Metabolomics Analyses from Tissues in Parkinson’s Disease

Abstract

Metabolomics has been successfully applied to study neurological and neurodegenerative disorders including Parkinson’s disease for: 1) the identification of potential biomarkers of onset and disease progression; 2) the identification of novel mechanisms of disease progression; and 3) the assessment of treatment prognosis and outcome. Reproducible and efficient extraction of metabolites is imperative to the success of any metabolomics investigation. Unlike other OMICS techniques, the composition of the metabolome can be negatively impacted by the preparation, processing and the handling of these samples. The proper choice of data collection, preprocessing and processing protocols are similarly important to the design of an effective metabolomics experiment. Likewise, the correct application of univariate and multivariate statistical methods are essential for providing biologically-relevant insights. In this chapter, we have outlined a detailed metabolomics workflow that addresses all of these issues. A step-by-step protocol from the preparation of neuronal cells and metabolomic tissue samples to their metabolic analyses using nuclear magnetic resonance, mass spectrometry, and chemometrics is presented.

Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron

“…One-dimensional (1D) 1 H NMR data collection and analysis were completed as described previously ( 40 – 42 , 67 – 69 ). Briefly, samples from each class were prepared for NMR analysis by dissolving the lyophilized culture medium into 600 μl of 50 mM phosphate buffer (pH 7.2, uncorrected) in 99.8% D 2 O with 50 μM 3-(tetramethylsilane)propionic acid-2,2,3,3-d4 (TMSP).…”

“…These original data were obtained using liquid chromatography technology, but since then, our ability to collect high-resolution untargeted one-dimensional proton nuclear magnetic resonance (1D 1 H NMR) data and the statistical methods to deconvolute complicated spectra has evolved considerably, making untargeted NMR metabolomics of B. theta cultures feasible ( 40 – 42 ). Our study aimed to use untargeted metabolomics, systems biology, and biological modeling techniques to revisit the metabolism of this important human symbiont to account for nutrient inputs and outputs and to gain insight into how B. theta responds to physiological concentrations of metabolic fermentation products that are encountered in the gut ecosystem.…”

Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications

“…Ultrafiltration has also been utilized, but may result in significant metabolite loss due to macromolecule binding, and should be used with caution when accurate quantification is desired [42,43]. Tissue samples are also commonly analyzed by solution state NMR, but must be homogenized prior to metabolite extraction [44]. Prior to sample storage, the effective concentration of biofluid samples may be improved by drying the sample and then, reconstituting in a phosphate buffer to the desired sample volume [44].…”

“…Tissue samples are also commonly analyzed by solution state NMR, but must be homogenized prior to metabolite extraction [44]. Prior to sample storage, the effective concentration of biofluid samples may be improved by drying the sample and then, reconstituting in a phosphate buffer to the desired sample volume [44]. This is particularly useful when a limited sample is available for NMR analysis, but it does require extra preparation time and may perturb the sample leading to erroneous quantification.…”

Advances of Mechanisms-Related Metabolomics in Parkinson’s Disease

“…Similarly, metabolic profiles of blood in idiopathic PD are also different from healthy groups, such as alpha-synuclein, tau protein, urate, and a series of amino acid metabolism ( Bolner et al, 2011 ; Luan et al, 2015 ; Saiki et al, 2017 ; Chang et al, 2018 ; Goldman et al, 2018 ). These disturbances in the metabolic pathways are related to mitochondrial dysfunctions and the concomitant changes in energy homeostasis and redox reaction, which are thought to be the final common pathways of most endogenous and exogenous factors that are involved in the etiology of PD ( Bhinderwala et al, 2019 ). Recent studies have revealed that there are metabolic differences between treated and drug-naïve PD patients ( Bogdanov et al, 2008 ; Troisi et al, 2019 ), as well as patients with and without dementia or depression ( Hatano et al, 2016 ; Dong et al, 2018 ).…”