepsis- hopes and challenges

One of the main causes of morbidity and death in pediatric patients is sepsis. Of the 48.9 million cases of sepsis reported globally, 41.5% involve children under the age of five, with 2.9 million deaths associated with the disease. Clinicians must identify and treat patients at risk of sepsis or septic shock before late-stage organ dysfunction occurs since diagnosing sepsis in young patients is more difficult than in adult patients. As of right now, omics technologies that possess adequate diagnostic sensitivity and specificity can assist in locating biomarkers that indicate how the disease will progress clinically and how the patient will react to treatment. By identifying patients who are at a higher risk of dying or experiencing persistent organ dysfunction, risk stratification based on biomarkers generated from proteomics can enhance prognosis. A potentially helpful method for determining the proteins that serve as biomarkers for sepsis and formulating theories on the pathophysiological mechanisms behind complex sepsis symptoms is plasma proteomics.

Screening and identification of the hub genes in severe acute pancreatitis and sepsis

Background

Severe acute pancreatitis (SAP) is accompanied with acute onset, rapid progression, and complicated condition. Sepsis is a common complication of SAP with a high mortality rate. This research aimed to identify the shared hub genes and key pathways of SAP and sepsis, and to explore their functions, molecular mechanism, and clinical value.

Methods

We obtained SAP and sepsis datasets from the Gene Expression Omnibus (GEO) database and employed differential expression analysis and weighted gene co-expression network analysis (WGCNA) to identify the shared differentially expressed genes (DEGs). Functional enrichment analysis and protein-protein interaction (PPI) was used on shared DEGs to reveal underlying mechanisms in SAP-associated sepsis. Machine learning methods including random forest (RF), least absolute shrinkage and selection operator (LASSO) and support vector machine recursive feature elimination (SVM-RFE) were adopted for screening hub genes. Then, receiver operating characteristic (ROC) curve and nomogram were applied to evaluate the diagnostic performance. Finally, immune cell infiltration analysis was conducted to go deeply into the immunological landscape of sepsis.

Result

We obtained a total of 123 DEGs through cross analysis between Differential expression analysis and WGCNA important module. The Gene Ontology (GO) analysis uncovered the shared genes exhibited a significant enrichment in regulation of inflammatory response. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the shared genes were primarily involved in immunoregulation by conducting NOD-like receptor (NLR) signaling pathway. Three machine learning results revealed that two overlapping genes (ARG1, HP) were identified as shared hub genes for SAP and sepsis. The immune infiltration results showed that immune cells played crucial part in the pathogenesis of sepsis and the two hub genes were substantially associated with immune cells, which may be a therapy target.

Conclusion

ARG1 and HP may affect SAP and sepsis by regulating inflammation and immune responses, shedding light on potential future diagnostic and therapeutic approaches for SAP-associated sepsis.

Exploring the role of antioxidants in sepsis-associated oxidative stress: a comprehensive review

Sepsis is a potentially fatal condition characterized by organ dysfunction caused by an imbalanced immune response to infection. Although an increased inflammatory response significantly contributes to the pathogenesis of sepsis, several molecular mechanisms underlying the progression of sepsis are associated with increased cellular reactive oxygen species (ROS) generation and exhausted antioxidant pathways. This review article provides a comprehensive overview of the involvement of ROS in the pathophysiology of sepsis and the potential application of antioxidants with antimicrobial properties as an adjunct to primary therapies (fluid and antibiotic therapies) against sepsis. This article delves into the advantages and disadvantages associated with the utilization of antioxidants in the therapeutic approach to sepsis, which has been explored in a variety of animal models and clinical trials. While the application of antioxidants has been suggested as a potential therapy to suppress the immune response in cases where an intensified inflammatory reaction occurs, the use of multiple antioxidant agents can be beneficial as they can act additively or synergistically on different pathways, thereby enhancing the antioxidant defense. Furthermore, the utilization of immunoadjuvant therapy, specifically in septic patients displaying immunosuppressive tendencies, represents a promising advancement in sepsis therapy.

Proteomic methods for the study of porcine acute phase proteins - anything new to detect?

Acute phase proteins (APPs) reflect the health status of individuals and are important tools in diagnostics, as their altered levels are a sign of disturbed homeostasis. While, in most cases, quantitation of known serum APPs is routinely performed by immunoassays, proteomics is helpful in discovery of new biomarker candidates, especially in samples other than body fluids. Besides putting APP regulation into an overall context of differentially abundant proteins, this approach can detect further details or outright new features in protein structure or specific modifications, and help understand better their function. Thus, it can show up ways to make present diagnostic assays more sensitive and/or specific, or correlate regulations of disease-specific proteins. The APP repertoire is dependent on the species. The pig is both, an important farm animal and a model animal for human diseases, due to similarities in physiology. Besides reviewing existing literature, yet unpublished examples for two-dimensional electrophoresis in connection with pig APPs highlight some of the benefits of proteomics. Of further help would be the emerging targeted proteomics, offering the possibility to determine particular isoforms or proteoforms, without the need of specific antibodies, but this method is presently scarcely used in veterinary medicine.

Evaluation of the Molecular Mechanisms of Sepsis Using Proteomics

Sepsis is a complex syndrome promoted by pathogenic and host factors; it is characterized by dysregulated host responses and multiple organ dysfunction, which can lead to death. However, its underlying molecular mechanisms remain unknown. Proteomics, as a biotechnology research area in the post-genomic era, paves the way for large-scale protein characterization. With the rapid development of proteomics technology, various approaches can be used to monitor proteome changes and identify differentially expressed proteins in sepsis, which may help to understand the pathophysiological process of sepsis. Although previous reports have summarized proteomics-related data on the diagnosis of sepsis and sepsis-related biomarkers, the present review aims to comprehensively summarize the available literature concerning “sepsis”, “proteomics”, “cecal ligation and puncture”, “lipopolysaccharide”, and “post-translational modifications” in relation to proteomics research to provide novel insights into the molecular mechanisms of sepsis.

The application of omic technologies to research in sepsis-associated acute kidney injury

Acute kidney injury (AKI) is common in critically ill children and adults, and sepsis-associated AKI (SA-AKI) is the most frequent cause of AKI in the ICU. To date, no mechanistically targeted therapeutic interventions have been identified. High-throughput "omic" technologies (e.g., genomics, proteomics, metabolomics, etc.) offer a new angle of approach to achieve this end. In this review, we provide an update on the current understanding of SA-AKI pathophysiology. Omic technologies themselves are briefly discussed to facilitate interpretation of studies using them. We next summarize the body of SA-AKI research to date that has employed omic technologies. Importantly, omic studies are helping to elucidate a pathophysiology of SA-AKI centered around cellular stress responses, metabolic changes, and dysregulation of energy production that underlie its clinical features. Finally, we propose opportunities for future research using clinically relevant animal models, integrating multiple omic technologies and ultimately progressing to translational human studies focusing therapeutic strategies on targeted disease mechanisms.

Detection and Inhibition of Bacteria on a Dual-Functional Silver Platform

Detection and inhibition of bacteria are universally required in clinics and daily life for health care. Developing a dual-functional material is challenging and in demand, engaging advanced applications for both defined bioanalysis and targeted biotoxicity. Herein, magnetic silver nanoshells are designed as a multifunctional platform for the detection and inhibition of bacteria. The optimized magnetic silver nanoshells enable direct laser desorption/ionization mass spectrometry based metabolic analysis of bacteria (≈10 µL^-1 ), in complex biofluids. The serum infection process (0-10 h) is monitored by statistics toward clinical classification. Moreover, magnetic silver nanoshells facilitate surface adhesion on bacteria due to nanoscale surface roughness and thus display long-term antibacterial effects. Bacteria metabolism is studied with metabolic biomarkers (e.g., malate and lysine) identified during inhibition, showing cell membrane destruction and dysfunctional protein synthesis mechanisms. This work not only guides the design of material-based approaches for bioanalysis and biotoxicity, but contributes to bacteria-related diagnosis by using specific metabolic biomarkers for sensitive detection and new insights by monitoring metabolomic change of bacteria for antibacterial applications.

Sepsis Through the Eyes of Proteomics: The Progress in the Last Decade

Sepsis is a systemic inflammatory response caused by infection whose molecular mechanisms are still not completely understood. The early detection of sepsis remains a great challenge for clinicians because no single biomarker capable of its reliable prediction, hence, delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. There are several experimental approaches used to reveal the molecular mechanism of sepsis progression. Proteomics coupled with mass spectrometry made possible to identify differentially expressed proteins in clinical samples. Recent advancement in liquid chromatography-based separation methods and mass spectrometers resolution and sensitivity with absolute quantitation methods, made possible to use proteomics as a powerful tool for study of clinical samples with higher coverage proteome profiles. In recent years, number of proteomic studies have been done under sepsis and/or in response to endotoxin and showed various signaling pathways, functions, and biomarkers. This review enlightened the proteomic progress in the last decade in sepsis.

Use of immunoproteomics to identify immunogenic proteins in a rat model of acute respiratory distress syndrome

Acute respiratory distress syndrome (ARDS) is a common and life‑threatening clinical syndrome, and seeking biomarkers of ARDS has been an area of continuing research. The present study hypothesized that alterations to certain immunogenic substances occur in injured lungs and are able to specifically bind with corresponding proteins in the blood, and that these proteins may be readily detected. To investigate this hypothesis, a rat model of ARDS was established by cecal ligation and puncture surgery, and an immunoproteomics approach, using serum as the primary antibody in a western blot analysis, was used with the aim of identifying immunogenic proteins in the injured lungs. Ingenuity Pathway Analysis (IPA) was used for bioinformatics analysis, and mass spectrometric analysis was used to identify a total of 38 differentially expressed immunogenic proteins. Bioinformatics analysis revealed that the top canonical pathways in which the identified proteins may be involved were gluconeogenesis I, glycolysis I, choline degradation I, NADH repair and heme degradation. IPA Biomarker Filter analysis with the terms 'acute respiratory distress syndrome/acute lung injury' was used to screen 13 proteins as candidate biomarkers. These proteins were described as antigens, and suggested that paired antibodies may be detected in the plasma of patients at high risk of ARDS. Analysis of these identified proteins may provide novel insights into the potential pathological mechanisms of ARDS.

The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.

Identification of potential biomarkers by serum proteomics analysis in rats with sepsis

This study was aimed to find new biomarkers for diagnosis and prediction of prognosis of sepsis. Serum samples from nonsurvivor, survivor, and control groups were obtained at 12 h after the induction of sepsis and labeled with isobaric tags (iTRAQ) and then analyzed by two-dimensional liquid chromatography and tandem mass spectrometry. Protein identification and quantification were obtained using mass spectrometry and the ProteinPilot software. Bioinformatics annotation was performed by searching against the PANTHER database. Enzyme-linked immunosorbent assays were used to further confirm the protein identification and differential expression. A logistic regression was then used to screen the index set for diagnosis and prognosis of sepsis. We found that 47 proteins were preferentially elevated in septic rats (both nonsurvivors and survivors) compared with the control rats, and 28 proteins were preferentially elevated in the NS rats as compared with the S group. Several biomarkers, such as multimerin 1, ficolin 1, carboxypeptidase N (CPN2), serine protease 1, and platelet factor 4, were tightly correlated with the diagnosis of sepsis. Logistic regression analyses established multimerin 1, pro-platelet basic protein, fibrinogen-α, and fibrinogen-β for prognosis of sepsis.

The role of proteomics in understanding biological mechanisms of sepsis

Sepsis is a systemic inflammatory state caused by infection. Complications of this infection with multiple organ failure lead to more lethal conditions, such as severe sepsis and septic shock. Sepsis is one of the leading causes of US deaths. Novel biomarkers with high sensitivity and specificity may be helpful for early diagnosis of sepsis and for improvement of patient outcomes through the development of new therapies. Mass spectrometry-based proteomics offers powerful tools to identify such biomarkers and furthermore to give insight to fundamental mechanisms of this clinical condition. In this review, we summarize findings from proteomics studies of sepsis and how their applications have provided more understanding into the pathogenesis of septic infection. Literatures related to "proteomics", "sepsis", "systemic inflammatory response syndrome", "severe sepsis", "septic infection", and "multiple organ dysfunction syndrome" were searched using PubMed. Findings about neonatal and adult sepsis are discussed separately. Within the adult sepsis studies, results are grouped based on the models (e.g., human or animal). Across investigations in clinical populations and in rodent and mammalian animal models, biological pathways, such as inflammatory and acute phase response, coagulation, complement, mitochondrial energy metabolism, chaperones, and oxidative stress, are altered at the protein level. These proteomics studies have discovered many novel biomarker candidates of septic infection. Validation the clinical use of these biomarker candidates may significantly impact the diagnosis and prognosis of sepsis. In addition, the molecular mechanisms revealed by these studies may also guide the development of more effective treatments.

Laboratory diagnostics of spontaneous bacterial peritonitis

The term peritonitis indicates an inflammatory process involving the peritoneum that is most frequently infectious in nature. Primary or spontaneous bacterial peritonitis (SBP) typically occurs when a bacterial infection spreads to the peritoneum across the gut wall or mesenteric lymphatics or, less frequently, from hematogenous transmission in combination with impaired immune system and in absence of an identified intra-abdominal source of infection or malignancy. The clinical presentation of SBP is variable. The condition may manifest as a relatively insidious colonization, without signs and symptoms, or may suddenly occur as a septic syndrome. Laboratory diagnostics play a pivotal role for timely and appropriate management of patients with bacterial peritonitis. It is now clearly established that polymorphonuclear leukocyte (PMN) in peritoneal fluid is the mainstay for the diagnosis, whereas the role of additional biochemical tests is rather controversial. Recent evidence also suggests that automatic cell counting in peritoneal fluid may be a reliable approach for early screening of patients. According to available clinical and laboratory data, we have developed a tentative algorithm for efficient diagnosis of SBP, which is based on a reasonable integration between optimization of human/economical resources and gradually increasing use of invasive and expensive testing. The proposed strategy entails, in sequential steps, serum procalcitonin testing, automated cell count in peritoneal fluid, manual cell count in peritoneal fluid, peritoneal fluid culture and bacterial DNA testing in peritoneal fluid.

Proteomics reveals age-related differences in the host immune response to sepsis

Sepsis is commonly caused by community-acquired pneumonia (CAP) and may develop into severe sepsis, characterized by multiple organ failure. The risk of severe sepsis among CAP patients and subsequent mortality increases sharply after the age of 65. The molecular mechanisms associated with this age-related risk are not fully understood. To better understand factors involved with increased incidence and mortality of severe sepsis in the elderly, we used a nested case-control study of patients enrolled in a multicenter observational cohort of 2320 participants with CAP. We identified a total of 39 CAP patients 50-65 and 70-85 years old who did or did not develop severe sepsis. Plasma samples were obtained on presentation to the emergency department and prior to therapeutic interventions. A semiquantitative plasma proteomics workflow was applied which incorporated tandem immunoaffinity depletion, iTRAQ labeling, strong cation exchange fractionation, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 772 proteins were identified, of which 58 proteins exhibit statistically significant differences in expression levels among patients with severe sepsis as a function of age. Differentially expressed proteins are involved in pathways such as acute phase response, coagulation signaling, atherosclerosis signaling, lipid metabolism, and production of nitric oxide and reactive oxygen species. This study provides insight into factors that may explain age-related differences in incidence of severe sepsis in the elderly.

Association between haptoglobin, hemopexin and mortality in adults with sepsis

Introduction

Plasma levels of cell-free hemoglobin are associated with mortality in patients with sepsis; however descriptions of independent associations with free hemoglobin and free heme scavengers, haptoglobin and hemopexin, are lacking beyond their description as acute phase reactants. We sought to determine the association of plasma levels of endogenous free hemoglobin and haptoglobin and hemopexin with in-hospital mortality in adults with sepsis.

Methods

We conducted a retrospective observational study of a total of 387 critically ill patients with sepsis in multiple intensive care units in an academic tertiary care hospital. Measurements of plasma haptoglobin and hemopexin were made on blood drawn within 24 hours of intensive care unit admission. The primary outcome was the association between plasma haptoglobin and hemopexin with in-hospital mortality.

Results

Survivors had significantly higher plasma haptoglobin concentrations (median 1234 μg/ml, interquartile range (IQR) 569 to 3037) and hemopexin concentrations (616 μg/ml, IQR 397 to 934) measured on enrollment compared to non-survivors (haptoglobin 750 μg/ml, IQR 404 to 2421, P = 0.008; hemopexin 470 μg/ml, IQR 303 to 891, P = 0.012). After controlling for potential confounders including cell-free hemoglobin concentration, patients with higher haptoglobin concentrations were significantly less likely to die in the hospital (odds ratio (OR) 0.653, 95% CI 0.433 to 0.984, P = 0.042), while the same association was not seen with hemopexin (OR 0.53, 95% CI 0.199 to 1.416, P = 0.206). In a subgroup analysis, the association between increased haptoglobin and hemopexin and decreased risk of mortality was no longer significant when analyzing patients with no detectable cell-free hemoglobin (P = 0.737 and P = 0.584, respectively).

Conclusion

In critically ill patients with sepsis, elevated plasma levels of haptoglobin were associated with a decreased risk of in-hospital mortality and this association was independent of confounders. Increased haptoglobin may play a protective role in sepsis patients who have elevated levels of circulating cell-free hemoglobin beyond its previous description as an acute phase reactant.

Proteomics in Veterinary Medicine

Advancement in electrophoresis and mass spectrometry techniques along with the recent progresses in genomics, culminating in bovine and pig genome sequencing, widened the potential application of proteomics in the field of veterinary medicine. The aim of the present review is to provide an in-depth perspective about the application of proteomics to animal disease pathogenesis, as well as its utilization in veterinary diagnostics. After an overview on the various proteomic techniques that are currently applied to veterinary sciences, the article focuses on proteomic approaches to animal disease pathogenesis. Included as well are recent achievements in immunoproteomics (ie, the identifications through proteomic techniques of antigen involved in immune response) and histoproteomics (ie, the application of proteomics in tissue processed for immunohistochemistry). Finally, the article focuses on clinical proteomics (ie, the application of proteomics to the identification of new biomarkers of animal diseases).

Plasma protein characteristics of long-term hemodialysis survivors

Hemodialysis (HD) patients are under recurrent circulatory stress, and hemodialysis has a high mortality rate. The characteristics of plasma proteomes in patients surviving long-term HD remain obscure, as well as the potential biomarkers in predicting prognoses. This study reports the proteome analyses of patient plasma from non-diabetic long-term HD (LHD, dialysis vintage 14.9±4.1 years, n = 6) and the age/sex/uremic etiology-comparable short-term HD (SHD, dialysis vintage 5.3±2.9 years, n = 6) using 2-DE and mass spectrometry. In addition, a 4-year longitudinal follow-up of 60 non-diabetic HD patients was subsequently conducted to analyze the baseline plasma proteins by ELISA in predicting prognosis. Compared to the SHD, the LHD survivors had increased plasma vitamin D binding proteins (DBP) and decreased clusterin, apolipoprotein A-IV, haptoglobin, hemopexin, complement factors B and H, and altered isoforms of α1-antitrypsin and fibrinogen gamma. During the 45.7±15 months for follow-up of the 60 HD patient cases, 16 patients died. Kaplan-Meier analysis demonstrated that HD patients with the lowest tertile of the baseline plasma DBP level have a significantly higher mortality rate. Multivariate Cox regression analysis further indicated that DBP is an independent predictor of mortality. In summary, the altered plasma proteins in LHD implicated accelerated atherosclerosis, defective antioxidative activity, increased inflammation/infection, and organ dysfunction. Furthermore, lower baseline plasma DBP in HD patients is related to mortality. The results suggest that the proteomic approach could help discover the potential biomarker in HD prognoses.

Mass spectrometry of peptides and proteins from human blood

It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

Comparative analysis of serum proteomes of patients with cardiovascular disease

OBJECTIVES

To monitor increases or decreases in cardiovascular disease (CVD)-related proteins that will be released from the deposits or plaque on the inner wall of blood vessels.

DESIGN AND METHODS

Protein profiles of sera from healthy subjects and CVD patients were determined via 2-DE. Differentially expressed spots in CVD patients were identified by ESI-Q-TOF MS/MS. Retinol binding protein 4 (RBP4), ceruloplasmin, and hemopexin were confirmed by Western blotting and RBP4 was further verified by ELISA.

RESULTS

Approximately, 400 spots were detected in each gel via comparisons of the serum proteome. Among these spots, 19 spots were selected and identified by ESI-Q-TOF MS/MS (P<0.05). The expression levels of RBP4 and ceruloplasmin were higher in CVD patients by Western blotting. The level of immunoreactive RBP4 in CVD patients was higher than that in healthy subjects.

CONCLUSIONS

The three proteins identified in the present study may constitute potential biomarkers for the diagnosis of CVD in patients.