Metabolomic Analysis Provides Insights on Paraquat-Induced Parkinson-Like Symptoms in Drosophila melanogaster

Novel metabolic biomarker for early detection and diagnosis to the patients with gastric cardia adenocarcinoma

BACKGROUND

Gastric cardia adenocarcinoma (GCA) is classified as Siewert type II adenocarcinoma at the esophagogastric junction in Western countries. The majority of GCA patients do not exhibit early warning symptoms, leading to over 90% of diagnoses at an advanced stage, resulting in a grim prognosis, with less than a 20% 5-year survival rate.

METHOD

Metabolic features of 276 GCA and 588 healthy controls were characterized through a widely-targeted metabolomics by UPLC-MS/MS analysis. This study encompasses a joint pathway analysis utilizing identified metabolites, survival analysis in both early and advanced stages, as well as high and negative and low expression of HER2 immunohistochemistry staining. Machine learning techniques and Cox regression models were employed to construct a diagnostic panel.

RESULTS

A total of 25 differential metabolites were consistently identified in both discovery and validation sets based on criteria of p < 0.05, (VIP) ≥ 1, and FC ≥ 2 or FC ≤ 0.5. Early-stage GCA patients exhibited a more favorable prognosis compared to those in advanced stages. HER2 overexpression was associated with a more positive outcome compared to the negative and low expression groups. Metabolite panel demonstrated a robust diagnostic performance with AUC of 0.869 in discovery set and 0.900 in validation set.

CONCLUSIONS

A total of 25 common and stable differential metabolites may hold promise as liquid non-invasive indicators for GCA diagnosis. HER2 may function as a tumor suppressor gene in GCA, as its overexpression is associated with improved survival. The downregulation of bile acid metabolism in GCA may offer valuable theoretical insights and innovative approaches for precision-targeted treatments in GCA patients.

Machine learning nominates the inositol pathway and novel genes in Parkinson's disease

There are 78 loci associated with Parkinson's disease in the most recent genome-wide association study (GWAS), yet the specific genes driving these associations are mostly unknown. Herein, we aimed to nominate the top candidate gene from each Parkinson's disease locus and identify variants and pathways potentially involved in Parkinson's disease. We trained a machine learning model to predict Parkinson's disease-associated genes from GWAS loci using genomic, transcriptomic and epigenomic data from brain tissues and dopaminergic neurons. We nominated candidate genes in each locus and identified novel pathways potentially involved in Parkinson's disease, such as the inositol phosphate biosynthetic pathway (INPP5F, IP6K2, ITPKB and PPIP5K2). Specific common coding variants in SPNS1 and MLX may be involved in Parkinson's disease, and burden tests of rare variants further support that CNIP3, LSM7, NUCKS1 and the polyol/inositol phosphate biosynthetic pathway are associated with the disease. Functional studies are needed to further analyse the involvements of these genes and pathways in Parkinson's disease.

Parkinson's disease: an update on preclinical studies of induced pluripotent stem cells

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease among adults worldwide. It is characterised by the death of dopaminergic neurons in the substantia nigra pars compacta and, in some cases, presence of intracytoplasmic inclusions of α-synuclein, called Lewy bodies, a pathognomonic sign of the disease. Clinical diagnosis of PD is based on the presence of motor alterations. The treatments currently available have no neuroprotective effect. The exact causes of PD are poorly understood. Therefore, more precise preclinical models have been developed in recent years that use induced pluripotent stem cells (iPSC). In vitro studies can provide new information on PD pathogenesis and may help to identify new therapeutic targets or to develop new drugs.

Chemical catalysis by biological amyloids

Toxic aggregation of proteins and peptides into amyloid fibers is the basis of several human diseases. In each disease, a particular peptide noncovalently assembles into long thin structures with an overall cross-β fold. Amyloids are not only related to disease: functional amyloids are found in many biological systems and artificial peptide amyloids are developed into novel nanomaterials. Amyloid fibers can act as template for the generation of more amyloids but are considered nonreactive in chemical catalysis. The perception of amyloids as chemically inert species was recently challenged by in vitro work on three human amyloid systems. With the use of model substrates, amyloid-β, α-synuclein and glucagon amyloids were found to catalyze biologically relevant chemical reactions. The detected catalytic activity was much less than that of 'real' enzymes, but like that of designed (synthetic) catalytic amyloids. I here describe the current knowledge around this new activity of natural amyloids and the putative connection to metabolic changes in amyloid diseases. These pioneering studies imply that catalytic activity is an unexplored gain-of-function activity of disease amyloids. In fact, all biological amyloids may harbor intrinsic catalytic activity, tuned by each amyloid's particular fold, that await discovery.

Amyloids of α-Synuclein Promote Chemical Transformations of Neuronal Cell Metabolites

The assembly of α-synuclein into cross-β structured amyloid fibers results in Lewy body deposits and neuronal degeneration in Parkinson's disease patients. As the cell environment is highly crowded, interactions between the formed amyloid fibers and a range of biomolecules can occur in cells. Although amyloid fibers are considered chemically inert species, recent in vitro work using model substrates has shown α-synuclein amyloids, but not monomers, to catalyze the hydrolysis of ester and phosphoester bonds. To search for putative catalytic activity of α-synuclein amyloids on biologically relevant metabolites, we here incubated α-synuclein amyloids with neuronal SH-SY5Y cell lysates devoid of proteins. LC-MS-based metabolomic (principal component and univariate) analysis unraveled distinct changes in several metabolite levels upon amyloid (but not monomer) incubation. Of 63 metabolites identified, the amounts of four increased (3-hydroxycapric acid, 2-pyrocatechuic acid, adenosine, and NAD), and the amounts of seventeen decreased (including aromatic and apolar amino acids, metabolites in the TCA cycle, keto acids) in the presence of α-synuclein amyloids. Many of these metabolite changes match what has been reported previously in Parkinson's disease patients and animal-model metabolomics studies. Chemical reactivity of α-synuclein amyloids may be a new gain-of-function that alters the metabolite composition in cells and, thereby, modulates disease progression.

Lamp1 Deficiency Enhances Sensitivity to α-Synuclein and Oxidative Stress in Drosophila Models of Parkinson Disease

Parkinson disease (PD) is a common neurodegenerative condition affecting people predominantly at old age that is characterized by a progressive loss of midbrain dopaminergic neurons and by the accumulation of α-synuclein-containing intraneuronal inclusions known as Lewy bodies. Defects in cellular degradation processes such as the autophagy-lysosomal pathway are suspected to be involved in PD progression. The mammalian Lysosomal-associated membrane proteins LAMP1 and LAMP2 are transmembrane glycoproteins localized in lysosomes and late endosomes that are involved in autophagosome/lysosome maturation and function. Here, we show that the lack of Drosophila Lamp1, the homolog of LAMP1 and LAMP2, severely increased fly susceptibility to paraquat, a pro-oxidant compound known as a potential PD inducer in humans. Moreover, the loss of Lamp1 also exacerbated the progressive locomotor defects induced by the expression of PD-associated mutant α-synuclein A30P (α-synA30P) in dopaminergic neurons. Remarkably, the ubiquitous re-expression of Lamp1 in a mutant context fully suppressed all these defects and conferred significant resistance towards both PD factors above that of wild-type flies. Immunostaining analysis showed that the brain levels of α-synA30P were unexpectedly decreased in young adult Lamp1-deficient flies expressing this protein in comparison to non-mutant controls. This suggests that Lamp1 could neutralize α-synuclein toxicity by promoting the formation of non-pathogenic aggregates in neurons. Overall, our findings reveal a novel role for Drosophila Lamp1 in protecting against oxidative stress and α-synuclein neurotoxicity in PD models, thus furthering our understanding of the function of its mammalian homologs.

Adult health and transition stage-specific rotenone-mediated Drosophila model of Parkinson’s disease: Impact on late-onset neurodegenerative disease models

Parkinson’s disease (PD) affects almost 1% of the population worldwide over the age of 50 years. Exposure to environmental toxins like paraquat and rotenone is a risk factor for sporadic PD which constitutes 95% of total cases. Herbicide rotenone has been shown to cause Parkinsonian symptoms in multiple animal models. Drosophila is an excellent model organism for studying neurodegenerative diseases (NDD) including PD. The aging process is characterized by differential expression of genes during different life stages. Hence it is necessary to develop life-stage-matched animal models for late-onset human disease(s) such as PD. Such animal models are critical for understanding the pathophysiology of age-related disease progression and important to understand if a genotropic drug/nutraceutical can be effective during late stages. With this idea, we developed an adult life stage-specific (health and transition phase, during which late-onset NDDs such as PD sets in) rotenone-mediated Drosophila model of idiopathic PD. Drosophila is susceptible to rotenone in dose-time dependent manner. Rotenone-mediated fly model of sporadic PD exhibits mobility defects (independent of mortality), inhibited mitochondrial complex I activity, dopaminergic (DAergic) neuronal dysfunction (no loss of DAergic neuronal number; however, reduction in rate-limiting enzyme tyrosine hydroxylase (TH) synthesis), and alteration in levels of dopamine (DA) and its metabolites; 3,4-Dihydroxyphenylacetic acid (DOPAC) and Homovanilic acid (HVA) in brain-specific fashion. These PD-linked behaviors and brain-specific phenotypes denote the robustness of the present fly model of PD. This novel model will be of great help to decipher life stage-specific genetic targets of small molecule mediated DAergic neuroprotection; understanding of which is critical for formulating therapeutic strategies for PD.

Phenotypic analyses, protein localization, and bacteriostatic activity of Drosophila melanogaster transferrin-1

Transferrin-1 (Tsf1) is an extracellular insect protein with a high affinity for iron. The functions of Tsf1 are still poorly understood; however, Drosophila melanogaster Tsf1 has been shown to influence iron distribution in the fly body and to protect flies against some infections. The goal of this study was to better understand the physiological functions of Tsf1 in D. melanogaster by 1) investigating Tsf1 null phenotypes, 2) determining tissue-specific localization of Tsf1, 3) measuring the concentration of Tsf1 in hemolymph, 4) testing Tsf1 for bacteriostatic activity, and 5) evaluating the effect of metal and paraquat treatments on Tsf1 abundance. Flies lacking Tsf1 had more iron than wild-type flies in specialized midgut cells that take up iron from the diet; however, the absence of Tsf1 had no effect on the iron content of whole midguts, fat body, hemolymph, or heads. Thus, as previous studies have suggested, Tsf1 appears to have a minor role in iron transport. Tsf1 was abundant in hemolymph from larvae (0.4 μM), pupae (1.4 μM), adult females (4.4 μM) and adult males (22 μM). Apo-Tsf1 at 1 μM had bacteriostatic activity whereas holo-Tsf1 did not, suggesting that Tsf1 can inhibit microbial growth by sequestering iron in hemolymph and other extracellular environments. This hypothesis was supported by detection of secreted Tsf1 in tracheae, testes and seminal vesicles. Colocalization of Tsf1 with an endosome marker in oocytes suggested that Tsf1 may provide iron to developing eggs; however, eggs from mothers lacking Tsf1 had the same amount of iron as control eggs, and they hatched at a wild-type rate. Thus, the primary function of Tsf1 uptake by oocytes may be to defend against infection rather than to provide eggs with iron. In beetles, Tsf1 plays a role in protection against oxidative stress. In contrast, we found that flies lacking Tsf1 had a typical life span and greater resistance to paraquat-induced oxidative stress. In addition, Tsf1 abundance remained unchanged in response to ingestion of iron, cadmium or paraquat or to injection of iron. These results suggest that Tsf1 has a limited role in protection against oxidative stress in D. melanogaster.

Pesticides Exposure-Induced Changes in Brain Metabolome: Implications in the Pathogenesis of Neurodegenerative Disorders

Pesticides have been used in agriculture, public health programs, and pharmaceuticals for many decades. Though pesticides primarily target pests by affecting their nervous system and causing other lethal effects, these chemical entities also exert toxic effects in inadvertently exposed humans through inhalation or ingestion. Mounting pieces of evidence from cellular, animal, and clinical studies indicate that pesticide-exposed models display metabolite alterations of pathways involved in neurodegenerative diseases. Hence, identifying common key metabolites/metabolic pathways between pesticide-induced metabolic reprogramming and neurodegenerative diseases is necessary to understand the etiology of pesticides in the rise of neurodegenerative disorders. The present review provides an overview of specific metabolic pathways, including tryptophan metabolism, glutathione metabolism, dopamine metabolism, energy metabolism, mitochondrial dysfunction, fatty acids, and lipid metabolism that are specifically altered in response to pesticides. Furthermore, we discuss how these metabolite alterations are linked to the pathogenesis of neurodegenerative diseases and to identify novel biomarkers for targeted therapeutic approaches.

Chemically induced models of Parkinson's disease

Environmental toxins are harmful substances detrimental to humans. Constant exposure to these fatal neurotoxins can cause various neurodegenerative disorders. Although poisonous, specific neurotoxins at optimal concentrations mimic the clinical features of neurodegenerative diseases in several animal models. Such chemically-induced model systems are beneficial in deciphering the molecular mechanisms of neurodegeneration and drug screening for these disorders. One such neurotoxin is 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a widely used chemical that recapitulates Parkinsonian features in various animal models. Apart from MPTP, other neurotoxins like 6-hydroxydopamine (6-OHDA), paraquat, rotenone also induce specific clinical features of Parkinson's disease in animal models. These chemically-induced Parkinson's disease models are playing a crucial role in understanding Parkinson's disease onset, pathology, and novel therapeutics. In this review, we provide a concise overview of various neurotoxins that can recapitulate Parkinsonian features in different in vivo and in vitro model systems specifically focusing on the different treatment methodologies of neurotoxins.

Metabolic Alterations in a Drosophila Model of Parkinson's Disease Based on DJ-1 Deficiency

Parkinson’s disease (PD) is the second-most common neurodegenerative disorder, whose physiopathology is still unclear. Moreover, there is an urgent need to discover new biomarkers and therapeutic targets to facilitate its diagnosis and treatment. Previous studies performed in PD models and samples from PD patients already demonstrated that metabolic alterations are associated with this disease. In this context, the aim of this study is to provide a better understanding of metabolic disturbances underlying PD pathogenesis. To achieve this goal, we used a Drosophila PD model based on inactivation of the DJ-1β gene (ortholog of human DJ-1). Metabolomic analyses were performed in 1-day-old and 15-day-old DJ-1β mutants and control flies using ¹H nuclear magnetic resonance spectroscopy, combined with expression and enzymatic activity assays of proteins implicated in altered pathways. Our results showed that the PD model flies exhibited protein metabolism alterations, a shift fromthe tricarboxylic acid cycle to glycolytic pathway to obtain ATP, together with an increase in the expression of some urea cycle enzymes. Thus, these metabolic changes could contribute to PD pathogenesis and might constitute possible therapeutic targets and/or biomarkers for this disease.

Longitudinal metabolomics profiling of serum amino acids in rotenone-induced Parkinson's mouse model

Recently, the detailed etiology and pathogenesis of Parkinson's disease (PD) have not been fully clarified yet. Increasing evidences suggested that the disturbance of peripheral branched-chain amino acids (BCAAs) metabolism can promote the occurrence and progression of neurodegenerative diseases through neuroinflammatory signaling. Although there are several studies on the metabolomics of PD, longitudinal study of metabolic pathways is still lacking. Therefore, the purpose of the present study was to determine the longitudinal alterations in serum amino acid profiles in PD mouse model. Gas chromatography-mass spectrometry (GC-MS) was applied to detect serum amino acid concentrations in C57BL/6 mice after 0, 3 and 4 weeks of oral administration with rotenone. Then the data were analysed by principal component analysis (PCA) and orthogonal projection to latent structures (OPLS) analysis. Finally, the correlations between different kinds of serum amino acids and behaviors in rotenone-treated mice were also explored. Compared with 0-week mice, the levels of L-isoleucine and L-leucine were down-regulated in 3-week and 4-week mice, especially in 4-week mice. Moreover, the comprehensive analysis showed that L-isoleucine and L-leucine were negatively correlated with pole-climbing time and positively correlated with fecal weight and water content of PD mice. These results not only suggested that L-isoleucine and L-leucine may be potential biomarkers, but also pointed out the possibility of treating PD by intervening in the circulating amino acids metabolism.

Metabolomics of neurological disorders in India

Metabolomics is the comprehensive study of the metabolome and its alterations within biological fluids and tissues. Over the years, applications of metabolomics have been explored in several areas, including personalised medicine in diseases, metabolome-wide association studies (MWAS), pharmacometabolomics and in combination with other branches of omics such as proteomics, transcriptomics and genomics. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the major analytical techniques widely employed in metabolomics. In addition, MS is coupled with chromatography techniques like gas chromatography (GC) and liquid chromatography (LC) to separate metabolites before analysis. These analytical techniques have made possible identification and quantification of large numbers of metabolites, encompassing characterization of diseases and facilitating a systematic and rational therapeutic strategy based on metabolic patterns. In recent years, the metabolomics approach has been used to obtain a deeper insight into the underlying biochemistry of neurodegenerative disorders and the discovery of biomarkers of clinical implications. The current review mainly focuses on an Indian perspective of metabolomics for the identification of metabolites and metabolic alterations serving as potential diagnostic biomarkers for neurological diseases including acute spinal cord injury, amyotrophic lateral sclerosis, tethered cord syndrome, spina bifida, stroke, Parkinson's disease, glioblastoma and neurological disorders with inborn errors of metabolism.

Evaluation of isoeugenol in inhibition of Staphylococcus aureus efflux pumps and their toxicity using Drosophila melanogaster model

The Staphylococcus aureus bacteria is a pathogen considered opportunistic and that has been acquiring resistance to several classes of antibiotics, mainly due to the synthesis of efflux pumps, which are proteins that expel these drugs intracellularly, reducing their effectiveness. The objective of this study was to evaluate the ability of isoeugenol to inhibit S. aureus efflux pumps and to determine its toxicity against a eukaryotic model (Drosophila melanogaster). IS-58, K2068 and K4414 S. aureus strains were used in the study. Isoeugenol minimum inhibitory concentration (MIC) and antibiotic modulation were evaluated in efflux pump inhibitory tests as well as in ethidium bromide (EtBr) assays. Toxicity tests against D. melanogaster assessed mortality and negative geotaxis. Isoeugenol obtained a relevant MIC result and a synergism was observed when isoeugenol was associated with the antibiotics, mainly with ciprofloxacin. Isoeugenol was able to affect all three efflux pumps tested, especially in strain K4414. The mortality of D. melanogaster caused by isoeugenol administration started after 12 h of exposure, being volume dependent and having an LC50 of 81.69 μL/L. In the negative geotaxis test, a statistical difference was observed after 24h of exposure compared to the control, demonstrating that damage to the locomotor apparatus had occurred. Based on the results, isoeugenol is a putative efflux pump inhibitor, becoming an alternative in blocking these proteins, and demonstrated acute toxicity against D. melanogaster.

A High-Throughput Chemical Screen in DJ-1β Mutant Flies Identifies Zaprinast as a Potential Parkinson's Disease Treatment

Dopamine replacement represents the standard therapy for Parkinson's disease (PD), a common, chronic, and incurable neurological disorder; however, this approach only treats the symptoms of this devastating disease. In the search for novel disease-modifying therapies that target other relevant molecular and cellular mechanisms, Drosophila has emerged as a valuable tool to study neurodegenerative diseases due to the presence of a complex central nervous system, the blood-brain barrier, and a similar neurotransmitter profile to humans. Human PD-related genes also display conservation in flies; DJ-1β is the fly ortholog of DJ-1, a gene for which mutations prompt early-onset recessive PD. Interestingly, flies mutant for DJ-1β exhibit PD-related phenotypes, including motor defects, high oxidative stress (OS) levels and metabolic alterations. To identify novel therapies for PD, we performed an in vivo high-throughput screening assay using DJ-1β mutant flies and compounds from the Prestwick® chemical library. Drugs that improved motor performance in DJ-1ß mutant flies were validated in DJ-1-deficient human neural-like cells, revealing that zaprinast displayed the most significant ability to suppress OS-induced cell death. Zaprinast inhibits phosphodiesterases and activates GPR35, an orphan G-protein-coupled receptor not previously associated with PD. We found that zaprinast exerts its beneficial effect in both fly and human PD models through several disease-modifying mechanisms, including reduced OS levels, attenuated apoptosis, increased mitochondrial viability, and enhanced glycolysis. Therefore, our results support zaprinast as a potential therapeutic for PD in future clinical trials.

Parkinson's disease: An update on preclinical studies of induced pluripotent stem cells

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease among adults worldwide. It is characterised by the death of dopaminergic neurons in the substantia nigra pars compacta and, in some cases, presence of intracytoplasmic inclusions of α-synuclein, called Lewy bodies, a pathognomonic sign of the disease. Clinical diagnosis of PD is based on the presence of motor alterations. The treatments currently available have no neuroprotective effect. The exact causes of PD are poorly understood. Therefore, more precise preclinical models have been developed in recent years that use induced pluripotent stem cells. In vitro studies can provide new information on PD pathogenesis and may help to identify new therapeutic targets or to develop new drugs.

Piperine-Coated Gold Nanoparticles Alleviate Paraquat-Induced Neurotoxicity in Drosophila melanogaster

Parkinson's disease (PD) is the most common progressive neurodegenerative disease known to impart bradykinesia leading to diverse metabolic complications. Currently, scarcity of effective drug candidates against this long-term devastating disorder poses a big therapeutic challenge. Here, we have synthesized biocompatible, polycrystalline, and uniform piperine-coated gold nanoparticles (AuNPs^piperine) to specifically target paraquat-induced metabolic complications both in Drosophila melanogaster and SH-SY5Y cells. Our experimental evidence clearly revealed that AuNPs^piperine can effectively reverse paraquat-induced lethal effects in both in vitro and in vivo model systems of PD. AuNPs^piperine were found to suppress oxidative stress and mitochondrial dysfunction, leading to inhibition of apoptotic cell death in paraquat-treated flies. AuNPs^piperine were also found to protect SH-SY5Y cells against paraquat-induced toxicity at the cellular level preferably by maintaining mitochondrial membrane potential. Both experimental and computational data point to the possible influence of AuNPs^piperine in regulating the homeostasis of parkin and p53 which may turn out to be the key factors in reducing PD symptoms. The findings of this work may facilitate the development of piperine-based nanoformulations against PD.

Circulating Metabolites as Potential Biomarkers for Neurological Disorders-Metabolites in Neurological Disorders

There are, still, limitations to predicting the occurrence and prognosis of neurological disorders. Biomarkers are molecules that can change in different conditions, a feature that makes them potential tools to improve the diagnosis of disease, establish a prognosis, and monitor treatments. Metabolites can be used as biomarkers, and are small molecules derived from the metabolic process found in different biological media, such as tissue samples, cells, or biofluids. They can be identified using various strategies, targeted or untargeted experiments, and by different techniques, such as high-performance liquid chromatography, mass spectrometry, or nuclear magnetic resonance. In this review, we aim to discuss the current knowledge about metabolites as biomarkers for neurological disorders. We will present recent developments that show the need and the feasibility of identifying such biomarkers in different neurological disorders, as well as discuss relevant research findings in the field of metabolomics that are helping to unravel the mechanisms underlying neurological disorders. Although several relevant results have been reported in metabolomic studies in patients with neurological diseases, there is still a long way to go for the clinical use of metabolites as potential biomarkers in these disorders, and more research in the field is needed.

Gut metagenomics-derived genes as potential biomarkers of Parkinson’s disease

Identification of the gut microbiome compositions associated with disease has become a research focus worldwide. Emerging evidence has revealed the presence of gut microbiota dysbiosis in Parkinson’s disease. In this study, we aimed to identify the gut microbiome associated with Parkinson’s disease and subsequently to screen and to validate potential diagnostic biomarkers of Parkinson’s disease. This case-control study investigated gut microbial genes in faeces from 40 volunteer Chinese patients with Parkinson’s disease and their healthy spouses using shotgun metagenomic sequencing. Furthermore, the identified specific gut microbial gene markers were validated with real-time PCR in an independent Chinese cohort of 78 Parkinson’s disease patients, 75 control subjects, 40 patients with multiple system atrophy and 25 patients with Alzheimer’s disease. We developed the first gut microbial gene catalogue associated with Parkinson’s disease. Twenty-five gene markers were identified that distinguished Parkinson’s disease patients from healthy control subjects, achieving an area under the receiver operating characteristic curve (AUC) of 0.896 (95% confidence interval: 83.1–96.1%). A highly accurate Parkinson’s disease index, which was not influenced by disease severity or Parkinson’s disease medications, was created. Testing these gene markers using quantitative PCR distinguished Parkinson’s disease patients from healthy controls not only in the 40 couples (AUC = 0.922, 95% confidence interval: 86.4–98.0%), but also in an independent group of 78 patients with Parkinson’s disease and 75 healthy control subjects (AUC = 0.905, 95% confidence interval: 86.0–95.1%). This classifier also performed a differential diagnosis power in discriminating these 78 patients with Parkinson’s disease from a cohort of 40 patients with multiple system atrophy and 25 patients with Alzheimer’s disease based on the panel of 25 biomarkers. Based on our results, the identified Parkinson’s disease index based on the gene set from the gut microbiome may be a potential diagnostic biomarker of Parkinson’s disease.

The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster

BACKGROUND

Genetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that attempt to map endophenotype such as the transcriptome, proteome or metabolome, that underlie complex traits. Here we used metabolomics to explore the nature of genetic variation for hydrogen peroxide (H2O2) resistance in the sequenced inbred Drosophila Genetic Reference Panel (DGRP).

RESULTS

We first studied genetic variation for H2O2 resistance in 179 DGRP lines and along with identifying the insulin signaling modulator u-shaped and several regulators of feeding behavior, we estimate that a substantial amount of phenotypic variation can be explained by a polygenic model of genetic variation. We then profiled a portion of the aqueous metabolome in subsets of eight 'high resistance' lines and eight 'low resistance' lines. We used these lines to represent collections of genotypes that were either resistant or sensitive to the stressor, effectively modeling a discrete trait. Across the range of genotypes in both populations, flies exhibited surprising consistency in their metabolomic signature of resistance. Importantly, the resistance phenotype of these flies was more easily distinguished by their metabolome profiles than by their genotypes. Furthermore, we found a metabolic response to H2O2 in sensitive, but not in resistant genotypes. Metabolomic data further implicated at least two pathways, glycogen and folate metabolism, as determinants of sensitivity to H2O2. We also discovered a confounding effect of feeding behavior on assays involving supplemented food.

CONCLUSIONS

This work suggests that the metabolome can be a point of convergence for genetic variation influencing complex traits, and can efficiently elucidate mechanisms underlying trait variation.

Modeling Neurodegenerative Disorders in Drosophila melanogaster

Drosophila melanogaster provides a powerful genetic model system in which to investigate the molecular mechanisms underlying neurodegenerative diseases. In this review, we discuss recent progress in Drosophila modeling Alzheimer's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis (ALS), Huntington's Disease, Ataxia Telangiectasia, and neurodegeneration related to mitochondrial dysfunction or traumatic brain injury. We close by discussing recent progress using Drosophila models of neural regeneration and how these are likely to provide critical insights into future treatments for neurodegenerative disorders.

A Neuron-Glial Trans-Signaling Cascade Mediates LRRK2-Induced Neurodegeneration

Pathogenic mutations in leucine-rich repeat kinase 2 (LRRK2) induce an age-dependent loss of dopaminergic (DA) neurons. We have identified Furin 1, a pro-protein convertase, as a translational target of LRRK2 in DA neurons. Transgenic knockdown of Furin1 or its substrate the bone morphogenic protein (BMP) ligand glass bottom boat (Gbb) protects against LRRK2-induced loss of DA neurons. LRRK2 enhances the accumulation of phosphorylated Mad (pMad) in the nuclei of glial cells in the vicinity of DA neurons but not in DA neurons. Consistently, exposure to paraquat enhances Furin 1 levels in DA neurons and induces BMP signaling in glia. In support of a neuron-glial signaling model, knocking down BMP pathway members only in glia, but not in neurons, can protect against paraquat toxicity. We propose that a neuron-glial BMP-signaling cascade is critical for mediating age-dependent neurodegeneration in two models of Parkinson's disease, thus opening avenues for future therapeutic interventions.

Saliva and urine metabolic profiling reveals altered amino acid and energy metabolism in male farmers exposed to pesticides in Madhya Pradesh State, India

Globally, the human population is exposed to low doses of pesticides due to its extensive use in agriculture. The chronic exposure to pesticides can lead to cancer, depression, anxiety, Parkinson's and Alzheimer's diseases etc. Here, we have made an attempt to use mass spectrometry based metabolomics to investigate the metabolic perturbations induced by the pesticides in the urine and saliva samples of farmers from the Madhya Pradesh State of India. The study was aimed to establish non-invasive matrices like urine and saliva as alternative diagnostic matrices to the occupational exposure studies. Saliva and urine samples were collected from 51 pesticides applicators and acquired metabolic profiles of urine and saliva samples using gas chromatography-mass spectrometry (GC-MS). Multivariate pattern recognition and pathway analysis were used to analyze and interpret the data. Investigation of endogenous metabolic profiles revealed remarkable discrimination in both saliva and urine samples of the exposed population strongly suggesting the changes in metabolic composition within the identified metabolites (for urine samples: accuracy 0.9766, R² = 0.9130, Q² = 0.8703; for saliva samples, an accuracy of 0.9961, R² = 0.9698, Q² = 0.9637). Thirteen metabolites of urine samples and sixteen metabolites of saliva samples were identified as differential metabolites specific to pesticide exposure. Pathway analysis of differential metabolites revealed that amino acid metabolism, energy metabolism (glycolysis and TCA cycle) and glutathione metabolism (oxidative stress) were found to affect in pesticide exposed population. The present study suggested that GC-MS based metabolomics can help to reveal the metabolic perturbations in human population after pesticides exposure.

Comparative effects of mercury chloride and methylmercury exposure on early neurodevelopment in zebrafish larvae

Mercury (Hg) is a ubiquitous environmental toxicant with important public health implications. Hg causes neurotoxicity through astrocytes, Ca2+, neurotransmitters, mitochondrial damage, elevations of reactive oxygen species and post-translational modifications. However, the similarities and differences between the neurotoxic mechanisms caused by different chemical forms of Hg remain unclear. Zebrafish embryos were exposed to methylmercury (MeHgCl) or mercury chloride (HgCl2) (0, 4, 40, 400 nM) up for 96 h. HgCl2 exposure could significantly decrease survival rate, body length and eye size, delay the hatching period, induce tail bending and reduce the locomotor activity, and these effects were aggravated in the MeHgCl group. The compounds could increase the number of apoptotic cells in the brain and downregulate the expression of Shha, Ngn1 and Nrd, which contribute to early nervous development. The underlying mechanisms were investigated by metabolomics data. Galactose metabolism, tyrosine metabolism and starch and sucrose metabolism pathways were disturbed after HgCl2 or MeHgCl exposure. In addition, the levels of three neurotransmitters including tyrosine, dopamine and tryptophan were reduced after HgCl2 or MeHgCl exposure. Oxidative stress is related to metabolite changes, such as changes in the putrescine, niacinamide and uric acid contents in the HgCl2 group, and squalene in the MeHgCl group. These data indicated that downregulation of these genes and abnormal metabolic profile and pathways contribute to the neurotoxicity of HgCl2 and MeHgCl.

Palmitate and Stearate are Increased in the Plasma in a 6-OHDA Model of Parkinson's Disease

INTRODUCTION

Parkinson's disease (PD) is the second most common neurodegenerative disorder, without any widely available curative therapy. Metabolomics is a powerful tool which can be used to identify unexpected pathway-related disease progression and pathophysiological mechanisms. In this study, metabolomics in brain, plasma and liver was investigated in an experimental PD model, to discover small molecules that are associated with dopaminergic cell loss.

METHODS

Sprague Dawley (SD) rats were injected unilaterally with 6-hydroxydopamine (6-OHDA) or saline for the vehicle control group into the medial forebrain bundle (MFB) to induce loss of dopaminergic neurons in the substantia nigra pars compacta. Plasma, midbrain and liver samples were collected for metabolic profiling. Multivariate and univariate analyses revealed metabolites that were altered in the PD group.

RESULTS

In plasma, palmitic acid (q = 3.72 × 10-2, FC = 1.81) and stearic acid (q = 3.84 × 10-2, FC = 2.15), were found to be increased in the PD group. Palmitic acid (q = 3.5 × 10-2) and stearic acid (q = 2.7 × 10-2) correlated with test scores indicative of motor dysfunction. Monopalmitin (q = 4.8 × 10-2, FC = -11.7), monostearin (q = 3.72 × 10-2, FC = -15.1) and myo-inositol (q = 3.81 × 10-2, FC = -3.32), were reduced in the midbrain. The liver did not have altered levels of these molecules.

CONCLUSION

Our results show that saturated free fatty acids, their monoglycerides and myo-inositol metabolism in the midbrain and enteric circulation are associated with 6-OHDA-induced PD pathology.

Recent advances and perspectives of metabolomics-based investigations in Parkinson's disease

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease of the central nervous system (CNS), which affects mostly older adults. In recent years, the incidence of PD has been dramatically increasing with the aging population expanding. Due to the lack of effective biomarkers, the accurate diagnosis and precise treatment of PD are currently compromised. Notably, metabolites have been considered as the most direct reflection of the physiological and pathological conditions in individuals and represent attractive candidates to provide deep insights into disease phenotypes. By profiling the metabolites in biofluids (cerebrospinal fluid, blood, urine), feces and brain tissues, metabolomics has become a powerful and promising tool to identify novel biomarkers and provide valuable insights into the etiopathogenesis of neurological diseases. In this review, we will summarize the recent advancements of major analytical platforms implemented in metabolomics studies, dedicated to the improvement and extension of metabolome coverage for in-depth biological research. Based on the current metabolomics studies in both clinical populations and experimental PD models, this review will present new findings in metabolomics biomarkers research and abnormal metabolic pathways in PD, and will discuss the correlation between metabolomic changes and clinical conditions of PD. A better understanding of the biological underpinning of PD pathogenesis might offer novel diagnostic, prognostic, and therapeutic approaches to this devastating disease.

High-dose acute exposure of paraquat induces injuries of swim bladder, gastrointestinal tract and liver via neutrophil-mediated ROS in zebrafish and their relevance for human health risk assessment

The exact toxicological mechanisms of paraquat (PQ) poisoning are not entirely clear, especially on the high-level acute exposure. To assess the health risk of PQ, especially to suicidal individuals, accidental ingestion eaters, occupational groups, and special multitude, firstly we explored the acute toxic effect and the possible mechanisms of high-level exposure of PQ using zebrafish. The mainly target organs of PQ were swim bladder which is the homolog of the mammalian lung, followed by gastrointestinal tract and liver. Morphological malformations which were further defined by histopathologic examination include smaller size, fibrosis and inflammatory cell invasion for swim bladder; irregularly arranged or dissolved epithelial folds, loss of villous architecture, and ecclasis of mucosal cells in a smaller lumen for gastrointestinal tract; as well as smaller size, degeneration, fibrous proliferation, atrophy for liver. In addition, PQ enhanced leukocyte recruitment (neutrophil migrated first, followed by macrophage) into swim bladder and induced ROS which can be scavenged by glutathione. Moreover, qRT-PCR results showed that PQ increased the expression level of genes involved in the inflammatory response, such as L-1β, IL-6, IL-8, TNF-α, TNF-β, IFN-1, TGF-β, and NF-kB. For the first time, our results demonstrated that acute exposure of PQ induced pulmonary toxicity which was followed by gastrointestinal and hepatic toxicity via neutrophil-mediated ROS in zebrafish. In summary, these findings generated here will contribute to our better understanding of characteristics of PQ acute poisoning and can provide valuable information on better PQ poisoning treatments, occupational disease prevention, and providing theoretical foundation for risk management measures.

PBPK/PD assessment for Parkinson's disease risk posed by airborne pesticide paraquat exposure

Exposure to several specific pesticides has led to an increase of Parkinson's disease (PD) risk. However, it is difficult to quantify the PD population risk related to certain pesticides in regions where environmental exposure data are scarce. Furthermore, the time trend of the prevalence and incidence of PD embedded in the background relationship between PD risk and pesticide exposures has not been well characterized. It has been convincingly identified that a key pesticide associated significantly with an increased risk trend of PD is paraquat (PQ). Here, we present a novel, probabilistic population-based exposure-response approach to quantify the contribution from PQ exposure to prevalence risk of PD. We found that the largest PQ exposure contributions occurred in its positive trend during 2004-2011, with the PQ contributing nearly 21 and 24%, respectively, to the PD prevalence rates among the age groups of 70-79 and ≥ 80 years in Taiwan. We also employed the present population risk model to predict the PQ-induced PD prevalence based on the projected rates of increase in PQ exposure associated with age-specific population. The predicted outcome can be used as an early warning signal for public health authorities. We suggest that a mechanistic understanding of the contribution of a specific pesticide exposure to PD risk trends is crucial to enhance our insights into the perspective on the impacts of environmental exposure on the neurodegenerative diseases.

Metabolomics: State-of-the-Art Technologies and Applications on Drosophila melanogaster

Metabolomics is one of the latest "omics" technology concerned with the high-throughput identification and quantification of metabolites, the final products of cellular processes. The revealed data provide an instantaneous snapshot of an organism's metabolic pathways, which can be used to explain its phenotype or physiology. On the other hand, Drosophila has shown its power in studying metabolism and related diseases. At this stage, we have the state-of-the-art knowledge in place: a potential candidate to study cellular metabolism (Drosophila melanogaster) and a powerful methodology for metabolic network decipherer (metabolomics). Yet missing is advanced metabolomics technologies like isotope-assisted metabolomics optimized for Drosophila. In this chapter, we will discuss on the current status and future perspectives in technologies and applications of Drosophila metabolomics.

Parkinson's Disease Model

Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide. It is known that there are many factors, either genetic or environmental factors, involved in PD, but the mechanism of PD is still not fully understood. Several animal models have been established to study the mechanisms of PD. Among these models, Drosophila melanogaster has been utilized as a valuable model to get insight into important features of PD. Drosophila melanogaster possesses a well-developed dopaminergic (DA) neuron system which is known to play an important role in PD pathogenesis. The well understanding of DA neurons from early larval through adult stage makes Drosophila as a powerful model for investigating the progressive neurodegeneration in PD. Besides, the short life cycle of Drosophila melanogaster serves an advantage in studying epidemiological features of PD. Most of PD symptoms can be mimicked in Drosophila model such as progressive impairment in locomotion, DA neuron degeneration, and some other non-motor symptoms. The Drosophila models of PD, therefore, show a great potential in application for PD genetic and drug screening.

Modulation of sestrin confers protection to Cr(VI) induced neuronal cell death in Drosophila melanogaster

Increased oxidative stress is one of the major causes of hexavalent chromium [Cr(VI)], a heavy metal with diverse applications and environmental presence, induced neuronal adversities in exposed organism including Drosophila. Sestrin (sesn), an oxidative stress responsive gene, emerges as a novel player in the management of oxidative stress response. It is reported to be regulated by Target of rapamycin (TOR) and the former regulates autophagy and plays an important role in the prevention of neurodegeneration. Due to limited information regarding the role of sesn in chemical induced cellular adversities, it was hypothesized that modulation of sesn may improve the Cr(VI) induced neuronal adversities in Drosophila. Upon exposure of Cr(VI) (5.0-20.0 μg/ml) to D. melanogaster larvae (w¹¹¹⁸; background control), neuronal cell death was observed at 20.0 μg/ml of Cr(VI) concentration which was found to be reversed by targeted sesn overexpression (Elav-GAL4>UAS-sesn) in those cells of exposed organism by the induction of autophagy concomitant with decreased reactive oxygen species (ROS) level, p-Foxo-, p-JNK- and p-Akt-levels with decreased apoptosis. Conversely, after sesn knockdown (Elav-GAL4>UAS-sesn^RNAi) in neuronal cells, they become more vulnerable to oxidative stress and apoptosis. Furthermore, knockdown of sesn in neuronal cells of exposed organism resulted in decreased autophagy with increased TOR and p-S6k levels while overexpression of sesn led to their decreased levels suggestive of decreased anabolic and increased catabolic activity in neuronal cells shifting energy towards the augmentation of cellular repair. Taken together, the study suggests therapeutic implications of sesn against chemical induced neuronal adversities in an organism.

Biomarker Research in Parkinson's Disease Using Metabolite Profiling

Biomarker research in Parkinson's disease (PD) has long been dominated by measuring dopamine metabolites or alpha-synuclein in cerebrospinal fluid. However, these markers do not allow early detection, precise prognosis or monitoring of disease progression. Moreover, PD is now considered a multifactorial disease, which requires a more precise diagnosis and personalized medication to obtain optimal outcome. In recent years, advanced metabolite profiling of body fluids like serum/plasma, CSF or urine, known as "metabolomics", has become a powerful and promising tool to identify novel biomarkers or "metabolic fingerprints" characteristic for PD at various stages of disease. In this review, we discuss metabolite profiling in clinical and experimental PD. We briefly review the use of different analytical platforms and methodologies and discuss the obtained results, the involved metabolic pathways, the potential as a biomarker and the significance of understanding the pathophysiology of PD. Many of the studies report alterations in alanine, branched-chain amino acids and fatty acid metabolism, all pointing to mitochondrial dysfunction in PD. Aromatic amino acids (phenylalanine, tyrosine, tryptophan) and purine metabolism (uric acid) are also altered in most metabolite profiling studies in PD.

Metabolomic Studies in Drosophila

Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila, often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research.

Minocycline protects, rescues and prevents knockdown transgenic parkin Drosophila against paraquat/iron toxicity: Implications for autosomic recessive juvenile parkinsonism

Autosomal recessive Juvenile Parkinsonism (AR-JP) is a chronic, progressive neurodegenerative disorder caused by mutation in the PARKIN gene, and invariably associated with dopaminergic (DAergic) neuronal loss and brain iron accumulation. Since current medical therapy is symptomatic and lacks significant disease-modifying effects, other treatment approaches are urgently needed it. In the present work, we investigate the role of minocycline (MC) in paraquat (PQ)/iron-induced neurotoxicity in the Drosophila TH>parkin-RNAi/+ (w[*]; UAS-parkin-RNAi; TH-GAL4) fly and have shown the following: (i) MC increased life span and restored the locomotor activity of knockdown (KD) transgenic parkin flies in comparison with the control (vehicle) group; (ii) MC at low (0.1 and 0.3mM) and middle (0.5mM) concentrations protected, rescued and prevented KD parkin Drosophila against PQ toxicity. However, MC at high (1mM) concentration aggravated the toxic effect of PQ; (iii) MC protected and rescued DAergic neurons against the PQ toxic effect according to tyrosine hydroxylase (TH)>green-fluorescent protein (GFP) reporter protein microscopy and anti-TH Western blotting analysis; (iv) MC protected DAergic neurons against PQ/iron toxicity; (v) MC significantly abridged lipid peroxidation (LPO) in the protection, rescue and prevention treatment in TH>parkin-RNAi/+ flies against PQ or iron alone or combined (PQ/iron)-induced neuronal oxidative stress (OS). Our results suggest that MC exerts neuroprotection against PQ/iron-induced OS in DAergic neurons most probably by the scavenging activity of reactive oxygen species (ROS), and by chelating iron. Therefore, MC might be a potential therapeutic drug to delay, revert, or prevent AR-JP.