Metabolomics-Based Discovery of Small Molecule Biomarkers in Serum Associated with Dengue Virus Infections and Disease Outcomes

Background

Epidemic dengue fever (DF) and dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) are overwhelming public health capacity for diagnosis and clinical care of dengue patients throughout the tropical and subtropical world. The ability to predict severe dengue disease outcomes (DHF/DSS) using acute phase clinical specimens would be of enormous value to physicians and health care workers for appropriate triaging of patients for clinical management. Advances in the field of metabolomics and analytic software provide new opportunities to identify host small molecule biomarkers (SMBs) in acute phase clinical specimens that differentiate dengue disease outcomes.

Methodology/Principal Findings

Exploratory metabolomic studies were conducted to characterize the serum metabolome of patients who experienced different dengue disease outcomes. Serum samples from dengue patients from Nicaragua and Mexico were retrospectively obtained, and hydrophilic interaction liquid chromatography (HILIC)-mass spectrometry (MS) identified small molecule metabolites that were associated with and statistically differentiated DHF/DSS, DF, and non-dengue (ND) diagnosis groups. In the Nicaraguan samples, 191 metabolites differentiated DF from ND outcomes and 83 differentiated DHF/DSS and DF outcomes. In the Mexican samples, 306 metabolites differentiated DF from ND and 37 differentiated DHF/DSS and DF outcomes. The structural identities of 13 metabolites were confirmed using tandem mass spectrometry (MS/MS). Metabolomic analysis of serum samples from patients diagnosed as DF who progressed to DHF/DSS identified 65 metabolites that predicted dengue disease outcomes. Differential perturbation of the serum metabolome was demonstrated following infection with different DENV serotypes and following primary and secondary DENV infections.

Conclusions/Significance

These results provide proof-of-concept that a metabolomics approach can be used to identify metabolites or SMBs in serum specimens that are associated with distinct DENV infections and disease outcomes. The differentiating metabolites also provide insights into metabolic pathways and pathogenic and immunologic mechanisms associated with dengue disease severity.     

Genome-Scale Discovery of DNA-Methylation Biomarkers for Blood-Based Detection of Colorectal Cancer

Background

There is an increasing demand for accurate biomarkers for early non-invasive colorectal cancer detection. We employed a genome-scale marker discovery method to identify and verify candidate DNA methylation biomarkers for blood-based detection of colorectal cancer.

Methodology/Principal Findings

We used DNA methylation data from 711 colorectal tumors, 53 matched adjacent-normal colonic tissue samples, 286 healthy blood samples and 4,201 tumor samples of 15 different cancer types. DNA methylation data were generated by the Illumina Infinium HumanMethylation27 and the HumanMethylation450 platforms, which determine the methylation status of 27,578 and 482,421 CpG sites respectively. We first performed a multistep marker selection to identify candidate markers with high methylation across all colorectal tumors while harboring low methylation in healthy samples and other cancer types. We then used pre-therapeutic plasma and serum samples from 107 colorectal cancer patients and 98 controls without colorectal cancer, confirmed by colonoscopy, to verify candidate markers. We selected two markers for further evaluation: methylated THBD (THBD-M) and methylated C9orf50 (C9orf50-M). When tested on clinical plasma and serum samples these markers outperformed carcinoembryonic antigen (CEA) serum measurement and resulted in a high sensitive and specific test performance for early colorectal cancer detection.

Conclusions/Significance

Our systematic marker discovery and verification study for blood-based DNA methylation markers resulted in two novel colorectal cancer biomarkers, THBD-M and C9orf50-M. THBD-M in particular showed promising performance in clinical samples, justifying its further optimization and clinical testing.     

Novel and Unique Diagnostic Biomarkers for Bacillus anthracis Infection

A search for bacterium-specific biomarkers in peripheral blood following infection with Bacillus anthracis was carried out with rabbits, using a battery of specific antibodies generated by DNA vaccination against 10 preselected highly immunogenic bacterial antigens which were identified previously by a genomic/proteomic/serologic screen of the B. anthracis secretome. Detection of infection biomarkers in the circulation of infected rabbits could be achieved only after removal of highly abundant serum proteins by chromatography using a random-ligand affinity column. Besides the toxin component protective antigen, the following three secreted proteins were detected in the circulation of infected animals: the chaperone and protease HtrA (BA3660), an NlpC/P60 endopeptidase (BA1952), and a protein of unknown function harboring two SH3 (Src homology 3) domains (BA0796). The three proteins could be detected in plasma samples from infected animals exhibiting 10³ to 10⁵ CFU/ml blood and also in standard blood cultures at 3 to 6 h post-bacterial inoculation at a bacteremic level as low as 10³ CFU/ml. Furthermore, the three biomarkers appear to be present only in the secretome of B. anthracis, not in those of the related pathogens B. thuringiensis and B. cereus. To the best of our knowledge, this is the first report of direct detection of B. anthracis-specific proteins, other than the toxin components, in the circulation of infected animals.The gram-positive spore-forming bacterium Bacillus anthracis is the causative agent of anthrax, a rare fatal disease which is initiated, in its most severe form, by inhalation of spores. Due to the severity of the disease, the ease of respiratory infection, and the extreme resistance of the spores to unfavorable environmental conditions, B. anthracis is considered a potential biological warfare agent (for a review, see references 8, 10, 35, 56, and 62), and in recent years, the need for novel reliable diagnostic approaches, improved vaccination strategies, novel therapeutic targets, and a better understanding of the pathogenesis of anthrax has been widely acknowledged.Inhaled B. anthracis spores are taken up by alveolar macrophages and germinate into vegetative bacilli which eventually invade the bloodstream, where they multiply massively and secrete toxins and virulence factors. Anthrax is toxinogenic in the sense that the bacterial binary exotoxin is necessary for the onset of the disease (54), yet other factors may be required for the colonization and expansion of bacteria in the host (15, 18, 31, 32, 37, 46, 65, 66, 70, 83). The toxin is composed of the following three proteins: protective antigen (PA), which mediates binding to the receptor on target cells and internalization of the toxin components (14, 74); lethal factor, a zinc protease targeting several mitogen-activated protein kinases (52); and edema factor (EF), a calmodulin-dependent adenylate cyclase (55, 57). The genes encoding the three exotoxin components are located on the native virulence plasmid pXO1. Genes encoding proteins with functions involved in the synthesis of the second major B. anthracis virulence determinant, an immunologically inert polyglutamyl capsule that protects bacteria from phagocytosis, are located on a second native virulence plasmid, pXO2 (56).In humans, the initial symptoms of inhalation anthrax are nonspecific and reminiscent of influenza-like upper respiratory tract infections. The second stage is characterized by high fever, respiratory failure, dyspnea, and shock. Unless patients are treated promptly, death occurs within 24 h of the onset of the second stage, preceded by massive bacteremia (27, 34, 73, 76). The mandatory treatment for anthrax is based on administration of antibiotics (17, 76), yet study of the disease in animal models has clearly established that the time of antibiotic administration postinfection is crucial for the effectiveness of the treatment, strongly supporting the importance of rapid diagnosis (2, 47, 48). At present, due to the severity of the disease and its rapid progression, treatment is administered to each person with confirmed contact with contaminated areas (76).Early accurate diagnosis of anthrax is complicated by the rarity of the disease and the nonspecific nature of the symptoms. Microbiologic identification of anthrax is based on the nonhemolytic nature of the typically white-gray colonies and the rod morphology of the gram-positive nonmotile bacilli detected in clinical samples or blood cultures (16, 19, 30, 73, 78). Immunofluorescence and immunohistochemistry targeted to bacterial proteins are not routinely conducted. Later in the course of the disease, seroconversion in response to the various components of the toxin may serve only as a retrospective confirmation of initial exposure. With the advent of genetic methodologies, B. anthracis in cultures inoculated with clinical and forensic samples can be detected specifically and accurately by PCR, usually designed to amplify genes located on the native virulence plasmids (30). Recently, the use of PA as a disease biomarker was suggested, owing to the presence of this protein in detectable amounts in the circulation of infected animals (53, 71). EF and lethal factor can be detected in the circulation only at later stages of infection (30).In recent years, the search for novel biomarkers of disease, including bacterial infections, has exploited the approach of global biological inspection based on functional genomic or proteomic studies (64, 85). We previously documented such global surveys, combined with a serological study of B. anthracis (5, 6, 20, 21, 22, 38, 39), for identification of vaccine and diagnostic marker candidates among extracellular (secreted or membranal) proteins. These studies indeed revealed a list of proteins that can serve as potential biomarkers, based on their immunogenicity (which probes their in vivo expression), abundance under various culture conditions, and functional relatedness to infection. In the present study, the search was extended by directly addressing the presence of bacterial secreted proteins in the circulation of B. anthracis-infected rabbits, using specific antibodies generated by DNA vaccination against the previously selected immunogenic proteins. Visualization of bacterial proteins in the circulation of infected animals was achieved only following depletion of highly abundant serum proteins by an affinity chromatography protocol. The search enabled the successful detection, in addition to PA, of three secreted proteins uniquely expressed by B. anthracis, i.e., HtrA (BA3660), the BA1952 endopeptidase, and a protein of unknown function (BA0796). All of these proteins are potential virulence-related factors. This is the first communication of the presence of B. anthracis secreted proteins other than the bacterial toxin in the circulation of infected animals, and their identification strongly supports the validity of the reductional screening approach for selection of disease biomarkers.     

Aptamer-Based Detection of Disease Biomarkers in Mouse Models for Chagas Drug Discovery

Drug discovery initiatives, aimed at Chagas treatment, have been hampered by the lack of standardized drug screening protocols and the absence of simple pre-clinical assays to evaluate treatment efficacy in animal models. In this study, we used a simple Enzyme Linked Aptamer (ELA) assay to detect T. cruzi biomarker in blood and validate murine drug discovery models of Chagas disease. In two mice models, Apt-29 ELA assay demonstrated that biomarker levels were significantly higher in the infected group compared to the control group, and upon Benznidazole treatment, their levels reduced. However, biomarker levels in the infected treated group did not reduce to those seen in the non-infected treated group, with 100% of the mice above the assay cutoff, suggesting that parasitemia was reduced but cure was not achieved. The ELA assay was capable of detecting circulating biomarkers in mice infected with various strains of T. cruzi parasites. Our results showed that the ELA assay could detect residual parasitemia in treated mice by providing an overall picture of the infection in the host. They suggest that the ELA assay can be used in drug discovery applications to assess treatment efficacy in-vivo.     

Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study

Serum metabolite profiling in Duchenne muscular dystrophy (DMD) may enable discovery of valuable molecular markers for disease progression and treatment response. Serum samples from 51 DMD patients from a natural history study and 22 age-matched healthy volunteers were profiled using liquid chromatography coupled to mass spectrometry (LC-MS) for discovery of novel circulating serum metabolites associated with DMD. Fourteen metabolites were found significantly altered (1% false discovery rate) in their levels between DMD patients and healthy controls while adjusting for age and study site and allowing for an interaction between disease status and age. Increased metabolites included arginine, creatine and unknown compounds at m/z of 357 and 312 while decreased metabolites included creatinine, androgen derivatives and other unknown yet to be identified compounds. Furthermore, the creatine to creatinine ratio is significantly associated with disease progression in DMD patients. This ratio sharply increased with age in DMD patients while it decreased with age in healthy controls. Overall, this study yielded promising metabolic signatures that could prove useful to monitor DMD disease progression and response to therapies in the future.     

Quantitative Network Measures as Biomarkers for Classifying Prostate Cancer Disease States: A Systems Approach to Diagnostic Biomarkers

Identifying diagnostic biomarkers based on genomic features for an accurate disease classification is a problem of great importance for both, basic medical research and clinical practice. In this paper, we introduce quantitative network measures as structural biomarkers and investigate their ability for classifying disease states inferred from gene expression data from prostate cancer. We demonstrate the utility of our approach by using eigenvalue and entropy-based graph invariants and compare the results with a conventional biomarker analysis of the underlying gene expression data.     

Discovery of Novel Serum Biomarkers for Prenatal Down Syndrome Screening by Integrative Data Mining

Background

To facilitate the experimental search for novel maternal serum biomarkers in prenatal Down Syndrome screening, we aimed to create a set of candidate biomarkers using a data mining approach.

Methodology/Principal Findings

Because current screening markers are derived from either fetal liver or placental trophoblasts, we reasoned that new biomarkers can primarily be found to be derived from these two tissues. By applying a three-stage filtering strategy on publicly available data from different sources, we identified 49 potential blood-detectable protein biomarkers. Our set contains three biomarkers that are currently widely used in either first- or second-trimester screening (AFP, PAPP-A and fβ-hCG), as well as ten other proteins that are or have been examined as prenatal serum markers. This supports the effectiveness of our strategy and indicates the set contains other markers potentially applicable for screening.

Conclusions/Significance

We anticipate the set will help support further experimental studies for the identification of new Down Syndrome screening markers in maternal blood.     

Biomarkers for Bone Tumors: Discovery from Genomics and Proteomics Studies and Their Challenges

Diagnosis of bone tumor currently relies on imaging and biopsy, and hence, the need to find less invasive ways for its accurate detection. More recently, numerous promising deoxyribonucleic acid (DNA) and protein biomarkers with significant prognostic, diagnostic and/or predictive abilities for various types of bone tumors have been identified from genomics and proteomics studies. This article reviewed the putative biomarkers for the more common types of bone tumors (that is, osteosarcoma, Ewing sarcoma, chondrosarcoma [malignant] and giant cell tumor [benign]) that were unveiled from the studies. The benefits and drawbacks of these biomarkers, as well as the technology platforms involved in the research, were also discussed. Challenges faced in the biomarker discovery studies and the problems in their translation from the bench to the clinical settings were also addressed.     

Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation

Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac rejection may offer a relevant post-transplant monitoring tool to effectively guide clinical care. The proposed computational pipeline is highly applicable to a wide range of biomarker proteomic studies.     

Study on Blood Biochemical Diagnostic Indices for Hepatic Function Biomarkers in Endemic Skeletal Fluorosis

The aim of the study was to determine the relationship of fluoride in drinking water to liver function in individuals living in normal and seven endemic fluorosis areas of Punjab, India. The concentration of fluoride in drinking water of different areas varied from 5.9 to 24.5 mg/L. Study group consisted of 705 patients in the age group between 20 and 60 years (mean age of 39.35 ± 11.27) affected with osteodental fluorosis were compared with 300 age- and sex-matched controls (with mean age of 35.28 ± 8.25 years). Biochemical data was analyzed by one-way analysis of variance (ANOVA) with post hoc Tukey–Kramer and Bonferroni multiple comparison tests. The relationship between hepatic enzymes was calculated by Pearson’s correlation and linear regression. The results revealed significantly (P < 0.001) higher concentration of serum fluoride in patients when compared to control. The mean activities of cyclic adenosine monophosphate (AMP), alkaline phosphatase (ALKP), acid phosphatase (ACP), aspartate aminotransaminase (AST), and alanine aminotransaminase (ALT) were significantly (P < 0.05–0.001) elevated in patients from all fluoride areas. ANOVA with post hoc Turkey–Kramer and Bonferroni multiple comparison test demonstrated a significant (P < 0.0001) variance in the activities of cAMP, ALKP, ACP, AST, and ALT in fluorotic patients, with elevation in water fluoride levels. Maximum elevation of 196.14% (ACP), 99.31% (cyclic adenosine monophosphate; cAMP), 72.08% (ALT), 60.14% (AST), and least 21.35% (ALKP) was recorded in patients exposed to 24.5 mg/L fluoride in drinking water. There was positive correlation between water fluoride, serum fluoride and AST (r = 0.77, 0.91), ALT (r = 0.82, 0.90), ALKP (r = 0.88, 0.97), and ACP (r = 0.74, 0.85). Pearson’s correlation demonstrated highly significant (P < 0.05) positive relationship between water fluoride and cAMP (regression equation: Y = 0.9807 ×+ 22.081 Y = 0.9807 \times + 22.081 , = 0.84; r = 0.92, P < 0.05). The increased levels of transaminases in fluorotic patients suggest alteration in liver functions. The level of alkaline and acid phosphatase was increased during fluoride intoxication which is also an early marker of hepatic cell damage because of its specificity and catalytic activity. The elevated levels of enzymes are reflective of bone disorders, which are characterized by increased osteoblastic activity. There levels increased several times if cellular damage occurs in the liver. The results suggest that fluoride exposure intensifies the activities of hepatic function enzymes in osteofluorosis.     

Top-Down Proteomics with Mass Spectrometry Imaging: A Pilot Study towards Discovery of Biomarkers for Neurodevelopmental Disorders

In the developing mammalian brain, inhibition of NMDA receptor can induce widespread neuroapoptosis, inhibit neurogenesis and cause impairment of learning and memory. Although some mechanistic insights into adverse neurological actions of these NMDA receptor antagonists exist, our understanding of the full spectrum of developmental events affected by early exposure to these chemical agents in the brain is still limited. Here we attempt to gain insights into the impact of pharmacologically induced excitatory/inhibitory imbalance in infancy on the brain proteome using mass spectrometric imaging (MSI). Our goal was to study changes in protein expression in postnatal day 10 (P10) rat brains following neonatal exposure to the NMDA receptor antagonist dizocilpine (MK801). Analysis of rat brains exposed to vehicle or MK801 and comparison of their MALDI MS images revealed differential relative abundances of several proteins. We then identified these markers such as ubiquitin, purkinje cell protein 4 (PEP-19), cytochrome c oxidase subunits and calmodulin, by a combination of reversed-phase (RP) HPLC fractionation and top-down tandem MS platform. More in-depth large scale study along with validation experiments will be carried out in the future. Overall, our findings indicate that a brief neonatal exposure to a compound that alters excitatory/inhibitory balance in the brain has a long term effect on protein expression patterns during subsequent development, highlighting the utility of MALDI-MSI as a discovery tool for potential biomarkers.     

The Diagnostic Value of Tumor Biomarkers for Detecting Hepatocellular Carcinoma Accompanied by Portal Vein Tumor Thrombosis

Tumor biomarkers commonly used for the detection of hepatocellular carcinoma (HCC) complicated with portal vein tumor thrombosis (PVTT) do not show satisfactory sensitivity and specificity. This study assesses the diagnostic value of the tumor biomarkers for the diagnosis of HCC with PVTT. A retrospective study was conducted on 475 patients diagnosed as HCC with PVTT and 977 patients diagnosed with HCC by imaging and requiring surgery at our hospital from January 1993 to January 2011. Serum alpha-fetoprotein AFP, carcinoembryonic antigen, and cancer antigen 125 (Ca125) of the patients were studied. No significant differences were observed in the patients’ general characteristics. The receiver operating characteristic (ROC) analysis showed that the cut-off of AFP and Ca125 was 32.91 ng/ml and 113.65 U/ml, respectively (AUC = 0.814 and 0.783). The parallel testing with AFP and Ca125 has a sensitivity of 0.909 and a specificity of 0.410; the serial testing has a sensitivity of 0.520 and a specificity of 0.97. The condition of AFP ≥ 20,000 ng/ml can detect HCC with PVTT with a sensitivity of 0.24, a specificity of 0.96, and an accuracy of 0.73 and positive screening of 0.76. The standard of both AFP > 32.91 ng/ml and Ca125 > 113.65 U/ml or AFP ≥ 20,000 ng/ml can detect HCC with PVTT with a specificity of 0.97 and 0.96, respectively, providing important guidance for clinical practice.