14 research outputs found
ADAP-GC 3.0: Improved Peak Detection and Deconvolution of Co-eluting Metabolites from GC/TOF-MS Data for Metabolomics Studies
ADAP-GC is an automated computational
pipeline for untargeted,
GC/MS-based metabolomics studies. It takes raw
mass spectrometry data as input and carries out a sequence of data
processing steps including construction of extracted ion chromatograms,
detection of chromatographic peak features, deconvolution of coeluting
compounds, and alignment of compounds across samples. Despite the
increased accuracy from the original version to version 2.0 in terms
of extracting metabolite information for identification and quantitation,
ADAP-GC 2.0 requires appropriate specification of a number of parameters
and has difficulty in extracting information on compounds that are
in low concentration. To overcome these two limitations, ADAP-GC 3.0
was developed to improve both the robustness and sensitivity of compound
detection. In this paper, we report how these goals were achieved
and compare ADAP-GC 3.0 against three other software tools including
ChromaTOF, AnalyzerPro, and AMDIS that are widely used in the metabolomics
community
Distinct Metabolomic Profiles of Papillary Thyroid Carcinoma and Benign Thyroid Adenoma
Papillary
thyroid carcinoma (PTC) and benign thyroid adenoma (BTA)
are the most common head and neck tumors. However, the metabolic differences
between PTC and BTA have not been characterized. The aim of this study
was to identify the metabolic profiles of these two types of tumors
using a metabolomics approach. Tumors and adjacent nontumor specimens
collected from 57 patients with PTC and 48 patients with BTA were
profiled using gas chromatography–time-of-flight mass spectrometry
and ultraperformance liquid chromatography-quadrupole time-of-flight
mass spectrometry. A panel of 46 and 44 differentially expressed metabolites
were identified in the PTC and BTA specimens, respetively, and compared
with nontumor tissues. Common metabolic signatures, as characterized
by increased glycolysis, amino acid metabolism, one carbon metabolism
and tryptophan metabolism, were found in both types of tumors. Purine
and pyrimidine metabolism was significantly elevated in the PTC specimens,
and taurine and hypotaurine levels were also higher in the PTC tissues.
Increased fatty acid and bile acid levels were found, especially in
the BTA tissues. The metabolic profiles of the PTC and BTA tissues
include both similar and remarkably different metabolites, suggesting
the presence of common and unique mechanistic pathways in these types
of tumors during tumorigenesis
ADAP-GC 2.0: Deconvolution of Coeluting Metabolites from GC/TOF-MS Data for Metabolomics Studies
ADAP-GC 2.0 has been developed to deconvolute coeluting
metabolites
that frequently exist in real biological samples of metabolomics studies.
Deconvolution is based on a chromatographic model peak approach that
combines five metrics of peak qualities for constructing/selecting
model peak features. Prior to deconvolution, ADAP-GC 2.0 takes raw
mass spectral data as input, extracts ion chromatograms for all the
observed masses, and detects chromatographic peak features. After
deconvolution, it aligns components across samples and exports the
qualitative and quantitative information of all of the observed components.
Centered on the deconvolution, the entire data analysis workflow is
fully automated. ADAP-GC 2.0 has been tested using three different
types of samples. The testing results demonstrate significant improvements
of ADAP-GC 2.0, compared to the previous ADAP 1.0, to identify and
quantify metabolites from gas chromatography/time-of-flight mass spectrometry
(GC/TOF-MS) data in untargeted metabolomics studies
Isotopic Ratio Outlier Analysis of the <i>S. cerevisiae</i> Metabolome Using Accurate Mass Gas Chromatography/Time-of-Flight Mass Spectrometry: A New Method for Discovery
Isotopic ratio outlier analysis (IROA)
is a <sup>13</sup>C metabolomics
profiling method that eliminates sample to sample variance, discriminates
against noise and artifacts, and improves identification of compounds,
previously done with accurate mass liquid chromatography/mass spectrometry
(LC/MS). This is the first report using IROA technology in combination
with accurate mass gas chromatography/time-of-flight mass spectrometry
(GC/TOF-MS), here used to examine the <i>S. cerevisiae</i> metabolome. <i>S. cerevisiae</i> was grown in YNB media,
containing randomized 95% <sup>13</sup>C, or 5%<sup>13</sup>C glucose
as the single carbon source, in order that the isotopomer pattern
of all metabolites would mirror the labeled glucose. When these IROA
experiments are combined, the abundance of the heavy isotopologues
in the 5%<sup>13</sup>C extracts, or light isotopologues in the 95%<sup>13</sup>C extracts, follows the binomial distribution, showing mirrored
peak pairs for the molecular ion. The mass difference between the <sup>12</sup>C monoisotopic and the <sup>13</sup>C monoisotopic equals
the number of carbons in the molecules. The IROA-GC/MS protocol developed,
using both chemical and electron ionization, extends the information
acquired from the isotopic peak patterns for formulas generation.
The process that can be formulated as an algorithm, in which the number
of carbons, as well as the number of methoximations and silylations
are used as search constraints. In electron impact (EI/IROA) spectra,
the artifactual peaks are identified and easily removed, which has
the potential to generate “clean” EI libraries. The
combination of chemical ionization (CI) IROA and EI/IROA affords a
metabolite identification procedure that enables the identification
of coeluting metabolites, and allowed us to characterize 126 metabolites
in the current study
Metabonomic Profiling Reveals Cancer Chemopreventive Effects of American Ginseng on Colon Carcinogenesis in <i>Apc</i><sup><i>Min/+</i></sup> Mice
American
ginseng (<i>Panax quinquefolius</i> L.) is one
of the most commonly used herbal medicines in the West. It has been
reported to possess significant antitumor effects that inhibit the
process of carcinogenesis. However, the mechanisms underlying its
anticancer effects remain largely unresolved. In this study, we investigated
the cancer chemopreventive effects of American ginseng on the progression
of high fat (HF) diet-enhanced colorectal carcinogenesis with a genetically
engineered <i>Apc</i><sup><i>Min/+</i></sup> mouse
model. The metabolic alterations in sera of experimental mice perturbed
by HF diet intervention as well as the American ginseng treatment
were measured by gas chromatography time-of-flight mass spectrometry
(GC-TOFMS) and liquid chromatography time-of-flight mass spectrometry
(LC-TOFMS) analysis. American ginseng treatment significantly extended
the life span of the <i>Apc</i><sup><i>Min/+</i></sup> mouse. Significant alterations of metabolites involving amino
acids, organic acids, fatty acids, and carbohydrates were observed
in <i>Apc</i><sup><i>Min/+</i></sup> mouse in
sera, which were attenuated by American ginseng treatment and concurrent
with the histopathological improvement with significantly reduced
tumor initiation, progression and gut inflammation. These metabolic
changes suggest that the preventive effect of American ginseng is
associated with attenuation of impaired amino acid, carbohydrates,
and lipid metabolism. It also appears that American ginseng induced
significant metabolic alterations independent of the <i>Apc</i><sup><i>Min/+</i></sup> induced metabolic changes. The
significantly altered metabolites induced by American ginseng intervention
include arachidonic acid, linolelaidic acid, glutamate, docosahexaenoate,
tryptophan, and fructose, all of which are associated with inflammation
and oxidation. This suggests that American ginseng exerts the chemopreventive
effects by anti-inflammatory and antioxidant mechanisms
Plasma Metabolite Biomarkers for the Detection of Pancreatic Cancer
Patients
with pancreatic cancer (PC) are usually diagnosed at late
stages, when the disease is nearly incurable. Sensitive and specific
markers are critical for supporting diagnostic and therapeutic strategies.
The aim of this study was to use a metabonomics approach to identify
potential plasma biomarkers that can be further developed for early
detection of PC. In this study, plasma metabolites of newly diagnosed
PC patients (<i>n</i> = 100) and age- and gender-matched
controls (<i>n</i> = 100) from Connecticut (CT), USA, and
the same number of cases and controls from Shanghai (SH), China, were
profiled using combined gas and liquid chromatography mass spectrometry.
The metabolites consistently expressed in both CT and SH samples were
used to identify potential markers, and the diagnostic performance
of the candidate markers was tested in two sample sets. A diagnostic
model was constructed using a panel of five metabolites including
glutamate, choline, 1,5-anhydro-d-glucitol, betaine, and
methylguanidine, which robustly distinguished PC patients in CT from
controls with high sensitivity (97.7%) and specificity (83.1%) (area
under the receiver operating characteristic curve [AUC] = 0.943, 95%
confidence interval [CI] = 0.908–0.977). This panel of metabolites
was then tested with the SH data set, yielding satisfactory accuracy
(AUC = 0.835; 95% CI = 0.777–0.893), with a sensitivity of
77.4% and specificity of 75.8%. This model achieved a sensitivity
of 84.8% in the PC patients at stages 0, 1, and 2 in CT and 77.4%
in the PC patients at stages 1 and 2 in SH. Plasma metabolic signatures
show promise as biomarkers for early detection of PC
Metabolic Transformation of DMBA-Induced Carcinogenesis and Inhibitory Effect of Salvianolic Acid B and Breviscapine Treatment
Oral cancer typically develops from hyperplasia through
dysplasia
to carcinoma with a multistep process of carcinogenesis involving
genetic alterations resulting in aberrant cellular appearance, deregulated
cell growth, and carcinoma. The metabolic transformation during the
process of oral carcinogenesis and its implications for cancer therapy
have not been extensively investigated. Here, we report a metabonomic
study on a classical model of 7,12-dimethylbenz(a)anthracene (DMBA)-induced
oral carcinogenesis in hamsters to delineate characteristic metabolic
transformation during the carcinogenesis using gas chromatography
time-of-flight mass spectrometry (GC–TOF MS). Salvianolic acid
B (Sal-B), isolated from <i>Salvia miltiorrhiza</i> Bge, and Breviscapine,
a flavonoid isolated from Herba Erigerontis, were used to treat the
hamsters exposed to DMBA to investigate the molecular mechanism of
the inhibitory effect of the two agents on oral carcinogenesis. The
dynamic changes of serum metabolic profiles indicated that both Sal-B
and Breviscapine were able to attenuate DMBA-induced metabolic perturbation,
which is consistent with the histopathological findings that Sal-B
and Breviscapine significantly decreased the squamous cell carcinoma
(SCC) incidence in the two treatment groups. Significant alterations
of key metabolic pathways, including elevated glutaminolysis and glycolysis,
and decreased cholesterol and myo-inositol metabolism, were observed
in the DMBA-induced model group, which were attenuated or normalized
by Sal-B or Breviscapine treatment. Elevated inflammation and tumor
angiogenesis at gene and metabolite expression levels were also observed
in DMBA-induced oral dysplasia and SCC but were attenuated or normalized
by Sal-B and Breviscapine along with significantly decreased incidences
of SCC formation
Serum Metabolic Signatures of Fulminant Type 1 Diabetes
Fulminant type 1 diabetes (FT1DM) is a relatively new
clinical
entity featured by acute destruction of pancreatic beta cells. Clinical
consequences of FT1DM could be fatal when timely medications are not
provided, suggesting the particular importance of rapid and accurate
diagnosis. Here we report a serum metabonomics study of FT1DM patients,
together with healthy control subjects (NC), type 2 diabetes (T2DM),
classic type 1 diabetes (T1DM), and diabetic ketoacidosis (DKA) patients,
with the aim of discovering metabolic markers associated with FT1DM.
A total of 79 subjects were enrolled (22 NC, 22 T1DM, 22 T2DM, 8 DKA
and 5 FT1DM) and the serum metabolic profiling of fasting blood samples
was performed using gas chromatography time-of-flight mass spectrometry
(GC-TOFMS) coupled with multivariate and univariate statistical analyses.
Serum metabolites differentially expressed in FT1DM relative to NC,
or to T2DM, T1DM and DKA were identified. Three metabolite markers,
5-oxoproline, glutamate, and homocysteine, were significantly altered
among FT1DM, T2DM, T1DM, and DKA. In addition, the three metabolite
markers, 5-oxoproline, glutamate, and homocysteine, presented similar
patterns of distribution across groups. The results showed that the
metabolic signatures of FT1DM identified in this study could be of
potential clinical significance for the accurate diagnosis of FT1DM
Metabonomic Phenotyping Reveals an Embryotoxicity of Deca-Brominated Diphenyl Ether in Mice
Recent studies have demonstrated that polybrominated diphenyl ethers (PBDEs), a group of industrial chemicals, could disrupt thyroid hormone homeostasis and exhibit neurotoxicity, reproductive toxicity, and embryotoxicity. However, clear evidence of embryotoxicity and neurotoxicity of many of these congeners, such as deca-BDE, one of the least bioactive congeners of PBDEs, is still lacking. In the present study, we investigated deca-BDE embryotoxicity by quantitative analysis of two essential thyroid hormones (T4 and T3) and a variety of small-molecule metabolites in the serum of deca-BDE-dosed pregnant mice. Four groups of pregnant C57 mice were administrated with deca-BDE in 20% fat emulsion at a dose of 150, 750, 1 500, or 2 500 mg/kg body weight via gastric intubation on gestation days (g.d.s) 7 to 9, while a control group was given 20% fat emulsion. Maternal mice were euthanized on g.d. 16 and examined for external malformations of the fetus. Maternal serum samples were collected and analyzed by the enzyme linked immunosorbent assay (ELISA) and gas chromatography–time-of-flight mass spectrometry (GC–TOF MS). Using multivariate statistical analysis, we observed a significantly altered metabolic profile associated with deca-BDE embryotoxicity in maternal serum. Our results also demonstrated that deca-BDE at a dose of 2 500 mg/kg body weight induced significant disruption of thyroid hormone metabolism, the TCA cycle, and lipid metabolism in maternal mice, which subsequently led to a significant inhibition of fetal growth and development. We concluded that deca-BDE-induced embryotoxicity closely correlated with global metabolic disruption that can be characterized by thyroid hormone deficiency, disrupted lipid metabolism, and a depleted level of cholesterol in maternal mice
Transcriptomic and Metabonomic Profiling Reveal Synergistic Effects of Quercetin and Resveratrol Supplementation in High Fat Diet Fed Mice
Dietary quercetin and resveratrol have been frequently
used in treating various diseases, but the underlying mechanisms are
not entirely clear. Here, we report combined transcriptomic and metabonomic
profiling that showed that the combined supplementation with quercetin
and resveratrol produced synergistic effects on a high-fat diet-induced
metabolic phenotype in mice. Histological and phenotypic improvements
in serum and hepatic total cholesterol, insulin, fasting blood glucose,
and HbA1c were also observed in mice receiving combined quercetin
and resveratrol supplementation. This combined quercetin and resveratrol
supplementation resulted in significant restoration of gene sets in
functional pathways of glucose/lipid metabolism, liver function, cardiovascular
system, and inflammation/immunity, which were altered by high fat
diet feeding. The integration of transcriptomic and metabonomic data
indicated quercetin and resveratrol supplementation enhanced processes
of glycolysis and fatty acid oxidation, as well as suppressed gluconeogenesis.
These alterations discovered at both the transcriptional and metabolic
levels highlight the significance of combined “omics”
platforms for elucidating mechanistic pathways altered by dietary
polyphenols, such as quercetin and resveratrol, in a synergistic manner