Application of pattern recognition and feature extraction techniques to volatile constituent metabolic profiles obtained by capillary gas chromatography

The applicability of threshold logic units, a form of nonparametric pattern recognition, to the processing of metabolic profile data obtained by high-efficiency glass capillary column gas chromatography has been investigated. The test data included profiles of the volatile constituents of urine from normal individuals and from individuals with diabetes mellitus. A feature extraction algorithm allowed for dimensionality reduction and indicated the constituents most important in the normal versus pathological distinction. With an optimum number of dimensions, a normal versus pathological prediction rate of 93.75% was achieved. Gas chromatography—mass spectrometry was utilized to identify important profile constituents.     

Hypermethylation of the CpG Island Near the G4C2 Repeat in ALS with a C9orf72 Expansion

The G₄C₂ repeat expansion in C9orf72 is the most common known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). We tested the hypothesis that the repeat expansion causes aberrant CpG methylation near the G₄C₂ repeat, which could be responsible for the downregulation of gene expression. We investigated the CpG methylation profile by two methods using genomic DNA from the blood of individuals with ALS (37 expansion carriers and 64 noncarriers), normal controls (n = 76), and family members of 7 ALS probands with the expansion. We report that hypermethylation of the CpG island 5′ of the G₄C₂ repeat is associated with the presence of the expansion (p < 0.0001). A higher degree of methylation was significantly correlated with a shorter disease duration (p < 0.01), associated with familial ALS (p = 0.009) and segregated with the expansion in 7 investigated families. Notably, we did not detect methylation for either normal or intermediate alleles (up to 43 repeats), bringing to question the current cutoff of 30 repeats for pathological alleles. Our study raises several important questions for the future investigation of large data sets, such as whether the degree of methylation corresponds to clinical presentation (ALS versus FTLD).     

Semen samples showing an increased rate of spermatozoa with imprinting errors have a negligible effect in the outcome of assisted reproduction techniques

The topic of imprinting defects present in the sperm of infertile patients has been addressed by several reports in the last few years. However, whether methylation abnormalities at one or few CpGs within an imprinted locus are pathological is a matter of debate. Moreover, whether imprinting anomalies in sperm could interfere with fertility treatment outcomes is still unknown. In this report we analyze the sperm DNA methylation profile of H19-ICR, KvDMR, SNRPN-ICR, IG-DMR and MEG3-DMR by pyrosequencing in 107 infertile men series and a control population of 30 proven fertile males. DNA methylation was statistically evaluated from two points of view: first, the methylation of each CpG was analyzed in the control population and the mean, standard deviation and range were determined and compared with infertile population data; second, in order to define altered methylation patterns for each region, a hierarchical cluster analysis was performed by which individuals were grouped in different clusters according to the degree of similarity of their methylation pattern. Two pieces of data supported the results obtained in the multi-variate analysis: the classification of the vast majority of control individuals in clusters with normal methylation patterns and the significant differences in methylation levels found between individuals within the normal and abnormal clusters. Individuals included in normal and abnormal methylation clusters were compared according to seminal parameters as well as to the outcome of assisted reproduction.     

Semen samples showing an increased rate of spermatozoa with imprinting errors have a negligible effect in the outcome of assisted reproduction techniques

The topic of imprinting defects present in the sperm of infertile patients has been addressed by several reports in the last few years. However, whether methylation abnormalities at one or few CpGs within an imprinted locus are pathological is a matter of debate. Moreover, whether imprinting anomalies in sperm could interfere with fertility treatment outcomes is still unknown. In this report we analyze the sperm DNA methylation profile of H19-ICR, KvDMR, SNRPN-ICR, IG-DMR and MEG3-DMR by pyrosequencing in 107 infertile men series and a control population of 30 proven fertile males. DNA methylation was statistically evaluated from two points of view: first, the methylation of each CpG was analyzed in the control population and the mean, standard deviation and range were determined and compared with infertile population data; second, in order to define altered methylation patterns for each region, a hierarchical cluster analysis was performed by which individuals were grouped in different clusters according to the degree of similarity of their methylation pattern. Two pieces of data supported the results obtained in the multi-variate analysis: the classification of the vast majority of control individuals in clusters with normal methylation patterns and the significant differences in methylation levels found between individuals within the normal and abnormal clusters. Individuals included in normal and abnormal methylation clusters were compared according to seminal parameters as well as to the outcome of assisted reproduction.     

Electron-capture gas chromatographic–chemical ionization mass spectrometric study of sera from people vaccinated with bacille Calmette–Guerin for characteristic metabolites

Serum samples from 26 individuals vaccinated with bacille Calmette–Guerin (BCG) and from 26 controls (10 patients with pulmonary tuberculosis and 16 non BCG-vaccinated healthy individuals) were analyzed by frequency-pulsed electron-capture gas chromatography (FPEC-GC) and chemical ionization gas chromatography–mass spectrometry (CIGC–MS) for the presence of characteristic metabolites. A distinct pattern consisted of tuberculostearic acid (TSA) and a peak, labeled peak 1, was observed in all BCG-vaccinated individuals, whereas only three of 26 controls generated this chromatography profile. TSA was detected in all patients with pulmonary tuberculosis but peak 1 was absent. Sera drawn from 12 individuals 11 to 14 days after BCG vaccination yielded three transitional FPEC-GC profiles. A permanent FPEC-GC profile consisting of TSA and of a full scale peak 1 appeared 28 days to a few months after BCG vaccination. Peak 1 was tentatively identified by CIGC–MS as 9-methyl-hexacosanol. The findings suggest that peak 1 may serve as a marker to detect Mycobacterium bovis BCG and to distinguish individuals infected with M. tuberculosis from individuals vaccinated with BCG.     

An improved method for the identification and quantitation of biological lipids by HPLC using laser light-scattering detection

We have developed a simplified and improved high performance liquid chromatography (HPLC) method for the detection and quantitation of tissue lipid using a new laser light-scattering detector (Varex model ELSD II). This detector has a limit of sensitivity of 50 ng for neutral lipid and 200 ng for most phospholipids with excellent reproducibility. By coupling the ELSD II with a ternary gradient normal phase HPLC system, we were able to separate and quantify the major lipid constituents of extracted tissue. This system was used to profile and quantitate the major lipids from rat brain, liver, and heart with greater sensitivity than other available techniques, with the exception of high performance thin-layer chromatography (HPTLC). However, the convenience of HPLC allows for a significant improvement in analysis time with only a threefold reduction in sensitivity when compared to HPTLC.     

A novel micro-to-macro approach for cardiac tissue mechanics

For studying cardiac mechanics, hyperelastic anisotropic computational models have been developed which require the tissue anisotropic and hyperelastic parameters. These parameters are obtained by tissue samples mechanically testing. The validity of such parameters are limited to the specific tissue sample only. They are not adaptable for pathological tissues commonly associated with tissue microstructure alterations. To investigate cardiac tissue mechanics, a novel approach is proposed to model hyperelasticity and anisotropy. This approach is adaptable to various tissue microstructural constituent’s distributions in normal and pathological tissues. In this approach, the tissue is idealized as composite material consisting of cardiomyocytes distributed in extracellular matrix (ECM). The major myocardial tissue constituents are mitochondria and myofibrils while the main ECM’s constituents are collagen fibers and fibroblasts. Accordingly, finite element simulations of uniaxial and equibiaxial tests of normal and infarcted tissue samples with known amounts of these constituents were conducted, leading to corresponding tissue stress–strain data that were fitted to anisotropic/hyperelastic models. The models were validated where they showed good agreement characterized by maximum average stress-strain errors of 16.17 and 10.01% for normal and infarcted cardiac tissue, respectively. This demonstrate the effectiveness of the proposed models in accurate characterization of healthy and pathological cardiac tissues.     

The frequency of occurrence and discriminatory power of compounds found in human scent across a population determined by SPME-GC/MS

The composition of human scent collected from the hands is of interest to the medical community as a mechanism to diagnose disease and the forensic community as a means to investigate canine scent discriminations. An extensive survey of the volatile organic compounds (VOCs) identified in the headspace of hand odor samples utilizing solid phase micro-extraction gas chromatography/mass spectrometry (SPME-GC/MS) has been conducted to determine the constituents of the human base odor profile. Sixty-three compounds were extracted from the collected odor samples. The composition included acids, alcohols, aldehydes, hydrocarbons, esters, ketones and nitrogen-containing compounds. The majority of the compounds detected (79.4%) were present in less than one third of the individuals sampled. Spearman correlation coefficient comparisons at a match/no-match threshold of 0.9 produced a distinguish ability of 99.67% across the population.     

Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes

Nonenzymatic glycation of peptides and proteins by d-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. In this work, we report the first proteomics-based characterization of nonenzymatically glycated proteins in human plasma and erythrocyte membranes from individuals with normal glucose tolerance, impaired glucose tolerance, and type 2 diabetes mellitus. Phenylboronate affinity chromatography was used to enrich glycated proteins and glycated tryptic peptides from both human plasma and erythrocyte membranes. The enriched peptides were subsequently analyzed by liquid chromatography coupled with electron transfer dissociation-tandem mass spectrometry, resulting in the confident identification of 76 and 31 proteins from human plasma and erythrocyte membranes, respectively. Although most of the glycated proteins could be identified in samples from individuals with normal glucose tolerance, slightly higher numbers of glycated proteins and more glycation sites were identified in samples from individuals with impaired glucose tolerance and type 2 diabetes mellitus.     

Effect of pressure and ionic strength on the self-association of Apo-A-I from the human high density lipoprotein complex.

The self-association of apo-A-I isolated from the human high density lipoprotein complex has been investigated by gel permeation chromatography and sedimentation equilibrium. The apparent weight average molecular weight (MWapp) versus Apo-A-I concentration profile was found to be sensitive to ionic strength and pressure; MWapp increased with increasing ionic strength and decreasing rotor speed. The data were consistent with a monomer-dimer-tetrameroctamer association shceme over all conditions investigated if a change in the partial specific volume of apo-A-I upon association of 5.5 x 10(-2) ml/g is postulated.     

Obesity-dependent metabolic signatures associated with nonalcoholic fatty liver disease progression

Our understanding of the mechanisms by which nonalcoholic fatty liver disease (NAFLD) progresses from simple steatosis to steatohepatitis (NASH) is still very limited. Despite the growing number of studies linking the disease with altered serum metabolite levels, an obstacle to the development of metabolome-based NAFLD predictors has been the lack of large cohort data from biopsy-proven patients matched for key metabolic features such as obesity. We studied 467 biopsied individuals with normal liver histology (n=90) or diagnosed with NAFLD (steatosis, n=246; NASH, n=131), randomly divided into estimation (80% of all patients) and validation (20% of all patients) groups. Qualitative determinations of 540 serum metabolite variables were performed using ultraperformance liquid chromatography coupled to mass spectrometry (UPLC-MS). The metabolic profile was dependent on patient body-mass index (BMI), suggesting that the NAFLD pathogenesis mechanism may be quite different depending on an individual's level of obesity. A BMI-stratified multivariate model based on the NAFLD serum metabolic profile was used to separate patients with and without NASH. The area under the receiver operating characteristic curve was 0.87 in the estimation and 0.85 in the validation group. The cutoff (0.54) corresponding to maximum average diagnostic accuracy (0.82) predicted NASH with a sensitivity of 0.71 and a specificity of 0.92 (negative/positive predictive values=0.82/0.84). The present data, indicating that a BMI-dependent serum metabolic profile may be able to reliably distinguish NASH from steatosis patients, have significant implications for the development of NASH biomarkers and potential novel targets for therapeutic intervention.     

Italian cohort of patients affected by inflammatory bowel disease is characterised by variation in glycerophospholipid,free fatty acids and amino acid levels

Background

Inflammatory bowel disease is a group of pathologies characterised by chronic inflammation of the intestine and an unclear aetiology. Its main manifestations are Crohn’s disease and ulcerative colitis. Currently, biopsies are the most used diagnostic tests for these diseases and metabolomics could represent a less invasive approach to identify biomarkers of disease presence and progression.

Objectives

The lipid and the polar metabolite profile of plasma samples of patients affected by inflammatory bowel disease have been compared with healthy individuals with the aim to find their metabolomic differences. Also, a selected sub-set of samples was analysed following solid phase extraction to further characterise differences between pathological samples.

Methods

A total of 200 plasma samples were analysed using drift tube ion mobility coupled with time of flight mass spectrometry and liquid chromatography for the lipid metabolite profile analysis, while liquid chromatography coupled with triple quadrupole mass spectrometry was used for the polar metabolite profile analysis.

Results

Variations in the lipid profile between inflammatory bowel disease and healthy individuals were highlighted. Phosphatidylcholines, lyso-phosphatidylcholines and fatty acids were significantly changed among pathological samples suggesting changes in phospholipase A₂ and arachidonic acid metabolic pathways. Variations in the levels of cholesteryl esters and glycerophospholipids were also found. Furthermore, a decrease in amino acids levels suggests mucosal damage in inflammatory bowel disease.

Conclusions

Given good statistical results and predictive power of the model produced in our study, metabolomics can be considered as a valid tool to investigate inflammatory bowel disease.

     

GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data

Glycosylation modifies the physicochemical properties and protein binding functions of glycoconjugates. These modifications are biosynthesized in the endoplasmic reticulum and Golgi apparatus by a series of enzymatic transformations that are under complex control. As a result, mature glycans on a given site are heterogeneous mixtures of glycoforms. This gives rise to a spectrum of adhesive properties that strongly influences interactions with binding partners and resultant biological effects. In order to understand the roles glycosylation plays in normal and disease processes, efficient structural analysis tools are necessary. In the field of glycomics, liquid chromatography/mass spectrometry (LC/MS) is used to profile the glycans present in a given sample. This technology enables comparison of glycan compositions and abundances among different biological samples, i.e. normal versus disease, normal versus mutant, etc. Manual analysis of the glycan profiling LC/MS data is extremely time-consuming and efficient software tools are needed to eliminate this bottleneck. In this work, we have developed a tool to computationally model LC/MS data to enable efficient profiling of glycans. Using LC/MS data deconvoluted by Decon2LS/DeconTools, we built a list of unique neutral masses corresponding to candidate glycan compositions summarized over their various charge states, adducts and range of elution times. Our work aims to provide confident identification of true compounds in complex data sets that are not amenable to manual interpretation. This capability is an essential part of glycomics work flows. We demonstrate this tool, GlycReSoft, using an LC/MS dataset on tissue derived heparan sulfate oligosaccharides. The software, code and a test data set are publically archived under an open source license.     

Phosphorylation of U24 from Human Herpes Virus type 6 (HHV-6) and its potential role in mimicking myelin basic protein (MBP) in multiple sclerosis

Myelin basic protein (MBP) from multiple sclerosis (MS) patients contains lower levels of phosphorylation at Thr97 than normal individuals. The significance of phosphorylation at this site is not fully understood, but it is proposed to play a role in the normal functioning of MBP. Human Herpesvirus Type 6 encodes the protein U24, which has tentatively been implicated in the pathology of MS. U24 shares a 7 amino acid stretch encompassing the Thr97 phosphorylation site of MBP: PRTPPPS. We demonstrate using a combination of mass spectrometry, thin layer chromatography and autoradiography, that U24 can be phosphorylated at the equivalent threonine. Phospho-U24 may confound signalling or other pathways in which phosphorylated MBP may participate, precipitating a pathological process.     

Median estimation of chemical constituents for sampling on two occasions under a log‐normal model

Sampling from a finite population on multiple occasions introduces dependencies between the successive samples when overlap is designed. Such sampling designs lead to efficient statistical estimates, while they allow estimating changes over time for the targeted outcomes. This makes them very popular in real‐world statistical practice. Sampling with partial replacement can also be very efficient in biological and environmental studies where estimation of toxicants and its trends over time is the main interest. Sampling with partial replacement is designed here on two occasions in order to estimate the median concentration of chemical constituents quantified by means of liquid chromatography coupled with tandem mass spectrometry. Such data represent relative peak areas resulting from the chromatographic analysis. They are therefore positive‐valued and skewed data, and are commonly fitted very well by the log‐normal model. A log‐normal model is assumed here for chemical constituents quantified in mainstream cigarette smoke in a real case study. Combining design‐based and model‐based approaches for statistical inference, we seek for the median estimation of chemical constituents by sampling with partial replacement on two time occasions. We also discuss the limitations of extending the proposed approach to other skewed population models. The latter is investigated by means of a Monte Carlo simulation study.     

Isolation and characterization of a pepsin C zymogen produced by human breast tissues.

An aspartic proteinase present in cyst fluid from women with gross cystic breast disease was purified by a procedure involving affinity chromatography on pepstatin-agarose and size-exclusion high performance liquid chromatography. The amino-terminal sequence of the purified breast proteinase was identical to that corresponding to gastric pepsinogen C. Additional data on cleavage specificity, pH optimum, and immunological properties supported the close relationship between both molecules. Northern blot analysis and polymerase chain reaction amplification studies performed on RNAs obtained from normal and pathological breast tissues demonstrated that the protein is produced by mammary carcinomas and cysts, but not by the normal resting mammary gland. Immunohistochemical staining of paraffin-embedded tissue sections confirmed the existence of a subset of tumors that have the ability to synthesize and secrete this pepsin zymogen. On the basis of these results, we suggest that pepsinogen C expression by human mammary epithelium may be involved in the development of breast diseases, being also of potential interest as a biochemical marker of the hormonal imbalance underlying these pathologies.     

Protein and lipid disturbances in rat liver microsomal membranes after bile duct ligation

An analysis of proteins, phospholipids and cholesterol from liver microsomal membranes was performed in normal and post-cholestatic rats. Bile duct ligated rats showed a progressive decrease of these membrane constituents. Minor changes in peptide analysis, a marked decrease of phosphatidylcholine and phosphatidylinositol, disappearance of phosphatidylethanolamine and sphingomyelin, and a clear increment of phosphatidylserine was observed in post-cholestatic as compared to normal group. It was concluded that extra-hepatic cholestasis produces structural changes on the liver microsomes, particularly on phospholipid profile.     

Metabolomic approaches to the normal aging process

Aging is a multifaceted process involving the accumulation of diverse deleterious changes in biological systems over time, so significant alterations in cellular metabolism are detected throughout aging. In the present study, the metabolic processes relevant to the normal aging process were investigated via non-targeted metabolomics using liquid chromatography–mass spectrometry. To exclude physiological and environmental differences, the metabolic profiles and the relevant metabolic pathways were analyzed in plasma from two separate study groups comprising two distinctly aged cohorts of healthy individuals, the elderly and the younger. The first group was recruited from an urban hospital, and the second group was recruited from a rural community. Alterations in fatty acid beta-oxidation, glycerophospholipid metabolism, and sphingolipid metabolism were identified as significant metabolic pathways relevant to normal aging. It was also found that sphingosine in sphingolipid metabolism, long-chain acylcarnitines in beta-oxidation, and lysophosphatidylcholines (LysoPCs) in glycerophospholipid metabolism could be critical candidate metabolites in the aging process. These results suggest that the metabolic profile of the healthiest individuals could be associated with the normal function of mitochondria, the primary organelle of redox homeostasis, as indicated by their low acylcarnitine to l-carnitine ratio and low levels of LysoPCs and sphingosine in plasma. The present study provides a critical contribution to the entire picture of the aging process.