Dataset Information

Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study.

ABSTRACT: The analysis of volatile organic compounds (VOC) as biomarkers of cancer is both promising and challenging. In this pilot study, we used an untargeted approach to compare volatile metabolomic signatures of melanoma and matched control non-neoplastic skin from the same patient. VOC from fresh (non-fixed) biopsied tissue were collected using the headspace solid phase micro extraction method (HS SPME) and analyzed by gas chromatography and mass spectrometry (GCMS). We applied the XCMS analysis platform and MetaboAnalyst software to reveal many differentially expressed metabolic features. Our analysis revealed increased levels of lauric acid (C12:0) and palmitic acid (C16:0) in melanoma. The identity of these compounds was confirmed by comparison with chemical standards. Increased levels of these fatty acids are likely to be a consequence of up-regulated de novo lipid synthesis, a known characteristic of cancer. Increased oxidative stress is likely to cause an additional increase in lauric acid. Implementation of this study design on larger number of cases will be necessary for the future metabolomics biomarker discovery applications.

SUBMITTER: Abaffy T

PROVIDER: S-EPMC3769583 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study.

Abaffy T T Möller M G MG Riemer D D DD Milikowski C C DeFazio R A RA

Metabolomics : Official journal of the Metabolomic Society 20130330 5

The analysis of volatile organic compounds (VOC) as biomarkers of cancer is both promising and challenging. In this pilot study, we used an untargeted approach to compare volatile metabolomic signatures of melanoma and matched control non-neoplastic skin from the same patient. VOC from fresh (non-fixed) biopsied tissue were collected using the headspace solid phase micro extraction method (HS SPME) and analyzed by gas chromatography and mass spectrometry (GCMS). We applied the XCMS analysis plat ...[more]

PMID: 24039618

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Project description:Perturbations in microRNA (miRNA) expression profiles has been reported for cutaneous malignant melanoma (CMM). With regards to a rapidly growing number of newly discovered miRNA sequences, the availability of up-to-date miRNA expression profiles for primary cutaneous malignant melanoma (PCMM), cutaneous malignant melanoma metastases (CMMM) and benign melanocytic naevi (BMN) is limited. Patients with PCMM (n=9), CMMM (n=4) and BMN (n=8) were included in the study. Specimens were obtained during surgery from the center of the tumors (lesional). An exploratory microarray analysis was performed by miRNA expression profiling based on miRBase V.16. Additionally, the expression levels of selected miRNA candidates were confirmed by TaqMan real-time quantitative polymerase chain reaction (RT-PCR). New miRNA candidates previously not described to be associated with CMM were found to be potentially dysregulated in CMM. Nine patients with PCMM (PCMM1-PCMM9), four patients with CMMM (CMMM1-CMMM4) and eight patients with BMN (BMN1-BMN8) were enrolled in the present study. All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation. Total RNA including miRNAs was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA). To be further considered for Microarray analysis a RIN ≥ 7.0 indicating medium to good RNA quality was defined as inclusion criteria. For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The spiked total RNA was treated with alkaline calf intestine phosphatase (CIP). The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions. Labeled miRNA samples were hybridized at 55°C for 20 hrs on separate Human miRNA Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile (Sigma-Aldich, St.Louis, USA). Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer´s instructions.

Project description:Background and aimNumerous women of reproductive age experience physical or mental discomfort during their natural menstrual cycle due to paramenstrual symptoms, such as premenstrual syndrome (PMS). To date, there is no established biomarker for the diagnosis of PMS. This study investigated the relationship between skin gas composition and menstruation cycles, and evaluated the possibility of skin gas composition as a biomarker of paramenstrual symptoms.MethodsWe conducted an exploratory pilot study. Healthy Japanese women (aged 20-29 years) underwent blood and skin gas analyses on 1 day corresponding to menstruation, preovulatory, middle luteal, and late luteal phases. Skin gas was collected from the cubital fossa and armpit using a Passive Flux Sampler; samples were analyzed for 65 volatile organic compounds (VOCs) by gas chromatography-mass spectrometry (GC-MS). Non-parametric statistical analysis was performed to identify VOCs related to the menstrual cycle, levels of female hormones, and severity of PMS.ResultsFourteen women participated; of those, 12 completed the study. Regarding the relationship with the menstrual cycles, seven and four VOCs were significantly and marginally changed, respectively, at the cubital fossa during menstruation. Of those 11 compounds, 10 were also correlated with the levels of serum female hormones. At the armpit, five and three compounds were significantly and marginally changed, respectively, during menstruation. Of those eight compounds, five were also correlated with the levels of serum female hormones. In the study of PMS severity, analysis of the changes in VOCs suggested that ketones and fatty acids are increased during menstruation in the severe PMS group versus the mild PMS group.ConclusionsThe results of this study suggest that certain VOCs emitted in skin gas related to the menstrual cycle, levels of female hormones, and severity of PMS. These findings may advance the metabolic understanding and development of diagnostic biomarkers for menstruation-related symptoms.

Dataset Information

Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study.

Publications

Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study.

Similar Datasets

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