Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis

Molecular diagnosis of sepsis: New aspects and recent developments

By shortening the time to pathogen identification and allowing for detection of organisms missed by blood culture, new molecular methods may provide clinical benefits for the management of patients with sepsis. While a number of reviews on the diagnosis of sepsis have recently been published we here present up-to-date new developments including multiplex PCR, mass spectrometry and array techniques. We focus on those techniques that are commercially available and for which clinical studies have been performed and published.

Sepsis biomarkers: an omics perspective

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

Biomarkers in sepsis

PURPOSE OF REVIEW

This review discusses the current developments in biomarkers for sepsis.

RECENT FINDINGS

With quantum leaps in technology, an array of biomarkers will become available within the next decade as point-of-care tools that will likely revolutionize the management of sepsis. These markers will facilitate early and accurate diagnosis, faster recognition of impending organ dysfunction, optimal selection and titration of appropriate therapies, and more reliable prognostication of risk and outcome. These diagnostics will also enable an improved characterization of the biological phenotype underlying sepsis and thus a better appreciation of the condition.

SUMMARY

The potential for novel biomarkers in sepsis will need to be properly realized with considerable funding, academic-industry collaborations, appropriate investigations and validation in heterogenous populations, but these developments do hold the capacity to transform patient care and outcomes.

In silico modeling: methods and applications to trauma and sepsis

OBJECTIVES

To familiarize clinicians with advances in computational disease modeling applied to trauma and sepsis.

DATA SOURCES

PubMed search and review of relevant medical literature.

SUMMARY

Definitions, key methods, and applications of computational modeling to trauma and sepsis are reviewed.

CONCLUSIONS

Computational modeling of inflammation and organ dysfunction at the cellular, organ, whole-organism, and population levels has suggested a positive feedback cycle of inflammation → damage → inflammation that manifests via organ-specific inflammatory switching networks. This structure may manifest as multicompartment "tipping points" that drive multiple organ dysfunction. This process may be amenable to rational inflammation reprogramming.

Diagnostic and prognostic markers in sepsis

Sepsis is a common and serious complication in intensive care unit patients. An important factor in optimizing survival rates in septic patients is the ability to start treatment early in the course of disease; there is, therefore, a need for accurate diagnostic tests. In recent years, there has been a move away from the rather vague and nonspecific signs that were previously used to diagnose sepsis towards the possible adjunctive role of biomarkers. Many biomarkers have been proposed and assessed clinically, but none alone is specific enough to definitively determine diagnosis. The future direction of research is most likely a greater focus on the use of panels or combinations of markers with clinical signs. Some biomarkers may also be useful for prognosis and guiding therapy. Here, the authors will review our changing approaches to sepsis diagnosis and discuss some of the markers that seem most relevant at the present time.

Age-independent co-expression of antimicrobial gene clusters in the blood of septic patients

Recent research has unravelled the clinical potential of profiling the blood transcriptome to diagnose diseases. However, resulting molecular marker sets comprised features with varying robustness and performance, depending on the dimension of training data. Thus, we investigated patterns that are inherent in large-scale data and suitable for feature selection in application to blood samples from septic patients. By integrating >300 microarray samples in correlation and enrichment analysis, we found general response patterns including a vast majority of co-expressed genes. Differentially expressed genes significantly mapped to immune response-associated categories and revealed strongly correlating upregulated genes related to antimicrobial functions. Classifiers using >20 uncorrelated features from enriched functional categories performed with 85% correct classification on average (10-fold cross-validation), comparable with correlated features, whilst single genes achieved up to 83% correct classifications in identifying septic patients. Independent interplatform comparison, however, validated only a subset of these features, including the antimicrobial cluster (area under the receiver operating characteristic curve >0.8). Based on these results, we propose feature selection for classification incorporating correlation and enriched functional categories to obtain robust marker candidates. Results of this transcriptomic meta-analysis suggest age-independent diagnostic opportunities, although further observational and animal interventional experiments are required to confirm the relevance of antimicrobial genes in sepsis.

Improving risk classification of critical illness with biomarkers: a simulation study

PURPOSE

Optimal triage of patients at risk for critical illness requires accurate risk prediction, yet few data on the performance criteria required of a potential biomarker to be clinically useful exists.

MATERIALS AND METHODS

We studied an adult cohort of nonarrest, nontrauma emergency medical services encounters transported to a hospital from 2002 to 2006. We simulated hypothetical biomarkers increasingly associated with critical illness during hospitalization and determined the biomarker strength and sample size necessary to improve risk classification beyond a best clinical model.

RESULTS

Of 57,647 encounters, 3121 (5.4%) were hospitalized with critical illness and 54,526 (94.6%) without critical illness. The addition of a moderate-strength biomarker (odds ratio, 3.0, for critical illness) to a clinical model improved discrimination (c statistic, 0.85 vs 0.8; P<.01) and reclassification (net reclassification improvement, 0.15; 95% confidence interval, 0.13-0.18) and increased the proportion of cases in the highest-risk category by +8.6% (95% confidence interval, 7.5%-10.8%). Introducing correlation between the biomarker and physiological variables in the clinical risk score did not modify the results. Statistically significant changes in net reclassification required a sample size of at least 1000 subjects.

CONCLUSIONS

Clinical models for triage of critical illness could be significantly improved by incorporating biomarkers, yet substantial sample sizes and biomarker strength may be required.

Rho-kinase-dependent F-actin rearrangement is involved in the release of endothelial microparticles during IFN-α-induced endothelial cell apoptosis

BACKGROUND

Activation of cytoskeleton regulator Rho-kinase during inflammatory stimulations plays a major role in cellular dysfunction and apoptosis. Because endothelial dysfunction may be influenced by increased circulating membrane microparticles (MPs), we hypothesized that inhibition of Rho-kinase can prevent interferon-α (IFN-α)-induced endothelial cell (EC) apoptosis and that protective effects of Rho-kinase inhibition are facilitated by prevention of F-actin rearrangement.

METHODS

In this study, Lewis rats were subjected to an intraperitoneal injection of IFN-α or IFN-α + Y-27632. FCM was performed to analyze circulating endothelial MPs (EMPs) from the blood samples of these animals by detecting the expression of CD144, CD62E, CD31, CD51, and CD54 on EMPs. IFN-α-induced pulmonary injury was assessed by measurement of lung wet-to-dry weight ratios and measurement of alveolar wall thickness. Human pulmonary microvascular ECs (HPMECs) were cultured with IFN-α or EMPs to elucidate the probable mechanisms of the release of EMPs.

RESULTS

Injection of IFN-α resulted in much higher levels of CD144 EMPs, CD62E EMPs, CD31 EMPs, CD51 EMPs, and CD54 EMPs. Pulmonary injury was also observed after injection of IFN-α. Furthermore, IFN-α induced F-actin rearrangement and apoptosis of HPMECs in vitro, and the Toll-like receptor 4/MyD88 and nuclear factor-κB pathways and EMPs per se played important roles in this process.

CONCLUSION

The results demonstrate that increased Rho-kinase activity causes the release of EMPs and cellular apoptosis. Moreover, HPMEC apoptosis that resulted from EMP stimulation indicates that EMPs can be considered as a potential target to regulate the rearrangement of cytoskeleton during endothelial cell apoptosis.

New approaches to sepsis: molecular diagnostics and biomarkers

Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.

Synthesis and Anti-inflammatory Evaluation of Novel Benzimidazole and Imidazopyridine Derivatives

Sepsis, an acute inflammatory disease, remains the most common cause of death in intensive care units. A series of benzimidazole and imidazopyridine derivatives were synthesized and screened for anti-inflammatory activities, and the imidazopyridine series showed excellent inhibition of the expression of inflammatory cytokines in LPS-stimulated macrophages. Compounds X10, X12, X13, X14, and X15 inhibited TNF-α and IL-6 release in a dose-dependent manner, and X12 showed no cytotoxicity in hepatic cells. Furthermore, X12 exhibited a significant protection against LPS-induced septic death in mouse models. Together, these data present a series of new imidazopyridines with potential therapeutic effects in acute inflammatory diseases.

Interleukin-27: a potential new sepsis biomarker exposed through genome-wide transcriptional profiling

Sepsis is a complex clinical condition that is driven predominantly by deviations from the orderly stereotypic immunological response to infection. Much effort has been undertaken in the search for biomarkers that can assist in discriminating critically ill patients with sterile inflammation from those with sepsis. Such biomarkers may aid the clinician in therapeutic decision making upon admission of a patient. Interleukin-27 may be such a discriminative biomarker, as suggested in the previous issue of Critical Care by a study of critically ill children.

Interleukin-27 is a novel candidate diagnostic biomarker for bacterial infection in critically ill children

Introduction

Differentiating between sterile inflammation and bacterial infection in critically ill patients with fever and other signs of the systemic inflammatory response syndrome (SIRS) remains a clinical challenge. The objective of our study was to mine an existing genome-wide expression database for the discovery of candidate diagnostic biomarkers to predict the presence of bacterial infection in critically ill children.

Methods

Genome-wide expression data were compared between patients with SIRS having negative bacterial cultures (n = 21) and patients with sepsis having positive bacterial cultures (n = 60). Differentially expressed genes were subjected to a leave-one-out cross-validation (LOOCV) procedure to predict SIRS or sepsis classes. Serum concentrations of interleukin-27 (IL-27) and procalcitonin (PCT) were compared between 101 patients with SIRS and 130 patients with sepsis. All data represent the first 24 hours of meeting criteria for either SIRS or sepsis.

Results

Two hundred twenty one gene probes were differentially regulated between patients with SIRS and patients with sepsis. The LOOCV procedure correctly predicted 86% of the SIRS and sepsis classes, and Epstein-Barr virus-induced gene 3 (EBI3) had the highest predictive strength. Computer-assisted image analyses of gene-expression mosaics were able to predict infection with a specificity of 90% and a positive predictive value of 94%. Because EBI3 is a subunit of the heterodimeric cytokine, IL-27, we tested the ability of serum IL-27 protein concentrations to predict infection. At a cut-point value of ≥5 ng/ml, serum IL-27 protein concentrations predicted infection with a specificity and a positive predictive value of >90%, and the overall performance of IL-27 was generally better than that of PCT. A decision tree combining IL-27 and PCT improved overall predictive capacity compared with that of either biomarker alone.

Conclusions

Genome-wide expression analysis has provided the foundation for the identification of IL-27 as a novel candidate diagnostic biomarker for predicting bacterial infection in critically ill children. Additional studies will be required to test further the diagnostic performance of IL-27.

The microarray data reported in this article have been deposited in the Gene Expression Omnibus under accession number GSE4607.

Surgical systems biology and personalized longitudinal phenotyping in critical care

Systems-wide molecular analysis of the metabolic, inflammatory and immune response to surgical trauma has yet to be translated into the operating room. Surgical patients are exposed to a large number of heterogeneous environmental insults that cannot only be quantified by genome-orientated 'omics platforms. Furthermore, surgery demands rapid or near real-time analysis. Systems-level metabolic phenotyping provides a novel 'global' perspective of an organism's metabolic response to surgical injury and, therefore, serves as an ideal platform for the development of personalized therapies in surgery. This article reviews current personalized approaches to healthcare in surgery and explores future directions for personalized surgical biomarker discovery and therapeutics. In particular, this article discusses our vision of 'personalized metabolic phenotyping' in surgery, and outlines next-generation technologies that will make this approach a reality.

Frontiers in preclinical safety biomarkers: microRNAs and messenger RNAs

The measurement of plasma microRNAs (miRNAs) and messenger RNAs (mRNAs) is the most recent effort to identify novel biomarkers in preclinical safety. These genomic markers often display tissue-specific expression, may be released from the tissues into the plasma during toxic events, change early and with high magnitude in tissues and in the blood during specific organ toxicities, and can be measured using multiplex formats. Their validation as biomarkers has been challenged by the technical difficulties. In particular, the concentration of miRNAs in the plasma depends on contamination by miRNAs originating from blood cells and platelets, and the relative fraction of miRNAs in complexes with Argonaute 2, high-density lipoproteins, and in exosomes and microvesicles. In spite of these hurdles, considerable progress has recently been made in assessing the potential value of miRNAs in the clinic, especially in cancer patients and cardiovascular diseases. The future of miRNAs and mRNAs as biomarkers of disease and organ toxicity depends on our ability to characterize their kinetics and to establish robust collection and measurement methods. This review covers the basic biology of miRNAs and the published literature on the use of miRNAs and mRNAs as biomarkers of specific target organ toxicity.

Targeted metabolomics for discrimination of systemic inflammatory disorders in critically ill patients

The occurrence of systemic inflammatory response syndrome (SIRS) remains a major problem in intensive care units with high morbidity and mortality. The differentiation between noninfectious and infectious etiologies of this disorder is challenging in routine clinical practice. Many biomarkers have been suggested for this purpose; however, sensitivity and specificity even of high-ranking biomarkers remain insufficient. Recently, metabolic profiling has attracted interest for biomarker discovery. The objective of this study was to identify metabolic biomarkers for differentiation of SIRS/sepsis. A total of 186 meta-bolites comprising six analyte classes were determined in 143 patients (74 SIRS, 69 sepsis) by LC-MS/MS. Two markers (C10:1 and PCaaC32:0) revealed significantly higher concentrations in sepsis. A classification model comprising these markers resulted in 80% and 70% correct classifications in a training set and a test set, respectively.This study demonstrates that acylcarnitines and glycerophosphatidylcholines may be helpful for differentiation of infectious from noninfectious systemic inflammation due to their significantly higher concentration in sepsis patients. Considering the well known pathophysiological relevance of lipid induction by bacterial components, metabolites as identified in this study are promising biomarker candidates in the differential diagnosis of SIRS and sepsis.

Computational and systems biology in trauma and sepsis: current state and future perspectives

Trauma, often accompanied by hemorrhage, is a leading cause of death worldwide, often leading to inflammation-related late complications that include sepsis and multiple organ failure. These secondary complications are a manifestation of the complexity of biological responses elicited by trauma/hemorrhage, responses that span most, if not all, cell types, tissues, and organ systems. This daunting complexity at the patient level is manifest by the near total dearth of available therapeutics, and we suggest that this dire condition is due in large part to the lack of a rational, systems-oriented framework for drug development, clinical trial design, in-hospital diagnostics, and post-hospital care. We have further suggested that mechanistic computational modeling can form the basis of such a rational framework, given the maturity of systems biology/computational biology. Herein, we briefly summarize the state of the art of these approaches, and highlight the biological insights and novel hypotheses derived from these approaches. We propose a rational framework for transitioning through the currently fragmented process from identification of biological networks that are potential therapeutic targets, through clinical trial design, to personalized diagnosis and care. Insights derived from systems and computational biology in trauma and sepsis include the centrality of Damage-Associated Molecular Pattern molecules as drivers of both beneficial and detrimental inflammation, along with a novel view of multiple organ dysfunction as a cascade of containment failures with distinct implications for therapy. Finally, we suggest how these insights might be best implemented to drive transformational change in the fields of trauma and sepsis.