Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles

Beyond the promise: Exploring the complex interactions of nanoparticles within biological systems

The exploration of nanoparticle applications is filled with promise, but their impact on the environment and human health raises growing concerns. These tiny environmental particles can enter the human body through various routes, such as the respiratory system, digestive tract, skin absorption, intravenous injection, and implantation. Once inside, they can travel to distant organs via the bloodstream and lymphatic system. This journey often results in nanoparticles adhering to cell surfaces and being internalized. Upon entering cells, nanoparticles can provoke significant structural and functional changes. They can potentially disrupt critical cellular processes, including damaging cell membranes and cytoskeletons, impairing mitochondrial function, altering nuclear structures, and inhibiting ion channels. These disruptions can lead to widespread alterations by interfering with complex cellular signaling pathways, potentially causing cellular, organ, and systemic impairments. This article delves into the factors influencing how nanoparticles behave in biological systems. These factors include the nanoparticles' size, shape, charge, and chemical composition, as well as the characteristics of the cells and their surrounding environment. It also provides an overview of the impact of nanoparticles on cells, organs, and physiological systems and discusses possible mechanisms behind these adverse effects. Understanding the toxic effects of nanoparticles on physiological systems is crucial for developing safer, more effective nanoparticle-based technologies.

Airborne magnetite nanoparticles induced early vascular pathologies by disrupting lipid metabolism under high-fat dietary patterns

Magnetite nanoparticles (MNPs) have been extensively detected in the atmospheric environment and implicated as a prominent threat to atherosclerosis, a chronic vascular inflammatory disease. Due to globalization and economic development, the dramatic shift in diet from traditional to high-fat dietary patterns aggravated atherosclerosis progression induced by environmental factors. However, limited knowledge is available regarding vascular risks and underlying mechanisms of airborne MNPs in high-risk populations with high-fat dietary habits. Herein, we demonstrated that MNPs exerted a proatherogenic effect under high-fat dietary patterns, leading to aortic wall thickening, elastic fiber disorganization, macrophage infiltration, and local inflammation. Based on the correlation analysis between MNPs and PM group, we identified that MNPs might be a key PM component in atherogenic toxicity. MNPs exposure disturbed the dynamic process of lipid metabolism, manifested as aortic lipid accumulation, dyslipidemia, and hepatic lipid metabolism disorder, which was modulated by the JAK-STAT pathway. Overall, these findings provide new insight into understanding the cardiovascular risks and mechanisms of MNPs among high-risk populations.

Metabolomics-derived biomarkers for biosafety assessment of Gd-based nanoparticle magnetic resonance imaging contrast agents

With the rapid development of nanotechnology and biomedicine, numerous gadolinium (Gd)-based nanoparticle MRI contrast agents have been widely investigated. Due to the unique physicochemical properties of nanoparticles and the complexity of biological systems, the biosafety of Gd-based nanoparticle MRI contrast agents has been paid more and more attention. Herein, for the first time, we employed an ultra-high performance liquid chromatography-electrospray ionization quadrupole time-of-flight/mass spectrometry (UPLC-ESI-QTOF/MS)-based metabolomics approach to investigate the potential toxicity of Gd-based nanoparticle MRI contrast agents. In this work, NaGdF4 and PEG-NaGdF4 nanoparticles were successfully constructed and selected as the representative Gd-based nanoparticle MRI contrast agents for the metabolomics analysis. Based on the results of metabolomics, more metabolic biomarkers and pathways were identified in the NaGdF4 group than those in the PEG-NaGdF4 group. Careful analysis of these metabolic biomarkers and pathways suggested that NaGdF4 nanoparticles induced disturbance of pyrimidine and purine metabolism, inflammatory response, and kidney injury to a certain extent compared with PEG-NaGdF4 nanoparticles. These results indicated that Gd-based nanoparticle contrast agents modified with PEG had better biosafety. Additionally, it was demonstrated that the discovery of characteristic metabolomics biomarkers induced by nanoparticles would provide a new approach for biosafety assessment and stimulate the development of nanomedicine.

Comparison of acute phase response in mice after inhalation and intratracheal instillation of molybdenum disulphide and tungsten particles

Inhalation studies are the gold standard for assessing the toxicity of airborne materials. They require considerable time, special equipment, and large amounts of test material. Intratracheal instillation is considered a screening and hazard assessment tool as it is simple, quick, allows control of the applied dose, and requires less test material. The particle-induced pulmonary inflammation and acute phase response in mice caused by intratracheal instillation or inhalation of molybdenum disulphide or tungsten particles were compared. End points included neutrophil numbers in bronchoalveolar lavage fluid, Saa3 mRNA levels in lung tissue and Saa1 mRNA levels in liver tissue, and SAA3 plasma protein. Acute phase response was used as a biomarker for the risk of cardiovascular disease. Intratracheal instillation of molybdenum disulphide or tungsten particles did not produce pulmonary inflammation, while molybdenum disulphide particles induced pulmonary acute phase response with both exposure methods and systemic acute phase response after intratracheal instillation. Inhalation and intratracheal instillation showed similar dose-response relationships for pulmonary and systemic acute phase response when molybdenum disulphide was expressed as dosed surface area. Both exposure methods showed similar responses for molybdenum disulphide and tungsten, suggesting that intratracheal instillation can be used for screening particle-induced acute phase response and thereby particle-induced cardiovascular disease.

Advances in tumor nanotechnology: theragnostic implications in tumors via targeting regulated cell death

Cell death constitutes an indispensable part of the organismal balance in the human body. Generally, cell death includes regulated cell death (RCD) and accidental cell death (ACD), reflecting the intricately molecule-dependent process and the uncontrolled response, respectively. Furthermore, diverse RCD pathways correlate with multiple diseases, such as tumors and neurodegenerative diseases. Meanwhile, with the development of precision medicine, novel nano-based materials have gradually been applied in the clinical diagnosis and treatment of tumor patients. As the carrier, organic, inorganic, and biomimetic nanomaterials could facilitate the distribution, improve solubility and bioavailability, enhance biocompatibility and decrease the toxicity of drugs in the body, therefore, benefiting tumor patients with better survival outcomes and quality of life. In terms of the most studied cell death pathways, such as apoptosis, necroptosis, and pyroptosis, plenty of studies have explored specific types of nanomaterials targeting the molecules and signals in these pathways. However, no attempt was made to display diverse nanomaterials targeting different RCD pathways comprehensively. In this review, we elaborate on the potential mechanisms of RCD, including intrinsic and extrinsic apoptosis, necroptosis, ferroptosis, pyroptosis, autophagy-dependent cell death, and other cell death pathways together with corresponding nanomaterials. The thorough presentation of RCD pathways and diverse nano-based materials may provide a wider cellular and molecular landscape of tumor diagnosis and treatments.

PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping

Toxicological evaluation of substances in regulation still often relies on animal experiments. Understanding the substances' mode-of-action is crucial to develop alternative test strategies. Omics methods are promising tools to achieve this goal. Until now, most attention was focused on transcriptomics, while proteomics is not yet routinely applied in toxicology despite the large number of datasets available in public repositories. Exploiting the full potential of these datasets is hampered by differences in measurement procedures and follow-up data processing. Here we present the tool PROTEOMAS, which allows meta-analysis of proteomic data from public origin. The workflow was designed for analyzing proteomic studies in a harmonized way and to ensure transparency in the analysis of proteomic data for regulatory purposes. It agrees with the Omics Reporting Framework guidelines of the OECD with the intention to integrate proteomics to other omic methods in regulatory toxicology. The overarching aim is to contribute to the development of AOPs and to understand the mode of action of substances. To demonstrate the robustness and reliability of our workflow we compared our results to those of the original studies. As a case study, we performed a meta-analysis of 25 proteomic datasets to investigate the toxicological effects of nanomaterials at the lung level. PROTEOMAS is an important contribution to the development of alternative test strategies enabling robust meta-analysis of proteomic data. This workflow commits to the FAIR principles (Findable, Accessible, Interoperable and Reusable) of computational protocols.

Acute phase response following pulmonary exposure to soluble and insoluble metal oxide nanomaterials in mice

BACKGROUND

Acute phase response (APR) is characterized by a change in concentration of different proteins, including C-reactive protein and serum amyloid A (SAA) that can be linked to both exposure to metal oxide nanomaterials and risk of cardiovascular diseases. In this study, we intratracheally exposed mice to ZnO, CuO, Al₂O₃, SnO₂ and TiO₂ and carbon black (Printex 90) nanomaterials with a wide range in phagolysosomal solubility. We subsequently assessed neutrophil numbers, protein and lactate dehydrogenase activity in bronchoalveolar lavage fluid, Saa3 and Saa1 mRNA levels in lung and liver tissue, respectively, and SAA3 and SAA1/2 in plasma. Endpoints were analyzed 1 and 28 days after exposure, including histopathology of lung and liver tissues.

RESULTS

All nanomaterials induced pulmonary inflammation after 1 day, and exposure to ZnO, CuO, SnO₂, TiO₂ and Printex 90 increased Saa3 mRNA levels in lungs and Saa1 mRNA levels in liver. Additionally, CuO, SnO₂, TiO₂ and Printex 90 increased plasma levels of SAA3 and SAA1/2. Acute phase response was predicted by deposited surface area for insoluble metal oxides, 1 and 28 days post-exposure.

CONCLUSION

Soluble and insoluble metal oxides induced dose-dependent APR with different time dependency. Neutrophil influx, Saa3 mRNA levels in lung tissue and plasma SAA3 levels correlated across all studied nanomaterials, suggesting that these endpoints can be used as biomarkers of acute phase response and cardiovascular disease risk following exposure to soluble and insoluble particles.

Assessment of primary and inflammation-driven genotoxicity of carbon black nanoparticles in vitro and in vivo

Carbon black nanoparticles (CBNPs) have a large surface area/volume ratio and are known to generate oxidative stress and inflammation that may result in genotoxicity and cancer. Here, we evaluated the primary and inflammatory response-driven (i.e. secondary) genotoxicity of two CBNPs, Flammruss101 (FL101) and PrintexXE2B (XE2B) that differ in size and specific surface area (SSA), and cause different amounts of reactive oxygen species. Three doses (low, medium and high) of FL101 and XE2B were assessed in vitro in the lung epithelial (A549) and activated THP-1 (THP-1a) monocytic cells exposed in submerged conditions for 6 and 24 h, and in C57BL/6 mice at day 1, 28 and 90 following intratracheal instillation. In vitro, we assessed pro-inflammatory response as IL-8 and IL-1β gene expression, and in vivo, inflammation was determined as inflammatory cell infiltrates in bronchial lavage (BAL) fluid and as histological changes in lung tissue. DNA damage was quantified in vitro and in vivo as DNA strand breaks levels by the alkaline comet assay. Inflammatory responses in vitro and in vivo correlated with dosed CBNPs SSA. Both materials induced DNA damage in THP-1a (correlated with dosed mass), and only XE2B in A549 cells. Non-statistically significant increase in DNA damage in vivo was observed in BAL cells. In conclusion, this study shows dosed SSA predicted inflammation both in vivo and in vitro, whereas dosed mass predicted genotoxicity in vitro in THP-1a cells. The observed lack of correlation between CBNP surface area and genotoxicity provides little evidence of inflammation-driven genotoxicity in vivo and in vitro.

Systematic review on primary and secondary genotoxicity of carbon black nanoparticles in mammalian cells and animals

Carbon black exposure causes oxidative stress, inflammation and genotoxicity. The objective of this systematic review was to assess the contributions of primary (i.e. direct formation of DNA damage) and secondary genotoxicity (i.e., DNA lesions produced indirectly by inflammation) to the overall level of DNA damage by carbon black. The database is dominated by studies that have measured DNA damage by the comet assay. Cell culture studies indicate a genotoxic action of carbon black, which might be mediated by oxidative stress. Many in vivo studies originate from one laboratory that has investigated the genotoxic effects of Printex 90 in mice by intra-tracheal instillation. Meta-analysis and pooled analysis of these results demonstrate that Printex 90 exposure is associated with a slightly increased level of DNA strand breaks in bronchoalveolar lavage cells and lung tissue. Other types of genotoxic damage have not been investigated as thoroughly as DNA strand breaks, although there is evidence to suggest that carbon black exposure might increase the mutation frequency and cytogenetic endpoints. Stratification of studies according to concurrent inflammation and DNA damage does not indicate that carbon black exposure gives rise to secondary genotoxicity. Even substantial pulmonary inflammation is at best only associated with a weak genotoxic response in lung tissue. In conclusion, the review indicates that nanosized carbon black is a weak genotoxic agent and this effect is more likely to originate from a primary genotoxic mechanism of action, mediated by e.g., oxidative stress, than inflammation-driven (secondary) genotoxicity.

Characterization of ENM Dynamic Dose-Dependent MOA in Lung with Respect to Immune Cells Infiltration

The molecular effects of exposures to engineered nanomaterials (ENMs) are still largely unknown. In classical inhalation toxicology, cell composition of bronchoalveolar lavage (BAL) is a toxicity indicator at the lung tissue level that can aid in interpreting pulmonary histological changes. Toxicogenomic approaches help characterize the mechanism of action (MOA) of ENMs by investigating the differentially expressed genes (DEG). However, dissecting which molecular mechanisms and events are directly induced by the exposure is not straightforward. It is now generally accepted that direct effects follow a monotonic dose-dependent pattern. Here, we applied an integrated modeling approach to study the MOA of four ENMs by retrieving the DEGs that also show a dynamic dose-dependent profile (dddtMOA). We further combined the information of the dddtMOA with the dose dependency of four immune cell populations derived from BAL counts. The dddtMOA analysis highlighted the specific adaptation pattern to each ENM. Furthermore, it revealed the distinct effect of the ENM physicochemical properties on the induced immune response. Finally, we report three genes dose-dependent in all the exposures and correlated with immune deregulation in the lung. The characterization of dddtMOA for ENM exposures, both for apical endpoints and molecular responses, can further promote toxicogenomic approaches in a regulatory context.

Dynamic intracellular exchange of nanomaterials' protein corona perturbs proteostasis and remodels cell metabolism

SignificanceThis study analyzed the dynamic protein corona on the surface of nanoparticles as they traversed from blood to cell lysosomes and escaped from lysosomes to cytoplasm in the target cells. We found with proteomic analysis an abundance of chaperone and glycolysis coronal proteins (i.e., heat shock cognate protein 70, heat shock protein 90, and pyruvate kinase M2 [PKM2]) after escape of the nanoparticles from lysosomes to the cytosol. Alterations of the coronal proteins (e.g., PKM2 and chaperone binding) induced proteostasis collapse, which subsequently led to elevated chaperone-mediated autophagy (CMA) activity in cells. As PKM2 is a key molecule in cell metabolism, we also revealed that PKM2 depletion was causative to CMA-induced cell metabolism disruption from glycolysis to lipid metabolism.

Acute lung inflammation induced by zinc oxide nanoparticles: Evolution and intervention via NRF2 activator

Zinc oxide nanoparticles (ZnONPs) are widely used worldwide. Human inhalation exposure to ZnONPs induces acute lung inflammation (ALI); however, the characteristics and therapeutic targets of ALI are unclear. In this study, female C57BL/6J mice were subjected to a single intratracheal instillation of 20 μg of ZnONPs. Increased lung malondialdehyde levels and decreased total antioxidant capacity at 6 h, as well as increased lactate dehydrogenase levels in bronchoalveolar lavage fluid (BALF) at 1 day (d) post treatment were observed. A significant inflammatory response was observed at 3 d and 7 d, as evidenced by increased leukocyte numbers and total protein concentration in BALF, and histological abnormalities. Pulmonary NRF2 signaling was significantly activated at 3 d post treatment. To investigate a protective role of NRF2 activator against ZnONP-induced ALI, the mice were intraperitoneally injected with 2-cyano-3,12-dioxooleana-1,9-dien-28-imidazolide (CDDO-Im) (2 mg/kg) 1 d before and 1 d after ZnONPs treatment. CDDO-Im significantly decreased leukocyte numbers and total protein concentration in BALF and pulmonary inflammatory gene expression, and ameliorated histopathological abnormalities induced by ZnONPs. Collectively, the present study indicates that ZnONPs exposure leads to oxidative stress, cell injury and inflammation in the lung successively. Moreover, the NRF2 activator protects against ZnONPs-induced ALI.

On the potential of micro-flow LC-MS/MS in proteomics

INTRODUCTION

Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples.

AREAS COVERED

This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications.

EXPERT OPINION

Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.

[Advances in high-throughput proteomic analysis]

基于质谱的蛋白质组学技术已经日趋成熟,可以对细胞和组织中的成千上万种蛋白质进行全面的定性和定量分析,逐步实现“深度覆盖”。随着生物医学日益增长的大队列蛋白质组学分析需求,如何在保持较为理想的覆盖深度下实现短时间、快速的“高通量”蛋白质组学分析已成为当前亟需解决的关键问题之一。常规的蛋白质组学分析流程通常包括样品前处理、色谱分离、质谱检测和数据分析。该文从以上4个方面展开介绍近10年以来高通量蛋白质组学分析技术取得的一系列研究进展,主要包括:(1)基于高通量、自动化移液工作站的蛋白质组样品前处理方法;(2)基于微升流速液相色谱与质谱联用的高通量蛋白质组检测方法;(3)利用灵敏度高、扫描速度快的质谱仪实现短色谱梯度分离下蛋白质组深度覆盖的分析方法;(4)基于人工智能、深度神经网络、机器学习等的蛋白质组学大数据分析方法。此外,对高通量蛋白质组学面临的挑战及其发展进行展望。总而言之,预期在不久的将来高通量蛋白质组学技术将会逐步“落地转化”,成为大队列蛋白质组学分析的利器。

Proteomics in systems toxicology

Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.

Environmentally Relevant Iron Oxide Nanoparticles Produce Limited Acute Pulmonary Effects in Rats at Realistic Exposure Levels

Iron is typically the dominant metal in the ultrafine fraction of airborne particulate matter. Various studies have investigated the toxicity of inhaled nano-sized iron oxide particles (FeO_xNPs) but their results have been contradictory, with some indicating no or minor effects and others finding effects including oxidative stress and inflammation. Most studies, however, did not use materials reflecting the characteristics of FeO_xNPs present in the environment. We, therefore, analysed the potential toxicity of FeO_xNPs of different forms (Fe₃O₄, α-Fe₂O₃ and γ-Fe₂O₃) reflecting the characteristics of high iron content nano-sized particles sampled from the environment, both individually and in a mixture (FeO_x-mix). A preliminary in vitro study indicated Fe₃O₄ and FeO_x-mix were more cytotoxic than either form of Fe₂O₃ in human bronchial epithelial cells (BEAS-2B). Follow-up in vitro (0.003, 0.03, 0.3 µg/mL, 24 h) and in vivo (Sprague–Dawley rats, nose-only exposure, 50 µg/m³ and 500 µg/m³, 3 h/d × 3 d) studies therefore focused on these materials. Experiments in vitro explored responses at the molecular level via multi-omics analyses at concentrations below those at which significant cytotoxicity was evident to avoid detection of responses secondary to toxicity. Inhalation experiments used aerosol concentrations chosen to produce similar levels of particle deposition on the airway surface as were delivered in vitro. These were markedly higher than environmental concentrations. No clinical signs of toxicity were seen nor effects on BALF cell counts or LDH levels. There were also no significant changes in transcriptomic or metabolomic responses in lung or BEAS-2B cells to suggest adverse effects.

Particle characterization and toxicity in C57BL/6 mice following instillation of five different diesel exhaust particles designed to differ in physicochemical properties

Background

Diesel exhaust is carcinogenic and exposure to diesel particles cause health effects. We investigated the toxicity of diesel exhaust particles designed to have varying physicochemical properties in order to attribute health effects to specific particle characteristics. Particles from three fuel types were compared at 13% engine intake O₂ concentration: MK1 ultra low sulfur diesel (DEP13) and the two renewable diesel fuels hydrotreated vegetable oil (HVO13) and rapeseed methyl ester (RME13). Additionally, diesel particles from MK1 ultra low sulfur diesel were generated at 9.7% (DEP9.7) and 17% (DEP17) intake O₂ concentration. We evaluated physicochemical properties and histopathological, inflammatory and genotoxic responses on day 1, 28, and 90 after single intratracheal instillation in mice compared to reference diesel particles and carbon black.

Results

Moderate variations were seen in physical properties for the five particles: primary particle diameter: 15–22 nm, specific surface area: 152–222 m²/g, and count median mobility diameter: 55–103 nm. Larger differences were found in chemical composition: organic carbon/total carbon ratio (0.12–0.60), polycyclic aromatic hydrocarbon content (1–27 μg/mg) and acid-extractable metal content (0.9–16 μg/mg). Intratracheal exposure to all five particles induced similar toxicological responses, with different potency. Lung particle retention was observed in DEP13 and HVO13 exposed mice on day 28 post-exposure, with less retention for the other fuel types. RME exposure induced limited response whereas the remaining particles induced dose-dependent inflammation and acute phase response on day 1. DEP13 induced acute phase response on day 28 and inflammation on day 90. DNA strand break levels were not increased as compared to vehicle, but were increased in lung and liver compared to blank filter extraction control. Neutrophil influx on day 1 correlated best with estimated deposited surface area, but also with elemental carbon, organic carbon and PAHs. DNA strand break levels in lung on day 28 and in liver on day 90 correlated with acellular particle-induced ROS.

Conclusions

We studied diesel exhaust particles designed to differ in physicochemical properties. Our study highlights specific surface area, elemental carbon content, PAHs and ROS-generating potential as physicochemical predictors of diesel particle toxicity.