Integrative Chemical Proteomics-Metabolomics Approach Reveals Acaca/Acacb as Direct Molecular Targets of PFOA

Advances in Integrated Multi-omics Analysis for Drug-Target Identification

As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.

Species Difference? Bovine, Trout, and Human Plasma Protein Binding of Per- and Polyfluoroalkyl Substances

Per- and polyfluoroalkyl substances (PFAS) strongly bind to proteins and lipids in blood, which govern their accumulation and distribution in organisms. Understanding the plasma binding mechanism and species differences will facilitate the quantitative in vitro-to-in vivo extrapolation and improve risk assessment of PFAS. We studied the binding mechanism of 16 PFAS to bovine serum albumin (BSA), trout, and human plasma using solid-phase microextraction. Binding of anionic PFAS to BSA and human plasma was found to be highly concentration-dependent, while trout plasma binding was linear for the majority of the tested PFAS. At a molar ratio of PFAS to protein ν < 0.1 molPFAS/molprotein, the specific protein binding of anionic PFAS dominated their human plasma binding. This would be the scenario for physiological conditions (ν < 0.01), whereas in in vitro assays, PFAS are often dosed in excess (ν > 1) and nonspecific binding becomes dominant. BSA was shown to serve as a good surrogate for human plasma. As trout plasma contains more lipids, the nonspecific binding to lipids affected the affinities of PFAS for trout plasma. Mass balance models that are parameterized with the protein-water and lipid-water partitioning constants (chemical characteristics), as well as the protein and lipid contents of the plasma (species characteristics), were successfully used to predict the binding to human and trout plasma.

Integrative chemoproteomics reveals anticancer mechanisms of silver(i) targeting the proteasome regulatory complex

Silver compounds have favorable properties as promising anticancer drug candidates, such as low side effects, anti-inflammatory properties, and high potential to overcome drug resistance. However, the exact mechanism by which Ag(i) confers anticancer activity remains unclear, which hinders further development of anticancer applications of silver compounds. Here, we combine thermal proteome profiling, cysteine profiling, and ubiquitome profiling to study the molecular mechanisms of silver(i) complexes supported by non-toxic thiourea (TU) ligands. Through the formation of AgTU complexes, TU ligands deliver Ag+ ions to cancer cells and tumour xenografts to elicit inhibitory potency. Our chemical proteomics studies show that AgTU acts on the ubiquitin-proteasome system (UPS) and disrupts protein homeostasis, which has been identified as a main anticancer mechanism. Specifically, Ag+ ions are released from AgTU in the cellular environment, directly target the 19S proteasome regulatory complex, and may oxidize its cysteine residues, thereby inhibiting proteasomal activity and accumulating ubiquitinated proteins. After AgTU treatment, proteasome subunits are massively ubiquitinated and aberrantly aggregated, leading to impaired protein homeostasis and paraptotic death of cancer cells. This work reveals the unique anticancer mechanism of Ag(i) targeting the 19S proteasome regulatory complex and opens up new avenues for optimizing silver-based anticancer efficacy.

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.

In utero exposures to perfluoroalkyl substances and the human fetal liver metabolome in Scotland: a cross-sectional study

BACKGROUND

Perfluoroalkyl and polyfluoroalkyl substances are classed as endocrine disrupting compounds but continue to be used in many products such as firefighting foams, flame retardants, utensil coatings, and waterproofing of food packaging. Perfluoroalkyl exposure aberrantly modulates lipid, metabolite, and bile acid levels, increasing susceptibility to onset and severity of metabolic diseases, such as diabetes and metabolic dysfunction-associated steatotic liver disease. To date, most studies in humans have focused on perfluoroalkyl-exposure effects in adults. In this study we aimed to show if perfluoroalkyls are present in the human fetal liver and if they have metabolic consequences for the human fetus.

METHODS

In this cross-sectional study, human fetal livers from elective termination of pregnancies at the Aberdeen Pregnancy Counselling Service, Aberdeen, UK, were analysed by both targeted (bile acids and perfluoroalkyl substances) and combined targeted and untargeted (lipids and polar metabolites) mass spectrometry based metabolomic analyses, as well as with RNA-Seq. Only fetuses from normally progressing pregnancies (determined at ultrasound scan before termination), terminated for non-medical reasons, from women older than 16 years, fluent in English, and between 11 and 21 weeks of gestation were collected. Women exhibiting considerable emotional distress or whose fetuses had anomalies identified at ultrasound scan were excluded. Stringent bioinformatic and statistical methods such as partial correlation network analysis, linear regression, and pathway analysis were applied to this data to investigate the association of perfluoroalkyl exposure with hepatic metabolic pathways.

FINDINGS

Fetuses included in this study were collected between Dec 2, 2004, and Oct 27, 2014. 78 fetuses were included in the study: all 78 fetuses were included in the metabolomics analysis (40 female and 38 male) and 57 fetuses were included in the RNA-Seq analysis (28 female and 29 male). Metabolites associated with perfluoroalkyl were identified in the fetal liver and these varied with gestational age. Conjugated bile acids were markedly positively associated with fetal age. 23 amino acids, fatty acids, and sugar derivatives in fetal livers were inversely associated with perfluoroalkyl exposure, and the bile acid glycolithocholic acid was markedly positively associated with all quantified perfluoroalkyl. Furthermore, 7α-hydroxy-4-cholesten-3-one, a marker of bile acid synthesis rate, was strongly positively associated with perfluoroalkyl levels and was detectable as early as gestational week 12.

INTERPRETATION

Our study shows direct evidence for the in utero effects of perfluoroalkyl exposure on specific key hepatic products. Our results provide evidence that perfluoroalkyl exposure, with potential future consequences, manifests in the human fetus as early as the first trimester of gestation. Furthermore, the profiles of metabolic changes resemble those observed in perinatal perfluoroalkyl exposures. Such exposures are already linked with susceptibility, initiation, progression, and exacerbation of a wide range of metabolic diseases.

FUNDING

UK Medical Research Council, Horizon Europe Program of the European Union, Seventh Framework Programme of the European Union, NHS Grampian Endowments grants, European Partnership for the Assessment of Risks from Chemicals, Swedish Research Council, Formas, Novo Nordisk Foundation, and the Academy of Finland.

Applications of multi-omics analysis in human diseases

Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi-omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi-omics. This review outlines the existing technical categories of multi-omics, cautions for experimental design, focuses on the integrated analysis methods of multi-omics, especially the approach of machine learning and deep learning in multi-omics data integration and the corresponding tools, and the application of multi-omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open-source analysis tools and databases, and finally, discusses the challenges and future directions of multi-omics integration and application in precision medicine. With the development of high-throughput technologies and data integration algorithms, as important directions of multi-omics for future disease research, single-cell multi-omics and spatial multi-omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi-omics medical research.

Plasma levels of per- and polyfluoroalkyl substances (PFAS) are associated with altered levels of proteins previously linked to inflammation, metabolism and cardiovascular disease

BACKGROUND

Per- and polyfluoroalkyl substances (PFAS) have been linked to immunotoxic and cardiometabolic effects in both experimental and epidemiological studies, but with conflicting results.

AIM

The aim of the present study was to investigate potential associations between plasma PFAS levels and plasma levels of preselected proteomic biomarkers previously linked to inflammation, metabolism and cardiovascular disease.

METHODS

Three PFAS (perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorohexane sulfonic acid (PFHxS)) were measured by non-targeted metabolomics and 249 proteomic biomarkers were measured by the proximity extension assay (PEA) in plasma from 2,342 individuals within the Epidemiology for Health (EpiHealth) study from Sweden (45-75 years old, 50.6 % men).

RESULTS

After adjustment for age and sex, 92% of the significant associations between PFOS concentrations and proteins were inverse (p < 0.0002, Bonferroni-adjusted). The results were not as clear for PFOA and PFHxS, but still with 80% and 64 % of the significant associations with proteins being inverse. After adjustment for age, sex, smoking, education, exercise habits and alcohol consumption, levels of epidermal growth factor receptor (EGFR), and paraoxonase type 3 (PON3) remained positively associated with all three PFAS, while resistin (RETN) and urokinase plasminogen activator surface receptor (uPAR) showed inverse associations with all three PFAS.

CONCLUSIONS

Our findings imply that PFAS exposure is cross-sectionally linked to altered levels of proteins previously linked to inflammation, metabolism and cardiovascular disease in middle-aged humans.

Profiling protein targets of cellular toxicant exposure

Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically susceptible to damage from individual types of exposure. Amino acid content is not completely predictive of protein susceptibility, as secondary, tertiary, and quaternary structures of proteins strongly influence the reactivity of the proteome to individual exposures. Because we cannot readily predict which proteins will be affected by which chemical exposures, mass spectrometry-based proteomic strategies are necessary to determine the protein targets of environmental toxins and toxicants. This review describes the mechanisms by which environmental exposure to toxins and toxicants can damage proteins and affect their function, and emerging omic methodologies that can be used to identify the protein targets of a given agent. These methods include target identification strategies that have recently revolutionized the drug discovery field, such as activity-based protein profiling, protein footprinting, and protein stability profiling technologies. In particular, we highlight the necessity of multiple, complementary approaches to fully interrogate how protein integrity is challenged by individual exposures.

A review of omics-based PFAS exposure studies reveals common biochemical response pathways

Per and Polyfluoroalkyl Substances (PFAS) are a diverse group of man-made chemicals with a range of industrial applications and which are widespread in the environment. They are structurally diverse but comprise a common chemical feature of at least one (though usually more) perfluorocarbon moiety (-C_nF_2n-) attached to a functional group such as a carboxylic or sulphonic acid. The strength of the Carbon-Fluorine bond means the compounds do not break down easily and can thus bioaccumulate. PFAS are of high concern to regulators and the public due to their potential toxicity and high persistence. At high exposure levels, PFAS have been implicated in a range of harmful effects on human and environmental health, particularly problems in/with development, cholesterol and endocrine disruption, immune system function, and oncogenesis. However, most environmental toxicology studies use far higher levels of PFAS than are generally found in the environment. Additionally, since the type of exposure, the PFAS used, and the organisms tested all vary between studies, so do the results. Traditional ecotoxicology studies may thus not identify PFAS effects at environmentally relevant exposures. Here we conduct a review of omics-based PFAS exposure studies using laboratory ecotoxicological methodologies and environmentally relevant exposure levels and show that common biochemical response pathways are identified in multiple studies. A major pathway identified was the pentose phosphate shunt pathway. Such molecular markers of sublethal PFAS exposure will greatly benefit accurate and effective risk assessments to ensure that new PFAS regulations can consider the full effects of PFAS exposure on environmental and human health receptors.

Polystyrene microplastics increase Pb bioaccumulation and health damage in the Chinese mitten crab Eriocheir sinensis

Microplastics may be potential vectors for environmental contaminants such as heavy metals in the aquatic ecosystem due to their highly hydrophobic surfaces and fugacity property. To investigate the combined effects of microplastics with Pb, we exposed juvenile Chinese mitten crabs Eriocheir sinensis to different Pb concentrations (0, 5 and 50 μg/L) combined with microplastics (0 and 400 μg/L) for 21 days to determine the Pb bioaccumulation, oxidative stress, lipid anabolism, and histopathology of hepatopancreas. In general, the results showed that compared to single Pb exposure, the combination of MPs and Pb significantly increased the bioaccumulation of Pb, activities/content of antioxidant biomarkers and lipid metabolism enzymes, and liver injury parameters in crabs, indicating MPs are potential vector of heavy metals and co-exposure exerts more severe effects on crabs. This study provides the insights into the oxidative defense and preliminary lipid anabolism of economic crustaceans in response to combined stress of Pb and MPs.

Molecular Gatekeeper Discovery: Workflow for Linking Multiple Exposure Biomarkers to Metabolomics

The exposome reflects multiple exposures across the life-course that can affect health. Metabolomics can reveal the underlying molecular basis linking exposures to health conditions. Here, we explore the concept and general data analysis framework of "molecular gatekeepers"─key metabolites that link single or multiple exposure biomarkers with correlated clusters of endogenous metabolites─to inform health-relevant biological targets. We performed untargeted metabolomics on plasma from 152 adolescent girls participating in the Growing Up Healthy Study in New York City. We then performed network analysis to link metabolites to exposure biomarkers including five trace elements (Cd, Mn, Pb, Se, and Hg) and five perfluorinated chemicals (PFCs; n-PFOS, Sm-PFOS, n-PFOA, PFHxS, and PFNA). We found 144 molecular gatekeepers and annotated 22 of them. Lysophosphatidylcholine (16:0) and taurodeoxycholate were correlated with both n-PFOA and n-PFOS, suggesting a shared dysregulation from multiple xenobiotic exposures. Sphingomyelin (d18:2/14:0) was significantly associated with age at menarche; yet, no direct association was detected between any exposure biomarkers and age at menarche. Thus, molecular gatekeepers can also discover molecular linkages between exposure biomarkers and health outcomes that may otherwise be obscured by complex interactions in direct measurements.

Environmental estrogens in surface water and their interaction with microalgae: A review

Environmental estrogens (EEs) have received extensive attention because they interfere with biological endocrine and reproduction systems by mimicking, antagonizing, or otherwise affecting the actions of endogenous hormones. Additionally, harmful algal blooms have become a global problem in surface water. Microalgae, as an essential primary producer, is especially important for aquatic life and the entire ecosystem. The presence of EEs in surface water may be a potential promoting factor for algal blooms, and microalgae may have effects on the degradation of EEs. This review focuses on the distribution and pollution characteristics of EEs in global surface waters, effects of single and mixed EEs on microalgae regarding growth and toxin production, mechanisms of EEs on microalgae at the cellular and molecular level. The impacts of microalgae on EEs were also discussed. This review provides a risk assessment of EEs and identifies essential clues that will aid in formulating and revising the relevant standards of surface water regarding EEs, which is significant for ecosystems and human health.

Novel perspectives of environmental proteomics

The connection among genome expression, proteome alteration, metabolism regulation and phenotype change under environmental stresses is very vague. It is a tough task for the traditional research approaches to reveal the related scientific mechanisms of the above connection at molecular and systematic levels. Proteomics approach is an insightful tool for revealing the biological functions, metabolic networks and functional protein interaction networks of cells and organisms under stresses at the systematic level. The purpose of this review is to provide an insightful guideline on how to set up a proteomic investigation for revealing biomolecule mechanisms, protein biomarkers and metabolism networks related to stress response, pollutant recognition, transport and biodegradation, and providing an insightful high-throughput approach for screening functional enzymes and effective microbes based on bioinformatics and functional verification method. Furthermore, the toxicity evaluation of pollutants and byproducts by proteomics approaches provides a scientific insight for early diagnosis of ecological risk and determination of the effectiveness of pollutant treatment techniques.

Chemoproteomic Approach toward Probing the Interactomes of Perfluoroalkyl Substances

Poly- and perfluoroalkyl substances (PFASs) are widely used in industrial products and consumer goods. Due to their extremely recalcitrant nature and potential bioaccumulation and toxicity, exposure to PFASs may result in adverse health outcomes in humans and wildlife. In this study, we developed a chemoproteomic strategy, based on the use of isotope-coded desthiobiotin-perfluorooctanephosphonic acid (PFOPA) probe and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis, to profile PFAS-binding proteins. Targeted proteins were labeled with the desthiobiotin-PFOPA probe, digested with trypsin, and the ensuing desthiobiotin-conjugated peptides were enriched with streptavidin beads for LC-MS/MS analysis. We were able to identify 469 putative PFOPA-binding proteins. By conducting competitive binding experiments using low (10 μM) and high (100 μM) concentrations of stable isotope-labeled PFOPA probes, we further identified 128 nonredundant peptides derived from 75 unique proteins that exhibit selective binding toward PFOPA. Additionally, we demonstrated that one of these proteins, fatty acid-binding protein 5 (FABP5), could interact directly with PFASs, including perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorohexanesulfonic acid (PFHxS), and perfluorobutanesulfonic acid (PFBS). Furthermore, desthiobiotin-labeled lysine residues are located close to the fatty acid-binding pocket of FABP5, and the binding affinity varies with the structures of PFASs. Taken together, we developed a novel chemoproteomic method for interrogating the PFAS-interacting proteome. The identification of these proteins sets the stage for understanding the mechanisms through which exposure to PFASs confers adverse human health effects.

Application of omics- and multi-omics-based techniques for natural product target discovery

Natural products continue to be an unparalleled source of pharmacologically active lead compounds because of their unprecedented structures and unique biological activities. Natural product target discovery is a vital component of natural product-based medicine translation and development and is required to understand and potentially reduce mechanisms that may be associated with off-target side effects and toxicity. Omics-based techniques, including genomics, transcriptomics, proteomics, metabolomics, and bioinformatics, have become recognized as effective tools needed to construct innovative strategies to discover natural product targets. Although considerable progress has been made, the successful discovery of natural product targets remains a challenging time-consuming process that has come to increasingly rely on the effective integration of multi-omics-based technologies to create emerging panomics (a.k.a., integrative omics, pan-omics, multiomics)-based strategies. This review summarizes a series of successful studies regarding the application of integrative omics-based methods in natural product target discovery. The advantages and disadvantages of each technique are discussed, with a particular focus on the systematic integration of multi-omics strategies. Further, emerging micro-scale single-cell-based techniques are introduced, especially to deal with minute natural product samples.

Effects of maternal exposure to PFOA on testes of male offspring mice

This study was conducted to explore the effects of maternal exposure to perfluorooctanoic acid (PFOA) on testicular development of male offspring mice. 20 pregnant Kunming mice were randomly divided into control group and PFOA exposure group with 10 mice of each. In PFOA exposure group, pregnant mice were given 5 mg/kg BW PFOA daily by gavage during gestation. Male offspring mice were killed to separate serum and collect testis at postpartum day 21, then tested the experimental indicators. The results showed that compared with control group, the content of PFOA in the serum of PFOA-exposed mice increased significantly and testosterone content is significantly reduced. Histological observations revealed architectural damages in testis in PFOA exposed groups and the apoptosis was increased. Transcriptome sequencing results showed that the U4/U6 snRNA coding genes snu13 and prp19 complex coding genes HSP73 were up-regulated and the U5 snRNA coding genes Brr2, Prp8 and EJC/TREX coding THOC genes were down-regulated after PFOA exposure Real-time PCR confirmed this result. These results indicate that the exposure of pregnant mice to perfluorooctanoic acid will have a damaging effect on the development of testes in male offspring mice, which may be due to blocked activation of the shear body, changes in structural functions, and inability to perform shear functions.

Comparative toxicometabolomics of perfluorooctanoic acid (PFOA) and next-generation perfluoroalkyl substances

Owing to environmental health concerns, a number of per- and polyfluoroalkyl substances (PFAS) have been phased-out, and increasingly replaced by various chemical analogs. Most prominent among these replacements are numerous perfluoroether carboxylic acids (PFECA). Toxicity, and environmental health concerns associated with these next-generation PFAS, however, remains largely unstudied. The zebrafish embryo was employed, in the present study, as a toxicological model system to investigate toxicity of a representative sample of PFECA, alongside perfluorooctanoic acid (PFOA) as one of the most widely used, and best studied, of the "legacy" PFAS. In addition, high-resolution magic angle spin (HRMAS) NMR was utilized for metabolic profiling of intact zebrafish embryos in order to characterize metabolic pathways associated with toxicity of PFAS. Acute embryotoxicity (i.e., lethality), along with impaired development, and variable effects on locomotory behavior, were observed for all PFAS in the zebrafish model. Median lethal concentration (LC₅₀) was significantly correlated with alkyl chain-length, and toxic concentrations were quantitatively similar to those reported previously for PFAS. Metabolic profiling of zebrafish embryos exposed to selected PFAS, specifically including PFOA and two representative PFECA (i.e., GenX and PFO3TDA), enabled elaboration of an integrated model of the metabolic pathways associated with toxicity of these representative PFAS. Alterations of metabolic profiles suggested targeting of hepatocytes (i.e., hepatotoxicity), as well as apparent modulation of neural metabolites, and moreover, were consistent with a previously proposed role of mitochondrial disruption and peroxisome proliferator-activated receptor (PPAR) activation as reflected by dysfunctions of carbohydrate, lipid and amino acid metabolism, and consistent with a previously proposed contribution of PFAS to metabolic syndrome. Taken together, it was generally concluded that toxicity of PFECA is quantitatively and qualitatively similar to PFOA, and these analogs, likewise, represent potential concerns as environmental toxicants.

Quantitative Profiling of Protein-Derived Electrophilic Cofactors in Bacterial Cells with a Hydrazine-Derived Probe

Post-translational modification of proteins can form electrophilic cofactors that serve as a catalytic center. The derived electrophilic cofactors greatly expand protein activities and functions. However, there are few studies concerning how to profile the electrophiles in bacteria. Herein, we utilized a clickable probe called propargyl hydrazine to profile the protein-derived electrophilic cofactors in Escherichia coli (E. coli) cells. Since the cofactors are mostly carbonyl groups, the hydrazine-based probe can specifically react with the cofactors to form a Schiff base. The labeled proteins were then pulled down for mass spectrometry (MS) analysis. Fourteen proteins were shown to undergo enrichment by the probe and competitive binding by its analogue, propyl hydrazine. The identified proteins were further analyzed with targeted proteomics based on parallel reaction monitoring (PRM). Using this strategy, we obtained a global portrait of protein electrophiles in bacterial cells, among which the proteins of speD and panD were previously reported to derive pyruvoyl group as an electrophilic center while lpp can retain N-terminal formyl methionine. This quantitative chemical proteomics strategy can be used to find out protein electrophiles in bacteria and holds great potential to further characterize the protein functions.

Seminal plasma metabolites mediate the associations of multiple environmental pollutants with semen quality in Chinese men

Environmental exposure to arsenic, phthalate esters (PAEs) and perfluorinated compounds (PFCs) has been associated with human semen quality. However, the epidemiological "black-box" of these associations remains poorly uncovered. In this study, based on the association analysis between arsenic, PAE and PFC exposure and semen quality parameters (i.e., semen volume, sperm concentration, sperm count, progressive motility, total motility and normal morphology) in a Chinese male population, we explored the seminal plasma metabolic signatures that may mediate the exposure-outcome relations by using the meet-in-metabolite-analysis (MIMA) approach. As a result, a negative association was found between DMA and sperm concentration, whereas MEHP and PFHxS were positively associated with sperm count and concentration, respectively. Metabolomics analysis revealed that sixteen and twenty-two seminal plasma metabolites were related to sperm concentration and count, respectively, and they are mainly involved in fatty acid, lipid and amino acid metabolism. Moreover, it was further indicated that eicosatetraenoate, carnitines and DHA may impact the inverse association between DMA and sperm concentration, while eicosatetraenoate, carnitines, DHA, PGB2 and tocotrienol are possible mediators of the positive association between PFHxS and sperm concentration. As these metabolic biomarkers are relevant to antioxidation and fatty acid β-oxidation, we suggest that redox balance and energy generation shifts in seminal plasma are involved in the association of human semen quality with environmental DMA and PFHxS exposure.

Evaluating the performance of sample preparation methods for ultra-performance liquid chromatography/mass spectrometry based serum metabonomics

RATIONALE

Metabonomics investigating perturbation to endogenous metabolism in response to external stimuli is emerging as a powerful tool for clinical diagnosis as well as in many other areas. The ability to retrieve reliable and reproducible information from complex biological fluids such as serum is crucial for its further applications.

METHODS

In this study, the performance of the commonly used sample preparation methods for ultra-performance liquid chromatography/mass spectrometry (UPLC/MS)-based metabonomics was investigated. Specifically, we compared the extraction efficiencies, the method reproducibility, and the ability to identify potential biomarkers using solvent-based protein precipitation and solid-phase extraction (SPE) for serum metabonomic studies. Differences between extraction methods were explored using principal component analysis (PCA) and orthogonal partial least squares-discrimination analysis (OPLS-DA).

RESULTS

Among the sample preparation methods tested, solvent-based protein precipitation using methanol has demonstrated the best analytical precision and extraction efficiency. Furthermore, this study revealed, for the first time, gender-specific differences in levels of two lysophosphatidylcholines (lysoPC 18:0 and lysoPC 18:1) in rat serum samples.

CONCLUSIONS

The performance of sample preparation methods for UPLC/MS-based serum metabonomics was evaluated systematically. Results showed sample preparation by solvent precipitation using methanol provided the best analytical precision and extraction efficiency for UPLC/MS-based serum metabonomics.

Interactions between Microcystis aeruginosa and coexisting bisphenol A at different phosphorus levels

Microcystis aeruginosa is known as the main contributor to cyanobacterial bloom, which is prevalent globally and degrades freshwater systems worldwide. The argument that the introduction of anthropogenic contaminants in fresh water stimulates cyanobacterial growth and microcystin production has attracted widespread attention. Bisphenol A (BPA), one of the most abundant endocrine-disrupting compounds, is often detected in various water bodies due to its notably high annual levels of production and use. Research on the combined effects of endocrine-disrupting compounds and environmental factors on cyanobacteria remains limited. To investigate the mechanism of interactions between contaminants and cyanobacteria at the cellular and proteomic levels, the growth rate, chlorophyll-a content, photosynthetic activities, microcystin-LR (MC-LR) production and release, reactive oxygen species (ROS) content, superoxide dismutase (SOD) activities, malondialdehyde (MDA) content, and proteome expression of M. aeruginosa under 1 μM BPA stress at a standard phosphorus level were investigated. The results showed that stress responses to BPA included increases in the growth rate, chlorophyll-a content, and Fv/Fm and rETRmax values under the low phosphorus condition. Responses involving ROS, SOD, and MDA indicated that phosphorus sufficiency and BPA caused oxidative stress in M. aeruginosa. Moreover, phosphorus sufficiency and BPA stimulated the production and release of MCs. Compared to levels in the non-BPA-treated group, exposure of M. aeruginosa to BPA caused 72 up-regulated proteins, which were primarily associated with photosynthesis, ribosome, fatty acid biosynthesis, glycolysis/glyconeogenesis, and carbon fixation in photosynthetic organisms. The 105 down-regulated proteins were related to quorum sensing, base excision repair, ABC transporters, longevity regulating and cell cycle-caulobacter, suggesting that the cytotoxicity of cyanobacterial cells induced by BPA was significantly increased. These findings provide insights into the molecular mechanism of the effects of BPA and phosphorus on M. aeruginosa, suggesting that coexisting pollutants may cause greater harm to and health risks in the environment.