To the authors’ knowledge, this is the first reported study to identify sPD and LRRK2 PD specific metabolic signatures in CSF using a targeted metabolomics approach employing both 1H NMR spectroscopy and mass spectrometry. Using complementary techniques allows us to detect and quantify many more metabolites and as such we require much more robust and accurate analytical data tools to help us discriminate between sample types. In this study, we used several machine learning algorithms to systematically evaluate our data. All the metrics have been reported in the supplementary information (Table S4). When comparing the multivariate approach, which is the traditional classification approach in the field of metabolomics, machine learning algorithms demonstrated superior performance for the diagnoses of PD. Particularly, logistic regression, random forest and support vector machine algorithms resulted in the best diagnostic accuracy (Fig. 2). This is because these algorithms work well with high-dimensional data and can deal with unbalanced and missing values. Multivariate modelling is all about getting a simple formulation of a frontier in a classification model problem that potentially tend to fail if there are non-linear boundaries between the groups aimed to be classified. On the other hand, Machine Learning algorithm seems to capture all patterns beyond any boundaries of linearity or even continuity of the boundaries between any groups implying superior classification performance. In a recent study, Stoessel et al. (2017) investigated PD-specific metabolic changes in CSF using non-targeted mass spectrometry and identified a panel of biomarkers for the diagnosis of PD. Using Random forest and PLS-DA, they reported models with an AUC = 0.74 and 0.73, respectively (23). Goldstein et al. (2012) reported models using biomarker candidates in in CSFwith 0.89 sensitivity and 0.80 specificity (24). In another study Hong et al.(2010) reported predictive model using DJ-1 and α-synuclein levels in CSF provided predictive accuracies equal to 0.77 with sensitivity of 0.94 and specificity of 0.50 (25). In a recent study by Mondello et al. (2014) α-Synuclein and ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) levels in CSF were used to discriminate PD from controls. Both biomarkers discriminated PD from controls well with AUC of 0.82 with sensitivity of 0.87 and specificity of 0.79, respectively (26). In our study we go one step further. We profiled sporadic and LRRK2 positive patients and produced powerful models with AUC = 0.88 (sensitivity = 1; specificity = 0.75) for sporadic and AUC = 0.94 (sensitivity = 0.88; specificity = 1) for LRRK2 PD patients. To the authors knowledge these are one of the most highly sensitive and specific models to be reported in the literature.
The primary objective of this study was to identify a panel of biomarkers which could accurately diagnose PD using CSF and to gain an insight into the biochemistry behind PD. To ensure we got the most accurate snapshot of the disease metabolome only samples from unmedicated participants were utilized to minimize any confounding factors.
Evident form the heat map, we can see that there are dysregulations in several metabolite groups due to parkinsonism (Fig. 3). Characteristics of the metabolites indicate perturbations in the carnitine, glycerophospholipid, sphingolipid, and amino acid metabolism in PD. MSEA identified a marked alteration in bile acid metabolism in sPD (Fig. 4a). Bile acids are form of cholinic acids synthesized from cholesterol in the liver (27). They are involved in many essential biological and metabolic cascades including glucose, lipid, cholesterol, drug metabolism and closely associated with intestinal hormones, microbiotas and energy balance (28). However, very little is known about the molecular mechanisms of bile acids in the central nervous system (29). In a study by Chun et al. (2012), they reported that UDCA (Ursodeoxycholic acid) reduced reactive oxygen species (ROS), reactive nitrogen species (peroxynitrite and nitric oxide), and helped to maintain intracellular glutathione (GSH) levels in a cell model of PD (30). Correspondingly, significant reduction in apoptosis markers such as nuclear fragmentation, caspase activation, and cytochrome were detected. Further, they reported that inhibiting phosphatidylinositiol-3-kinase (PI3K) and Akt/PKB blocked the favorable effects of UDCA on SNP-induced cytotoxic cell death (30). The beneficial effect of UDCA on impairment of mitochondrial function has also been reported by Mortiboys et al.(2015) (31). Moreover, the naturally occurring taurine conjugate of UDCA (TUDCA) was tested for its neuroprotective effect in motor neuron disease (32).
Another important biochemical pathway found to be aberrant in the CSF of PD patients was taurine and hypotaurine metabolism. Taurine is a major intracellular free β-amino acid in mammalian tissues and intervenes in many physiological functions, such as neuromodulation, maintenance of calcium homeostasis, antioxidant and anti-inflammatory processes. The level of taurine has been reported to be elevated in the region of brain controlling the dopamine release and dopaminergic neuron activity (33). Moreover, taurine has been reported to reduce dopaminergic neurodegeneration and α-synuclein oligomerization through suppression of microglial M1 polarization via NOX2-NF-κB pathway in a pesticide-induced PD model (34). Thus, one may hypothesize that the perturbation of this particular metabolic pathway could be a neuroprotective reaction by the brain.
It is also noteworthy that this is the first metabolomics study to report ethanol degradation to be significantly perturbed in the CSF of PD patients. Interestingly, one of the key enzymes involved in the ethanol degradation pathway is alcohol dehydrogenase (ADH). Mutations in ADH genes could play a role in the etiology of Parkinson's disease (PD) because of the important function they undertake, particularly in retinoid and dopamine metabolism and/or aldehyde detoxification (35). In support of our hypothesis, Tan et al. (2001) reported that a polymorphism at allele A1 for ADH was correlated with an increased risk of PD (36).
Interestingly, propionate metabolism was found to be significantly disturbed between in sPD and corresponding controls. Propionate, the end-product of the microbial digestion of carbohydrates, presents together with other SCFA in the gastro-intestinal tract. Gut microbiota and their metabolic products are among potential candidates that could ignite a process that eventually leads to Lewy body formation in the enteric nervous system. In recent studies, differences in the abundance of certain gut microbiota and their metabolic products such as SCFA and propionate was reported (37).
MSEA also highlighted several metabolic pathways perturbed in the CSF harvested from LRRK2 PD patients (Fig. 4b). One such pathway was fatty acid metabolism. Perturbation in fatty acid metabolism in PD has also been previously reported (38). An enzymatic deficiency in either fatty acid breakdown or disturbance of fatty acid transport across the mitochondrial membrane due to defects in the carnitine transport system result in dysregulation of fatty acid (39). Supported by the significant change in the level of carnitines in CSF, we hypothesize that lipid metabolism is directly perturbed as a result of the change in carnitine levels. Brain acylcarnitines support lipid biosynthesis and the activity of antioxidants; they also enhance cholinergic neurotransmission (40). Further, when oxygen levels are low, the brain transitions from glucose metabolism to anaerobic respiration. Alternatively, it can also shift from glucose metabolism entirely, using fatty acids or ketones during pathological conditions such as neurodegeneration, hypoxia/ischemia, or post-traumatic brain injury (41). Therefore, the perturbation in fatty acid metabolism we observed could be a potential attempt at attenuating neuronal cell death, further supported by a significant change in the level of 1-methylhistamine which is a metabolite in histamine metabolism. Histamine, a neurotransmitter which is widely distributed throughout the human brain and an increase in it has been reported to be involved in the histaminergic system in PD (42). Notably, both Mitochondrial Beta oxidation of LCFA and Mitochondrial Beta oxidation of SCFA were significantly disturbed in LRRK2 PD. Taken together, these results suggest a profound change in energy metabolism.
Consistent with an essential role in cellular function, lack of inositol in cells leads to a rapid loss of viability (43). As inositol metabolic pathway was found to be perturbed, the association between LRRK2 gene and inositol metabolism needs to be further elucidated.
Our study is not without its limitations. Firstly, our small sample size limits what we deduce from the results. Secondly, the available clinical information is lacking such as UPDSR. This precluded us from considering key clinical variables in the models to optimize performance and to determine whether there are other confounding factors that could affect the metabolic profile.