Simultaneous Detection of 3-Nitrotyrosine and 3-Nitro-4-hydroxyphenylacetic Acid in Human Urine by Online SPE LC-MS/MS and Their Association with Oxidative and Methylated DNA Lesions

Microbiota in a long survival discourse with the human host

The relationship between human health and gut microbiota is becoming more apparent. It is now widely believed that healthy gut flora plays a vital role in the overall well-being of the individual. There are spatial and temporal variations in the distribution of microbes from the esophagus to the rectum throughout an individual's lifetime. Through the development of genome sequencing technologies, scientists have been able to study the interactions between different microorganisms and their hosts to improve the health and disease of individuals. The normal gut microbiota provides various functions to the host, whereas the host, in turn, provides nutrients and promotes the development of healthy and resilient microbiota communities. Thus, the microbiota provides and maintains the gut's structural integrity and protects the gut against pathogens. The development of the normal gut microbiota is influenced by various factors. Some of these include the mode of delivery, diet, and antibiotics. In addition, the environment can also affect the development of the gut microbiota. For example, one of the main concerns of antibiotic use is the alteration of the gut microbiota, which could lead to the development of multidrug-resistant organisms. When microbes are disturbed, it can potentially lead to various diseases. Depending on the species' ability to adapt to the human body's environment, the fate of the microbes in the host and their relationship with the human body are decided. This review aims to provide a comprehensive analysis of microbe, microbes-host immune interactions, and factors that can disturb their interactions.

Ribonucleotide reductase: Implications of thiol S-nitrosylation and tyrosine nitration for different subunits

Ribonucleotide reductase (RNR) is a multi-subunit enzyme responsible for catalyzing the rate-limiting step in the production of deoxyribonucleotides essential for DNA synthesis and repair. The active RNR complex is composed of multimeric R1 and R2 subunits. The RNR catalysis involves the formation of tyrosyl radicals in R2 subunits and thiyl radicals in R1 subunits. Despite the quaternary structure and cofactor diversity, all the three classes of RNR have a conserved cysteine residue at the active site which is converted into a thiyl radical that initiates the substrate turnover, suggesting that the catalytic mechanism is somewhat similar for all three classes of the RNR enzyme. Increased RNR activity has been associated with malignant transformation, cancer cell growth, and tumorigenesis. Efforts concerning the understanding of RNR inhibition in designing potent RNR inhibitors/drugs as well as developing novel approaches for antibacterial, antiviral treatments, and cancer therapeutics with improved radiosensitization have been made in clinical research. This review highlights the precise and potent roles of NO in RNR inhibition by targeting both the subunits. Under nitrosative stress, the thiols of the R1 subunits have been found to be modified by S-nitrosylation and the tyrosyl radicals of the R2 subunits have been modified by nitration. In view of the recent advances and progresses in the field of nitrosative modifications and its fundamental role in signaling with implications in health and diseases, the present article focuses on the regulations of RNR activity by S-nitrosylation of thiols (R1 subunits) and nitration of tyrosyl residues (R2 subunits) which will further help in designing new drugs and therapies.

A Fluorescent Cage for Supramolecular Sensing of 3-Nitrotyrosine in Human Blood Serum

3-Nitrotyrosine (NT) is generated by the action of peroxynitrite and other reactive nitrogen species (RNS), and as a consequence it is accumulated in inflammation-associated conditions. This is particularly relevant in kidney disease, where NT concentration in blood is considerably high. Therefore, NT is a crucial biomarker of renal damage, although it has been underestimated in clinical diagnosis due to the lack of an appropriate sensing method. Herein we report the first fluorescent supramolecular sensor for such a relevant compound: Fluorescence by rotational restriction of tetraphenylethenes (TPE) in a covalent cage is selectively quenched in human blood serum by 3-nitrotyrosine (NT) that binds to the cage with high affinity, allowing a limit of detection within the reported physiological concentrations of NT in chronic kidney disease.

Improvement of the fluorescent sensing biomarker 3-nitrotyrosine for a new luminescent coordination polymer by size regulation

A new 3D luminescent coordination polymer (LCP) 1 was synthesized for detecting biomarker 3-nitrotyrosine. By adjusting the reaction conditions, Nano-LCP 1 was synthesized, which has a more lower detection limit compared with LCP 1.

HILIC-MS/MS for the Determination of Methylated Adenine Nucleosides in Human Urine

N6-methyl-2'-deoxyadenosine (m6dA) is a newly discovered DNA epigenetic mark in mammals. N6-methyladenosine (m6A), 2'-O-methyladenosine (Am), N6,2'-O-dimethyladenosine (m6Am), and N6,N6-dimethyladenosine (m62A) are common RNA modifications. Previous studies illustrated the associations between the aberrations of these methylated adenosines in nucleic acids and cancer. Herein, we developed Fe3O4/graphene-based magnetic dispersive solid-phase extraction for the enrichment and hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS/MS) for the measurements of m6dA, m6A, Am, m6Am, and m62A in human urine samples. We found that malic acid could improve the HILIC-based separation of these modified nucleosides and markedly enhance the sensitivity of their MS detection. With this method, we accurately quantified the contents of these modified adenine nucleosides in urine samples collected from gastric and colorectal cancer patients as well as healthy controls. We found that, relative to healthy controls, urinary m6dA and Am levels are significantly lower for gastric and colorectal cancer patients; while gastric cancer patients also exhibited lower levels of urinary m6A, the trend was opposite for colorectal cancer patients. Together, we developed a robust analytical method for simultaneous measurements of five methylated adenine nucleosides in human urine, and our results revealed an association between the levels of urinary methylated adenine nucleosides and the occurrence of gastric as well as colorectal cancers, suggesting the potential applications of these modified nucleosides as biomarkers for the early detection of these cancers.

Recent progress in the LC-MS/MS analysis of oxidative stress biomarkers

The presence of a dynamic and balanced equilibrium between the production of reactive oxygen (ROS) and nitrogen (RNS) species and the in-house antioxidant defense mechanisms is characteristic for a healthy body. During oxidative stress (OS), this balance is switched to increased production of ROS and RNS, exceeding the capacity of physiological antioxidant systems. This can cause damage to biological molecules, leading to loss of function and even cell death. Nowadays, there is increasing scientific and clinical interest in OS and the associated parameters to measure the degree of OS in biofluids. An increasing number of reports using LC-MS/MS methods for the analysis of OS biomarkers can be found. Since bioanalysis is usually complicated by matrix effects, various types of cleanup procedures are used to effectively separate the biomarkers from the matrix. This is an essential part of the analysis to prepare a reproducible and homogenous solution suitable for injection onto the column. The present review gives a summary of the chromatographic methods used for the determination of OS biomarkers in both urine and plasma, serum, and whole blood samples. The first part mainly describes the biological background of the different OS biomarkers, while the second part reports examples of chromatographic methods for the analysis of different metabolites connected with OS in biofluids, covering a period from 2015 till early 2020. The selected examples mainly include LC-MS/MS methods for isoprostanes, oxidized proteins, oxidized lipoproteins, and DNA/RNA biomarkers. The last part explains the clinical relevance of this review.

Nephroprotective effect of Ferulago angulata flowers on N-nitrosodimethylamine-induced nephrotoxicity in rats and its phytochemical profile

The present study was designed to assess the phytochemical content of Ferulago angulata (FA) and possible in vivo nephroprotective effect of FA administration on trace elements, minerals, MDA and GSH in kidney and liver tissue samples, serum vitamin (α-tocopherol, retinol, cholecalciferol, phylloquinone), TSA, and LSA in a rat model of DMN-induced nephrotoxicity. In the study, Wistar albino rats were assigned to six groups: Control (0.9% NaCl), (DMN 10 mg/kg), (FA 150 mg/kg), (DMN + FA 150 mg/kg), (FA 300 mg/kg), and (DMN + FA 300 mg/kg). Rats were intraperitoneally given DMN for the first 7 days. Renal injury caused by DMN was proved by the histopathological alterations. The FA (300 mg/kg) treatment significantly normalized Se, Cr, Ca levels in liver and Co level in kidney tissue samples. These observed positive effects are due to the phytochemical content of the plant. The flower extract of FA (300 mg/kg) can be used for the prevention of kidney damage. PRACTICAL APPLICATIONS: Ferulago angulata flowers are used in traditional medicine for treat kidney and liver digestive system diseases. This species is endemic taxa of the family Apiaceae, which has been used both as food and therapeutics because of their phytochemical composition. In this study, the phenolic characterization of FA flower was used to a new RP-HPLC method, as well as the biological activity of FA flower and possible in vivo nephroprotective effect of FA flowers on trace elements, minerals, MDA and GSH in kidney and liver tissue samples and vitamins, TSA, and LSA in serum samples a rat model of DMN-induced nephrotoxicity. It was found that high level of phenolic compounds (chlorogenic acid, vanillic acid, 2-hydroxycinnamic acid) present in the flower extract of F. angulata has positive effects and antioxidant properties. Due to its phenolic content, FA flower extract could protect for kidney damage and can be used as antioxidants in the food additive and pharmaceutical industry.

Advances in detection and quantification of methylcytosine and its derivatives

Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.

Concentration characteristics, source apportionment, and oxidative damage of PM2.5-bound PAHs in petrochemical region in Xinjiang, NW China

Polycyclic aromatic hydrocarbons (PAHs) are of considerable concern due to their potential as human carcinogens. Thus, determining the characteristics, potential source, and examining the oxidative capacity of PAHs to protect human health is essential. This study investigated the PM_2.5-bound PAHs at Dushanzi, a large petrochemical region in Xinjiang as well as northwest China. A total of 33 PM_2.5 samples with 13 PAHs, together with molecular tracers (levoglucosan, and element carbon), were analyzed during the non-heating and heating periods. The results showed that the PM_2.5 concentrations were 70.22 ± 22.30 and 95.47 ± 61.73 μg/m³, while that of total PAHs were 4.07 ± 2.03 and 60.33 ± 30.80 ng/m³ in sampling period, respectively. The fluoranthene, pyrene, chrysene, benzo[b]fluoranthene, and benzo[k]fluoranthene were the most abundant (top five) PAHs, accounting for 71.74 and 72.80% of total PAH mass during non-heating and heating periods. The BaP equivalent (BaPeq) concentration exceeded 1 ng/m³ as recommended by National Ambient Air Quality Standards during heating period. The diagnostic ratios and positive matrix factorization indicated that oil industry, biomass burning, coal combustion, and vehicle emissions are the primary sources. The coal combustion remarkably increased during heating period. The plasmid scission assay (PSA) results showed that higher DNA damage rate was observed during heating period. PAHs in PM_2.5 such as Chr, BaP, and IcdP were found to have significantly positive correlations with the plasmid DNA damage rates. Additionally, the relationship among BaPeq and DNA damage rate suggested that synergistic reaction may modify the toxicity of PAHs.

The human microbiome and metabolomics: Current concepts and applications

The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host-microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases. Also, identification of these metabolic fingerprints could give us clues as to how to manipulate the microbiome to promote health or treat diseases. This review provides an overview of our current knowledge of the microbiome and metablomics, applications and the future perspectives.

Exposure to fine particulate matter causes oxidative and methylated DNA damage in young adults: A longitudinal study

An increased understanding is needed of the physiological effects and plausible biological mechanisms that link PM_2.5 (particulate matter with an aerodynamic diameter below 2.5μm) exposure to mortality and morbidities such as atherosclerosis and respiratory disease. PM_2.5 causes carcinogenic health effects. Biomonitoring in humans has suggested that 8-oxo-7, 8-dihydro-2-deoxyguanosine (8-oxodG) and N7-methylguanine (N7-MeG) are correlated with oxidative and methylated DNA damage. Thus, it is meaningful to explore the mechanisms of mutagenesis and carcinogenesis associated with oxidative and methylated DNA damage by simultaneously measuring these two markers. We recruited 72 participants from 2 areas (residential and commercial as well as residential and industrial) in the greater Taipei metropolitan area at baseline. Personal samplers were used to collect 24-hour PM_2.5-integrated samples. All participants completed an interview, and blood and urine samples were collected the next morning. All collection procedures were repeated twice after a two-month follow-up period. Urinary 8-oxodG and N7-MeG were assayed as biomarkers of oxidative and methylated DNA damage, respectively. Plasma superoxide dismutase (SOD) and glutathione peroxidase-1 (GPX-1) were measured as biomarkers of antioxidants. Urinary 1-hydroxypyrene (1-OHP) was used as a biomarker of exposure to polycyclic aromatic hydrocarbons (PAHs). The mean PM_2.5 level was 37.3μg/m³ at baseline. PM_2.5 concentrations were higher during winter than during spring and summer. After adjusting for confounds through a generalized estimating equation (GEE) analysis, N7-MeG was significantly increased by 8.1% (β=0.034, 95% CIs=0.001-0.068) per 10μg/m³ increment in PM_2.5. 8-oxodG levels were positively correlated with N7-MeG according to both cross-sectional and longitudinal analyses, and 1-OHP was significantly associated with increasing 8-oxodG and N7-MeG concentrations. Exposure to PM_2.5 increases methylated DNA damage. The mean level of urinary N7-MeG was 1000-fold higher than that of 8-oxodG.

Integration of Miniaturized Solid Phase Extraction and LC-MS/MS Detection of 3-Nitrotyrosine in Human Urine for Clinical Applications

Free 3-nitrotyrosine (3-NT) has been extensively used as a possible biomarker for oxidative stress. Increased levels of 3-NT have been reported in a wide variety of pathological conditions. However, existing methods lack the sufficient sensitivity and/or specificity necessary to measure the low endogenous level of 3-NT reliably and are too cumbersome for clinical applications. Hence, analytical improvement is urgently needed to accurately quantify the levels of 3-NT and verify the role of 3-NT in pathological conditions. This protocol presents the development of a novel liquid chromatography tandem mass spectrometry (LC-MS/MS) detection combined with a miniaturized solid phase extraction (SPE) for the rapid and accurate measurement of 3-NT in human urine as a non-invasive biomarker for oxidative stress. SPE using a 96-well plate markedly simplified the process by combining sample cleanup and analyte enrichment without tedious derivatization and evaporation steps, reducing solvent consumption, waste disposal, risk of contamination and overall processing time. The employment of 25 mM ammonium acetate (NH4OAc) at pH 9 as the SPE elution solution substantially enhanced the selectivity. Mass spectrometry signal response was improved through adjustment of the multiple reaction monitoring (MRM) transitions. Use of 0.01% HCOOH as additive on a pentafluorophenyl (PFP) column (150 mm x 2.1 mm, 3 µm) improved signal response another 2.5-fold and shortened the overall run time to 7 min. A lower limit of quantitation (LLOQ) of 10 pg/mL (0.044 nM) was achieved, representing a significant sensitivity improvement over the reported assays. This simplified, rapid, selective and sensitive method allows two plates of urine samples (n = 192) to be processed in a 24 h time-period. Considering the markedly improved analytical performance, and non-invasive and inexpensive urine sampling, the proposed assay is beneficial for pre-clinical and clinical studies.

Probing cigarette smoke-induced DNA single-strand breaks and screening natural protective compounds by use of magnetic bead-based chemiluminescence

Magnetic bead (MB)-based chemiluminescence (CL) ELISA can be a sample-thrifty, time-saving tool for evaluation of cigarette smoke-induced DNA single-strand breaks (SSBs) with high specificity. This article describes a novel approach using immobilized oligonucleotide on MBs to determine cigarette smoke-induced DNA SSBs and screen some protective natural compounds. Typically, fluorescein-labeled DNA (FAM-DNA) was immobilized on the MBs and then oxidized by the smoke in the absence or presence of natural compounds, and a part of FAM-DNA was fragmented due to cigarette smoke-induced DNA SSB and then detached from MBs whereas other non-broken FAM-DNA still remained on MBs. Then, any broken FAM-DNA fragments, complex tobacco smoke matrix, and other stuff related with natural compounds were conveniently washed away by a magnetic force, and thus possible interfering substances were completely removed. Finally, those remaining non-broken FAM-DNA on MBs were reacted with HRP-labeled anti-fluorescein antibody and then detected by CL ELISA. CL signal was converted to molar concentrations of the FAM-DNA by interpolation from a pre-determined standard linear calibration curve. The level of DNA SSBs induced by cigarette smoke was thus calculated using the method. A library of 30 natural products was subsequently screened, and two among them were found to protect DNA from oxidative damage and thus may be promising compounds for the development of new drugs. The method developed will be useful for quantitative screening of drug genotoxicity in terms of induction of DNA SSBs. Graphical abstract ᅟ.

Label-free detection of 3-nitro-l-tyrosine with nickel-doped graphene localized surface plasmon resonance biosensor

3-nitro-l-tyrosine (3-NT) is believed to be a biomarker of neurodegenerative diseases and metal doped graphene possess exceptionally high binding energy of 3-NT with metal-nitro chemisorption. Here we report a novel label-free detection scheme of 3-NT via nickel-doped graphene (NDG) as the functionalized receptor on our phase detecting localized surface plasmon resonance (LSPR) biosensor. When compared with reported 3-NT immunoassay with enzyme-linked immunosorbent assay (ELISA), our NDG-LSPR platform offers two advantages i.e. 1) label-free and 2) capture of 3-NT by direct chemisorption. Our limit of detection for 3-NT in PBS was found to be 0.13pg/ml and the linear dynamic range of response was from 0.5pg/ml to 1ng/ml, i.e. four orders of magnitude. The specificity of our NDG receptor to 3-NT was also verified with l-tyrosine of equivalent concentrations in PBS and diluted human serum, for which the NDG receptor shows negligible responses. In addition, the adsorption of 3-NT and l-tyrosine to the NDG receptor were also investigated by atomic force microscopy and further verified by surface enhanced Raman spectroscopy. Therefore, our NDG-LSPR biosensor competes favorably against ELISA and we believe it should be an attractive and economical solution to early diagnostic of 3-NT related disorders for clinical applications.

Metabolic biomarkers for chronic kidney disease

Chronic kidney disease (CKD) is an increasingly recognized burden for patients and health care systems with high (and growing) global incidence and prevalence, significant mortality, and disproportionately high treatment costs. Yet, the available diagnostic tools are either impractical in clinical routine or have serious shortcomings impeding a well-informed disease management although optimized treatment strategies with proven benefits for the patients have become available. Advances in bioanalytical technologies have facilitated studies that identified genomic, proteomic, and metabolic biomarker candidates, and confirmed some of them in independent cohorts. This review summarizes the CKD-related markers discovered so far, and focuses on compounds and pathways, for which there is quantitative data, substantiating evidence from translational research, and a mechanistic understanding of the processes involved. Also, multiparametric marker panels have been suggested that showed promising diagnostic and prognostic performance in initial analyses although the data basis from prospective trials is very limited. Large-scale studies, however, are underway and will provide the information for validating a set of parameters and discarding others. Finally, the path from clinical research to a routine application is discussed, focusing on potential obstacles such as the use of mass spectrometry, and the feasibility of obtaining regulatory approval for targeted metabolomics assays.