Phosphotyrosine profiling of human cerebrospinal fluid

Background

Cerebrospinal fluid (CSF) is an important source of potential biomarkers that affect the brain. Biomarkers for neurodegenerative disorders are needed to assist in diagnosis, monitoring disease progression and evaluating efficacy of therapies. Recent studies have demonstrated the involvement of tyrosine kinases in neuronal cell death. Thus, neurodegeneration in the brain is related to altered tyrosine phosphorylation of proteins in the brain and identification of abnormally phosphorylated tyrosine peptides in CSF has the potential to ascertain candidate biomarkers for neurodegenerative disorders.

Methods

In this study, we used an antibody-based tyrosine phosphopeptide enrichment method coupled with high resolution Orbitrap Fusion Tribrid Lumos Fourier transform mass spectrometer to catalog tyrosine phosphorylated peptides from cerebrospinal fluid. The subset of identified tyrosine phosphorylated peptides was also validated using parallel reaction monitoring (PRM)-based targeted approach.

Results

To date, there are no published studies on global profiling of phosphotyrosine modifications of CSF proteins. We carried out phosphotyrosine profiling of CSF using an anti-phosphotyrosine antibody-based enrichment and analysis using high resolution Orbitrap Fusion Lumos mass spectrometer. We identified 111 phosphotyrosine peptides mapping to 66 proteins, which included 24 proteins which have not been identified in CSF previously. We then validated a set of 5 tyrosine phosphorylated peptides in an independent set of CSF samples from cognitively normal subjects, using a PRM-based targeted approach.

Conclusions

The findings from this deep phosphotyrosine profiling of CSF samples have the potential to identify novel disease-related phosphotyrosine-containing peptides in CSF.

     

Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium

Background

The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing.

Methods

The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap). Statistical analysis using a one-way ANOVA followed by Bonferroni’s post-hoc test was used to show significant differences in protein expression. Ingenuity Pathway Analysis was used to observe networks of differentially expressed proteins, their biological processes, and associated diseases, while Cytoscape software was used to determine putative interactions with select biomarker proteins. These candidate biomarkers were further verified using Western blotting, while coimmunoprecipitation was used to verify putative partners determined using bioinformatics.

Results

We show that a comparison across all three proteomes shows that there are 447 differentially expressed proteins, with 387 differentially expressed between postnatal day 3 and 30. Ingenuity Pathway Analysis revealed ~?62% of postnatal day 3 downregulated proteins are involved in neurological diseases. Several proteins are expressed exclusively on P3, including Parvin α, Drebrin1 (Drb1), Secreted protein acidic and cysteine rich (SPARC), Transmembrane emp24 domain-containing protein 10 (Tmed10). Coimmunoprecipitations showed that Parvin and SPARC interact with integrin-linked protein kinase and the large conductance calcium-activated potassium channel, respectively.

Conclusions

Quantitative mass spectrometry revealed the identification of numerous differentially regulated proteins over three days of postnatal development. These data provide insights into functional pathways regulating normal sensory and supporting cell development in the cochlea that include potential biomarkers. Interacting partners of two of these markers suggest the importance of these complexes in regulating cellular structure and synapse development.

     

No diurnal variation of classical and candidate biomarkers of Alzheimer’s disease in CSF

Background

Cerebrospinal fluid (CSF) biomarkers have gained increasing importance in the diagnostic work-up of Alzheimer’s disease (AD). The core CSF biomarkers related to AD pathology (Aβ42, t-tau and p-tau) are currently used in CSF diagnostics, while candidate markers of amyloid metabolism (Aβ38, Aβ40, sAPPα, sAPPβ), synaptic loss (neurogranin), neuroinflammation (YKL-40), neuronal damage (VILIP-1) and genetic risk (apolipoprotein E) are undergoing evaluation. Diurnal fluctuation in the concentration of CSF biomarkers has been reported and may represent a preanalytical confounding factor in the laboratory diagnosis of AD. The aim of the present study was to investigate the diurnal variability of classical and candidate CSF biomarkers in a cohort of neurosurgical patients carrying a CSF drainage.

Method

Samples were collected from a cohort of 13 neurosurgical patients from either ventricular (n?=?6) or lumbar (n?=?7) CSF drainage at six time points during the day, 1–7 days following the neurosurgical intervention. Concentrations of the core biomarkers were determined by immunoassays.

Results

Although absolute values largely varied among subjects, none of the biomarkers showed significant diurnal variation. Site of drainage (lumbar vs. ventricular) did not influence this result. The different immunoassays used for tau and Aβ markers provided similar results.

Conclusion

Time of day at CSF collection does not ultimately affect the concentration levels of classical and candidate AD biomarkers. Similar trends were found when using different immunoassays, thus corroborating the consistency of the data.

     

Metabolomics approach for predicting response to neoadjuvant chemotherapy for colorectal cancer

Introduction

Colorectal cancer (CRC) is a clinically heterogeneous disease, which necessitates a variety of treatments and leads to different outcomes. Only some CRC patients will benefit from neoadjuvant chemotherapy (NACT).

Objectives

An accurate prediction of response to NACT in CRC patients would greatly facilitate optimal personalized management, which could improve their long-term survival and clinical outcomes.

Methods

In this study, plasma metabolite profiling was performed to identify potential biomarker candidates that can predict response to NACT for CRC. Metabolic profiles of plasma from non-response (n?=?30) and response (n?=?27) patients to NACT were studied using UHPLC–quadruple time-of-flight)/mass spectrometry analyses and statistical analysis methods.

Results

The concentrations of nine metabolites were significantly different when comparing response to NACT. The area under the receiver operating characteristic curve value of the potential biomarkers was up to 0.83 discriminating the non-response and response group to NACT, superior to the clinical parameters (carcinoembryonic antigen and carbohydrate antigen 199).

Conclusion

These results show promise for larger studies that could result in more personalized treatment protocols for CRC patients.

     

Identification of putative biomarkers for leptomeningeal invasion in B-cell non-Hodgkin lymphoma by NMR metabolomics

Introduction

B-cell non-Hodgkin lymphoma (B-NHL) is the most common hematological malignancy and different genetic alterations are frequently detected in transformed B lymphocytes. Within this heterogeneous disease, certain aggressive subgroups have an increased risk of central nervous system (CNS) involvement at diagnosis and/or relapse, resulting in parenchymal or leptomeningeal infiltration (LI) in 5–15% of cases. The current sensitivity limitations of cerebrospinal fluid (CSF) cytology and contrast-enhanced MRI for CNS involvement, mainly at early stages, motivates the search for alternative diagnostic methods.

Objectives

Here we aim at using untargeted ¹H-NMR metabolomics to identify putative biomarkers for LI in B-NHL patients.

Methods

CSF and peripheral blood samples were obtained from B-NHL patients with a positive (n?=?7, LI group) or negative LI diagnostic (n?=?13, control group). For seven patients, CSF samples were collected during the course of intrathecal chemotherapy, making it possible to assess the patient´s response to treatment. ¹H-NMR spectra were acquired and statistical multivariate and univariate analysis were performed to identify significant alterations.

Results

Significant metabolite differences were found between LI and control groups in CSF, but not in serum. A predictive PLS-DA cross-validated model identified significant pool changes in glycine, alanine, pyruvate, acetylcarnitine, carnitine, and phenylalanine. Additionally, increments in protein signals were detected in the LI group. Significantly, the PLS-DA model predicted correctly all samples obtained from the group of patients in remission during LI treatment.

Conclusions

The results show that the CSF NMR-metabolomics approach is a promising complementary method in clinical diagnosis and treatment follow-up of LI in B-NHL patients.

     

Crop metabolomics: from diagnostics to assisted breeding

Background

Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.

Aim of Review

We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.

Key Scientific Concepts of Review

Translational metabolomics applied to crop breeding programs.

     

Annotation of the human cerebrospinal fluid lipidome using high resolution mass spectrometry and a dedicated data processing workflow

Introduction

Due to its proximity with the brain, cerebrospinal fluid (CSF) could be a medium of choice for the discovery of biomarkers of neurological and psychiatric diseases using untargeted analytical approaches.

Objectives

This study explored the CSF lipidome in order to generate a robust mass spectral database using an untargeted lipidomic approach.

Methods

Cerebrospinal fluid samples from 45 individuals were analyzed by liquid chromatography coupled to high-resolution mass spectrometry method (LC-HRMS). A dedicated data processing workflow was implemented using XCMS software and adapted filters to select reliable features. In addition, an automatic annotation using an in silico lipid database and several MS/MS experiments were performed to identify CSF lipid species.

Results

Using this complete workflow, 771 analytically relevant monoisotopic lipid species corresponding to 550 unique lipids which represent five major lipid families (i.e., free fatty acids, sphingolipids, glycerophospholipids, glycerolipids, and sterol lipids) were detected and annotated. In addition, MS/MS experiments enabled to improve the annotation of 304 lipid species. Thanks to LC-HRMS, it was possible to discriminate between isobaric and also isomeric lipid species; and interestingly, our study showed that isobaric ions represent about 50 % of the total annotated lipid species in the human CSF.

Conclusion

This work provides an extensive LC/HRMS database of the human CSF lipidome which constitutes a relevant foundation for future studies aimed at finding biomarkers of neurological disorders.

     

Detection of human herpesviruses in the cerebrospinal fluid from patients diagnosed with or suspected of having progressive multifocal leukoencephalopathy

Background

Progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease caused by JC virus (JCV), occurs mainly in immunocompromised patients. While JCV DNA is detected in the cerebrospinal fluid (CSF) from a certain proportion of patients suspected of having PML, JCV-negative patients may also develop brain lesions due to other infectious agents. This study assessed the prevalence of six herpesviruses in the CSF from patients diagnosed with or suspected of PML.

Methods

Two hundred and ninety-nine CSF specimens and clinical data were collected from 255 patients, including 31 confirmed PML cases. Quantitative PCR assays were carried out to detect the genomic DNA of JCV, herpes simplex virus (HSV), varicella-zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus 6 (HHV-6).

Results

Herpesvirus DNAs were detected in the CSF specimens from 29 of 255 patients (11.4%). HSV-1 and CMV were detected in JCV-negative patients, whereas VZV and EBV were detected in both CSF JCV-positive and -negative individuals. The herpesvirus-positive patients had underlying disorders that caused immunosuppression, such as HIV infection, congenital immunodeficiencies, and hematologic malignancies, and presented with neurologic symptoms and MRI lesions, mainly in the cerebral white matter. The median values of CSF cell counts and protein levels in the herpesvirus-positive patients were slightly higher than those in the PML patients.

Conclusions

The results demonstrate that herpesviruses are occasionally detected in the CSF from PML patients and immunocompromised individuals suspected of having PML. Thus, this study provides a significant basis for the diagnosis and treatment of neurological disorders in immunocompromised patients.

     

Metabolic characterization of hepatitis B virus-related liver cirrhosis using NMR-based serum metabolomics

Introduction

Liver cirrhosis (LC) is an advanced liver disease that can develop into hepatocellular carcinoma. Hepatitis B virus (HBV) infection is one of the main causes of LC. Therefore, there is an urgent need for developing a new method to monitor the progression of HBV-related LC (HBV-LC).

Objectives

In this study, we attempted to examine serum metabolic changes in healthy individuals as well as patients with HBV and HBV-LC. Furthermore, potential metabolite biomarkers were identified to evaluate patients progressed from health to HBV-LC.

Methods

Metabolic profiles in the serum of healthy individuals as well as patients with HBV and HBV-LC were detected using an NMR-based metabolomic approach. Univariate and multivariate analyses were conducted to analyze serum metabolic changes during HBV-LC progression. Moreover, potential metabolite biomarkers were explored by receiver operating characteristic curve analysis.

Results

Serum metabolic changes were closely associated with the progression of HBV-LC, mainly involving energy metabolism, protein metabolism, lipid metabolism and microbial metabolism. Serum histidine was identified as a potential biomarker for HBV patients. Acetate, formate, pyruvate and glutamine in the serum were identified as a potential biomarker panel for patients progressed from HBV to HBV-LC. In addition, phenylalanine, unsaturated lipid, n-acetylglycoprotein and acetone in the serum could be considered as a potential common biomarkers panel for these patients.

Conclusion

NMR-based serum metabolomic approach could be a promising tool to monitor the progression of liver disease. Different metabolites may reflect different stages of liver disease.

     

Non-invasive urinary metabolomic profiling discriminates prostate cancer from benign prostatic hyperplasia

Introduction

Prostate cancer (PCa) is one of the most common malignancies in men worldwide. Serum prostate specific antigen (PSA) level has been extensively used as a biomarker to detect PCa. However, PSA is not cancer-specific and various non-malignant conditions, including benign prostatic hyperplasia (BPH), can cause a rise in PSA blood levels, thus leading to many false positive results.

Objectives

In this study, we evaluated the potential of urinary metabolomic profiling for discriminating PCa from BPH.

Methods

Urine samples from 64 PCa patients and 51 individuals diagnosed with BPH were analysed using ¹H nuclear magnetic resonance (¹H-NMR). Comparative analysis of urinary metabolomic profiles was carried out using multivariate and univariate statistical approaches.

Results

The urine metabolomic profile of PCa patients is characterised by increased concentrations of branched-chain amino acids (BCAA), glutamate and pseudouridine, and decreased concentrations of glycine, dimethylglycine, fumarate and 4-imidazole-acetate compared with individuals diagnosed with BPH.

Conclusion

PCa patients have a specific urinary metabolomic profile. The results of our study underscore the clinical potential of metabolomic profiling to uncover metabolic changes that could be useful to discriminate PCa from BPH in a clinical context.

     

Transient increase in CSF GAP-43 concentration after ischemic stroke

Background

Cerebrospinal fluid (CSF) biomarkers reflect ongoing processes in the brain. Growth-associated protein 43 (GAP-43) is highly upregulated in brain tissue shortly after experimental ischemia suggesting the CSF GAP-43 concentration may be altered in ischemic brain disorders. CSF GAP-43 concentration is elevated in Alzheimer’s disease patients; however, patients suffering from stroke have not been studied previously.

Methods

The concentration of GAP-43 was measured in longitudinal CSF samples from 28 stroke patients prospectively collected on days 0–1, 2–4, 7–9, 3?weeks, and 3–5?months after ischemia and cross-sectionally in 19 controls. The stroke patients were clinically evaluated using a stroke severity score system. The extent of the brain lesion, including injury size and degrees of white matter lesions and atrophy were evaluated by CT and magnetic resonance imaging.

Results

Increased GAP-43 concentration was detected from day 7–9 to 3?weeks after stroke, compared to day 1–4 and to levels in the control group (P?=?0.02 and P?=?0.007). At 3–5?months after stroke GAP-43 returned to admission levels. The initial increase in GAP-43 during the nine first days was associated to stroke severity, the degree of white matter lesions and atrophy and correlated positively with infarct size (r_s?=?0.65, P?=?0.001).

Conclusions

The transient increase of CSF GAP-43 is important to take into account when used as a biomarker for other neurodegenerative diseases such as Alzheimer’s disease. Furthermore, GAP-43 may be a marker of neuronal responses after stroke and additional studies confirming the potential of CSF GAP-43 to reflect severity and outcome of stroke in larger cohorts are warranted.

     

Iridoid and phenylethanoid/phenylpropanoid metabolite profiles of <Emphasis Type="Italic">Scrophularia</Emphasis> and <Emphasis Type="Italic">Verbascum</Emphasis> species used medicinally in North America

Introduction

Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.

Objectives

We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.

Methods

Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.

Results

Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.

Conclusions

Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.

     

Identification of biomarkers of chromophobe renal cell carcinoma by weighted gene co-expression network analysis

Background

Chromophobe renal cell carcinoma (ChRCC) is the second common subtype of non-clear cell renal cell carcinoma (nccRCC), which accounting for 4–5% of renal cell carcinoma (RCC). However, there is no effective bio-marker to predict clinical outcomes of this malignant disease. Bioinformatic methods may provide a feasible potential to solve this problem.

Methods

In this study, differentially expressed genes (DEGs) of ChRCC samples on The Cancer Genome Atlas database were filtered out to construct co-expression modules by weighted gene co-expression network analysis and the key module were identified by calculating module-trait correlations. Functional analysis was performed on the key module and candidate hub genes were screened out by co-expression and MCODE analysis. Afterwards, real hub genes were filter out in an independent dataset GSE15641 and validated by survival analysis.

Results

Overall 2215 DEGs were screened out to construct eight co-expression modules. Brown module was identified as the key module for the highest correlations with pathologic stage, neoplasm status and survival status. 29 candidate hub genes were identified. GO and KEGG analysis demonstrated most candidate genes were enriched in mitotic cell cycle. Three real hub genes (SKA1, ERCC6L, GTSE-1) were selected out after mapping candidate genes to GSE15641 and two of them (SKA1, ERCC6L) were significantly related to overall survivals of ChRCC patients.

Conclusions

In summary, our findings identified molecular markers correlated with progression and prognosis of ChRCC, which might provide new implications for improving risk evaluation, therapeutic intervention, and prognosis prediction in ChRCC patients.

     

Comparison of iTRAQ and SWATH in a clinical study with multiple time points

Background

Advances in mass spectrometry have accelerated biomarker discovery in many areas of medicine. The purpose of this study was to compare two mass spectrometry (MS) methods, isobaric tags for relative and absolute quantitation (iTRAQ) and sequential window acquisition of all theoretical fragment ion spectra (SWATH), for analytical efficiency in biomarker discovery when there are multiple methodological constraints such as limited sample size and several time points for each patient to be analyzed.

Methods

A total of 140 tear samples were collected from 28 glaucoma patients at 5 time points in a glaucoma drug switch study. Samples were analyzed with iTRAQ and SWATH methods using NanoLC-MSTOF mass spectrometry.

Results

We discovered that even though iTRAQ is faster than SWATH with respect to analysis time per sample, it loses in sensitivity, reliability and robustness. While SWATH analysis yielded complete data of 456 proteins in all samples, with iTRAQ we were able to quantify 477 proteins in total but on average only 125 proteins were quantified in a sample. 283 proteins were common in the datasets produced by the two methods. Repeatability of the methods was assessed by calculating percent relative standard deviation (% RSD) between replicate MS analyses: SWATH was more repeatable (56% of proteins?<?20% RSD), compared to iTRAQ (43% of proteins?<?20% RSD). Despite the overall benefits of SWATH, both methods showed less than 1 log fold change difference in the expression of 74% common proteins. In addition, comparison to MS/MS peptide results using 8 isotopically labeled peptide standards, SWATH and iTRAQ showed similar results in terms of accuracy. Moreover, both methods detected similar trends in a longitudinal analysis of protein expression of two known tear biomarkers.

Conclusions

Overall, we conclude that SWATH should be preferred for biomarker discovery studies when analyzing limited volumes of clinical samples collected at multiple time points.

Trial Registeration

The study was approved by the Ethics Committee at Tampere University Hospital and was registered in EU clinical trials register (EudraCT Number: 2010-021039-14).

     

Heart fatty acid binding protein and Aβ-associated Alzheimer’s neurodegeneration

Background

Epidemiological and molecular findings suggest a relationship between Alzheimer’s disease (AD) and dyslipidemia, although the nature of this association is not well understood.

Results

Using linear mixed effects models, we investigated the relationship between CSF levels of heart fatty acid binding protein (HFABP), a lipid binding protein involved with fatty acid metabolism and lipid transport, amyloid-β (Aβ), phospho-tau, and longitudinal MRI-based measures of brain atrophy among 295 non-demented and demented older individuals. Across all participants, we found a significant association of CSF HFABP with longitudinal atrophy of the entorhinal cortex and other AD-vulnerable neuroanatomic regions. However, we found that the relationship between CSF HABP and brain atrophy was significant only among those with low CSF Aβ_1–42 and occurred irrespective of phospho-tau_181p status.

Conclusions

Our findings indicate that Aβ-associated volume loss occurs in the presence of elevated HFABP irrespective of phospho-tau. This implicates a potentially important role for fatty acid binding proteins in Alzheimer’s disease neurodegeneration.

     

Serum metabolomic study for detecting biomarkers of non-traumatic osteonecrosis of the femoral head

Introduction

Non-traumatic osteonecrosis of the femoral head (NTONFH) is a progressive disease, always leading to hip dysfunction if no early intervention was applied. The difficulty for early diagnosis of NTONFH is due to the slight symptoms at early stages as well as the high cost for screening patients by using magnetic resonance imaging.

Objective

The aim was to detect biomarkers of early-stage NTONFH, which was beneficial to the exploration of a cost-effective approach for the early diagnose of the disease.

Methods

Metabolomic approaches were employed in this study to detect biomarkers of early-stage NTONFH (22 patients, 23 controls), based on the platform of ultra-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and the uses of multivariate statistic analysis, putative metabolite identification, metabolic pathway analysis and biomarker analysis.

Results

In total, 33 serum metabolites were found altered between NTONFH group and control group. In addition, glycerophospholipid metabolism and pyruvate metabolism were highly associated with the disease.

Conclusion

The combination of LysoPC (18:3), l-tyrosine and l-leucine proved to have a high diagnostic value for early-stage NTONFH. Our findings may contribute to the protocol for early diagnosis of NTONFH and further elucidate the underlying mechanisms of the disease.

     

Global proteomic mapping of alkali stress regulated molecular networks in <Emphasis Type="Italic">Helianthus tuberosus</Emphasis> L.

Background and aims

Soil salinization with high pH condition is a major abiotic stress to plant growth and crop productivity. Helianthus tuberosus L. is an important stress tolerant plant and can survive in the saline-alkali soil and semiarid areas. The aim of this study is to identify the effect of alkali stress on H. tuberosus through global proteomics analysis and improve understanding of the alkalinity resistance of plants.

Methods

H. tuberosus seedlings were exposed to different level alkali stress for 7 days. Protein profiling was quantified by conducting MS-based comparative proteomics analysis. RT-PCR study was carried out to analyze the mRNA expression levels of candidate alkali stress response proteins.

Results

The response of H. tuberosus to alkali stress was detected at both physiological and molecular levels. 104 differentially expressed proteins from H. tuberosus leaves response to Na₂CO₃ treatment were successfully identified. Functional categorization of these identified proteins showed that the accumulation level of proteins involved in glycolysis, TCA cycle, PSI system, ROS scavenging and signal transduction increased under alkali stress.

Conclusions

Based on the observation of plant growth and the investigation of molecular regulation, H.tuberosus could resist certain alkali stress by modulating carbohydrate metabolism and redox homeostasis. These findings provide a new sight into the underlying molecular mechanisms of alkali resistance in plant.

     

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome

Background

Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40–50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used to demonstrate that the network regulating stress signaling by the c-Jun N-terminal kinase pathway played a crucial role in survival of patients with neuroblastoma irrespective of their MYCN amplification status. This demonstrates the enormous potential of computational models of biological modules for the discovery of underlying molecular mechanisms of diseases.

Results

Since signaling is known to be highly relevant in cancer, we have used a computational model of the whole cell signaling network to understand the molecular determinants of bad prognostic in neuroblastoma. Our model produced a comprehensive view of the molecular mechanisms of neuroblastoma tumorigenesis and progression.

Conclusion

We have also shown how the activity of signaling circuits can be considered a reliable model-based prognostic biomarker.

Reviewers

This article was reviewed by Tim Beissbarth, Wenzhong Xiao and Joanna Polanska. For the full reviews, please go to the Reviewers’ comments section.

     

Hypertension in adult Fabry’s disease: is cardiotrophin-1 a diagnostic biomarker?

Background

Cardiotrophin-1 (CT-1), a cytokine produced by cardiomyocytes and non-cardiomyocytes in conditions of stress, can be used as a biomarker of left ventricular hypertrophy and dysfunction in hypertensive patients. Hypertension is one of the main adverse events in the third and last phase of Fabry’s disease (FD). We measured CT-1 in order to examine its correlation with the vascular and cardiac alterations at different ages and assess its potential for use as a biomarker of hypertension in FD.

Findings

The level of CT-1 was clearly higher in hypertensive adults than in adult FD patients. FD patients show a small, non-significant decrease in plasma CT-1 with age, while in hypertensive patients CT-1 in plasma rises strongly and highly significantly with age.

Conclusions

CT-1 can be considered a good biomarker of the progression of hypertension with age, but particular care is needed when following hypertension in FD patients, since CT-1 does not correlate the same way with this disease.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.