Abundance of Modifications in Mature miRNAs Revealed by LC-MS/MS Method Coupled with a Two-Step Hybridization Purification Strategy.

Accurate detection of endogenous miRNA modifications, such as N6-methyladenosine (m6A), 7-methylguanosine (m7G), and 5-methylcytidine (m5C), poses significant challenges, resulting in considerable uncertainty regarding their presence in mature miRNAs. In this study, we demonstrate for the first time that liquid chromatography coupled with a tandem mass spectrometry (LC-MS/MS) nucleoside analysis method is a practical tool for quantitatively analyzing human miRNA modifications. The newly designed liquid-solid two-step hybridization (LSTH) strategy enhances specificity for miRNA purification, while LC-MS/MS offers robust capability in recognizing modifications and sufficient sensitivity with detection limits ranging from attomoles to low femtomoles. Therefore, it provides a more reliable approach compared to existing techniques for revealing modifications in endogenous miRNAs. With this approach, we characterized m6A, m7G, and m5C modifications in miR-21-5p, Let-7a/e-5p, and miR-10a-5p isolated from cultured cells and observed unexpectedly low abundance (<1% at each site) of these modifications.

An estimate assay for low-level exposure to ionizing radiation based on mass spectrometry quantification of γ-H2AX in human peripheral blood lymphocytes.

Exposure to environmental ionizing radiation (IR) is ubiquitous, and large-dose exposure to IR is known to cause DNA damage and genotoxicity which is associated with an increased risk of cancer. Whether such detrimental effects are caused by exposure to low-dose IR is still debated. Therefore, rapid and early estimation of absorbed doses of IR in individuals, especially at low levels, using radiation response markers is a pivotal step for early triage during radiological incidents to provide adequate and timely clinical interventions. However, there is currently a crucial shortage of methods capable of determining the extent of low-dose IR exposure to human beings. The phosphorylation of histone H2AX on serine 139 (designated γ-H2AX), a classic biological dosimeter, can be used to evaluate the DNA damage response. We have developed an estimation assay for low-level exposure to IR based on the mass spectrometry quantification of γ-H2AX in blood. Human peripheral blood lymphocytes sensitive to low-dose IR, maintaining low temperature (4°C) and adding enzyme inhibitor are proven to be key steps, possibly insuring that a stable and marked γ-H2AX signal in blood cells exposed to low-dose IR could be detected. For the first time, DNA damage at low dose exposures to IR as low as 0.01 Gy were observed using the sensitive variation of γ-H2AX with high throughput mass spectrometry quantification in human peripheral blood, which is more accurate than the previously reported methods by virtue of isotope-dilution mass spectrometry, and can observe the time effect of DNA damage. These in vitro cellular dynamic monitoring experiments show that DNA damage occurred rapidly and then was repaired slowly over the passage of post-irradiation time even after exposure to very low IR doses. This assay was also used to assess different radiation exposures at the in vitro cellular level. These results demonstrate the potential utility of this assay in radiation biodosimetry and environmental risk assessment.

Differential comparison of genotoxic effects of aristolochic acid I and II in human cells by the mass spectroscopic quantification of γ-H2AX.

Aristolochic acids (AAs) are known to be the potent genotoxic carcinogens, of which aristolochic acid I (AAI) and aristolochic acid II (AAII) are the two representative compounds. As the carcinogenic risk of herbs containing AAs is a global health issue, quantitative evaluation of genotoxicity is needed for the risk assessment of AAs. γ-H2AX, which is an acknowledged attractive bifunctional biomarker for simultaneously reflect the DNA damage response and repair, was used to quantitatively determine the DNA damage and repair properties of AAI and AAII in human cell lines, based on our previously developed mass spectrometry method. Results indicated that both AAI and AAII could increase the level of γ-H2AX in cells in a concentration-dependent manner, and the increased level of γ-H2AX induced by AAI was relatively higher than that induced by AAII. Time-effect curves showed that the change tendency of the proportion of γ-H2AX was obviously different in the later period, particularly afterwards 8 h post exposure. Additionally, AAI and AAII induced an opposite change of expression levels of DNA damage repair-associated proteins (ERCC1 and p53) in HepG2 cells, revealing their distinct molecular mechanisms. Findings of the present study are helpful for understanding the genotoxicity mechanism of AAI and AAII.

Dynamically monitoring cellular γ-H2AX reveals the potential of carcinogenicity evaluation for genotoxic compounds.

Amongst all toxicological endpoints, carcinogenicity might pose the greatest concern. Genetic damage has been considered an important underlying mechanism for the carcinogenicity of chemical substances. The demand for in vitro genotoxic tests as alternative approaches is growing rapidly with the implementation of new regulations for compounds. However, currently available in vitro genotoxicity tests are often limited by relatively high false positive rates. Moreover, few studies have explored carcinogenicity potential by in vitro genotoxicity testing due to the shortage of suitable toxicological biomarkers to link gene damage with cancer risk. γ-H2AX is a recently acknowledged attractive endpoint (biomarker) for evaluating DNA damage and can simultaneously reflect the DNA damage response and repair of cells. We previously reported an ultrasensitive and reliable method, namely stable-isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS), for detecting cellular γ-H2AX and evaluating genotoxic chemicals. More importantly, our method can dynamically monitor the specific processes of genotoxic compounds affecting DNA damage and repair reflected by the amount of γ-H2AX. To clarify the possibility of using this method to assess the potential carcinogenicity of genotoxic chemicals, we applied it to a set of 69 model compounds recommended by the European Center for the Validation of Alternative Methods (ECVAM), with already-characterized genotoxic potential. Compared to conventional in vitro genotoxicity assays, including the Ames test, the γ-H2AX assay by MS has high accuracy (94-96%) due to high sensitivity and specificity (88% and 100%, respectively). The dynamic profiles of model compounds after exposure in HepG2 cells were explored, and a mathematical approach was employed to simulate and quantitatively model the DNA repair kinetics of genotoxic carcinogens (GCs) based on γ-H2AX time-effect curves up to 8 h. Two crucial parameters, i.e., k (rate of γ-H2AX decay) and t50 (time required for γ-H2AX from maximum decrease to half) estimated by the least squares method, were achieved. An open web server to help researchers calculate these two key parameters and profile simulated curves of the tested compound is available online ( http://ccb1.bmi.ac.cn:81/shiny-server/sample-apps/prediction1/ ). We detected a positive association between carcinogenic levels and k and t50 values of γ-H2AX in tested GCs, validating the potential of using this MS-based γ-H2AX in vitro assay to help preliminarily evaluate carcinogenicity and assess genotoxicity. This approach may be used alone or integrated into an existing battery of in vitro genetic toxicity tests.

Facile and sensitive measurement of GSH/GSSG in cells by surface-enhanced Raman spectroscopy.

Reduced glutathione (GSH) and the oxidized glutathione (GSSG) are well-known biomolecules in the main constituents of intracellular redox homeostasis system. A rapid, accurate measurement of cellular GSH and GSSG is quite needed in investigating important biochemical events. In this work, we present a novel and sensitive method to monitor intracellular GSH and GSSG concentrations by a portable surface-enhanced Raman spectroscopy (SERS) technique. We introduced a reduction-sensitive reaction-type Raman probe, 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) to initiate GSH reduction, itself concomitantly converts to 2-nitro-5-thiobenzoic acid (TNB) to release a strong SERS signal. In a convenient way of inorganic salt MgSO4 induced aggregation of silver nanoparticles substrate, we easily implemented a good discrimination between DTNB and TNB, and a quantitative measurement of GSH and GSSG with a high sensitivity of 10 nM. This SERS method proved its feasible applicability in rapidly and sensitively monitoring GSH depletion behaviors of some notorious alkylating agents, i.e., sulfur mustard and nitrogen mustards in ex vitro or in vitro (cellular response). This SERS method may be very worthwhile in cellular detoxication event via the GSH approach and other GSH involved biomedical researches.

Distinct Orchestration and Dynamic Processes on γ-H2AX and p-H3 for Two Major Types of Genotoxic Chemicals Revealed by Mass Spectrometry Analysis.

Genotoxic chemicals act by causing DNA damage, which, if left unrepaired, can have deleterious consequences for cell survival. DNA damage response (DDR) gets activated to repair or mitigate the effects of DNA damage. Histone H2AX and H3 phosphorylation biomarkers (γ-H2AX and p-H3) have attracted great attention as they play pivotal roles in the DDR. Simultaneous quantitation of γ-H2AX and p-H3 in exposed cells may monitor the toxicity of genotoxic chemicals and to some extent reflect the subsequent DDR process. Reported here is the first comprehensive characterization of distinct orchestration and dynamic processes on cellular γ-H2AX and p-H3 for two major types of genotoxic chemicals, clastogens and aneugens, by stable isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS). We find that clastogens significantly induce an increase in γ-H2AX and a decrease in p-H3; aneugens have no obvious effect on γ-H2AX, whereas induce either an increase or a decrease in p-H3. In addition, the specific profiles of clastogens and aneugens affecting DNA damage may be dynamically observed, which in turn provides insights into the processes involving DNA damage repair as well as transcription. Taken together, these results suggest that robust LC-MS/MS analysis of γ-H2AX and p-H3 can not only quantitatively differentiate mechanistic information on clastogens and aneugens but also dynamically present the detail profiles of DNA damage and repair processes.