Characterization of the proteome and lipidome profiles of human lung cells after low dose and chronic exposure to multiwalled carbon nanotubes

Omics approaches for the assessment of biological responses to nanoparticles

Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.

Human and environmental impacts of nanoparticles: a scoping review of the current literature

Use of nanoparticles have established benefits in a wide range of applications, however, the effects of exposure to nanoparticles on health and the environmental risks associated with the production and use of nanoparticles are less well-established. The present study addresses this gap in knowledge by examining, through a scoping review of the current literature, the effects of nanoparticles on human health and the environment. We searched relevant databases including Medline, Web of Science, ScienceDirect, Scopus, CINAHL, Embase, and SAGE journals, as well as Google, Google Scholar, and grey literature from June 2021 to July 2021. After removing duplicate articles, the title and abstracts of 1495 articles were first screened followed by the full-texts of 249 studies, and this resulted in the inclusion of 117 studies in the presented review.In this contribution we conclude that while nanoparticles offer distinct benefits in a range of applications, they pose significant threats to humans and the environment. Using several biological models and biomarkers, the included studies revealed the toxic effects of nanoparticles (mainly zinc oxide, silicon dioxide, titanium dioxide, silver, and carbon nanotubes) to include cell death, production of oxidative stress, DNA damage, apoptosis, and induction of inflammatory responses. Most of the included studies (65.81%) investigated inorganic-based nanoparticles. In terms of biomarkers, most studies (76.9%) used immortalised cell lines, whiles 18.8% used primary cells as the biomarker for assessing human health effect of nanoparticles. Biomarkers that were used for assessing environmental impact of nanoparticles included soil samples and soybean seeds, zebrafish larvae, fish, and Daphnia magna neonates.From the studies included in this work the United States recorded the highest number of publications (n = 30, 25.64%), followed by China, India, and Saudi Arabia recording the same number of publications (n = 8 each), with 95.75% of the studies published from the year 2009. The majority of the included studies (93.16%) assessed impact of nanoparticles on human health, and 95.7% used experimental study design. This shows a clear gap exists in examining the impact of nanoparticles on the environment.

The toxicity of nanoparticles and their interaction with cells: an in vitro metabolomic perspective

Nowadays, nanomaterials (NMs) are widely present in daily life due to their significant benefits, as demonstrated by their application in many fields such as biomedicine, engineering, food, cosmetics, sensing, and energy. However, the increasing production of NMs multiplies the chances of their release into the surrounding environment, making human exposure to NMs inevitable. Currently, nanotoxicology is a crucial field, which focuses on studying the toxicity of NMs. The toxicity or effects of nanoparticles (NPs) on the environment and humans can be preliminary assessed in vitro using cell models. However, the conventional cytotoxicity assays, such as the MTT assay, have some drawbacks including the possibility of interference with the studied NPs. Therefore, it is necessary to employ more advanced techniques that provide high throughput analysis and avoid interferences. In this case, metabolomics is one of the most powerful bioanalytical strategies to assess the toxicity of different materials. By measuring the metabolic change upon the introduction of a stimulus, this technique can reveal the molecular information of the toxicity induced by NPs. This provides the opportunity to design novel and efficient nanodrugs and minimizes the risks of NPs used in industry and other fields. Initially, this review summarizes the ways that NPs and cells interact and the NP parameters that play a role in this interaction, and then the assessment of these interactions using conventional assays and the challenges encountered are discussed. Subsequently, in the main part, we introduce the recent studies employing metabolomics for the assessment of these interactions in vitro.

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.

Nutrient molecule corona: An update for nanomaterial-food component interactions

The adsorption of biological molecules to nanomaterials (NMs) will significantly impact NMs' behavior in complex microenvironments. Previously we proposed the need to consider the interactions between food components and NMs for the evaluation of oral toxicity of NMs. This review updated this concept as nutrient molecule corona, that the adsorption of nutrient molecules alters the uptake of nutrient molecules and/or NMs, as well as the signaling pathways to induce a combined toxicity due to the biologically active nature of nutrient molecules. Even with the presence of protein corona, nutrient molecules may still bind to NMs to change the identities of NMs in vivo. Furthermore, this review proposed the binding of excessive nutrient molecules to NMs to induce a combined toxicity under pathological conditions such as metabolic diseases. The structures of nutrient molecules and physicochemical properties of NMs determine nutrient molecule corona formation, and these aspects should be considered to limit the unwanted effects brought by nutrient molecule corona. In conclusion, similar to other biological molecule corona, the formation of nutrient molecule corona due to the presence of food components or excessive nutrient molecules in pathophysiological microenvironments will alter the behaviors of NMs.

Multiwalled Carbon Nanotubes Induce Fibrosis and Telomere Length Alterations

Telomere shortening can result in cellular senescence and in increased level of genome instability, which are key events in numerous of cancer types. Despite this, few studies have focused on the effect of nanomaterial exposure on telomere length as a possible mechanism involved in nanomaterial-induced carcinogenesis. In this study, effects of exposure to multiwalled carbon nanotubes (MWCNT) on telomere length were investigated in mice exposed by intrapleural injection, as well as in human lung epithelial and mesothelial cell lines. In addition, cell cycle, apoptosis, and regulation of genes involved in DNA damage repair were assessed. Exposure to MWCNT led to severe fibrosis, infiltration of inflammatory cells in pleura, and mesothelial cell hyperplasia. These histological alterations were accompanied by deregulation of genes involved in fibrosis and immune cell recruitment, as well as a significant shortening of telomeres in the pleura and the lung. Assessment of key carcinogenic mechanisms in vitro confirmed that long-term exposure to the long MWCNT led to a prominent telomere shortening in epithelial cells, which coincided with G1-phase arrest and enhanced apoptosis. Altogether, our data show that telomere shortening resulting in cell cycle arrest and apoptosis may be an important mechanism in long MWCNT-induced inflammation and fibrosis.

In vitro toxicity of carbon nanotubes: a systematic review

Carbon nanotube (CNT) toxicity-related issues provoke many debates in the scientific community. The controversial and disputable data about toxicity doses, proposed hazard effects, and human health concerns significantly restrict CNT applications in biomedical studies, laboratory practices, and industry, creating a barrier for mankind in the way of understanding how exactly the material behaves in contact with living systems. Raising the toxicity question again, many research groups conclude low toxicity of the material and its potential safeness at some doses for contact with biological systems. To get new momentum for researchers working on the intersection of the biological field and nanomaterials, i.e., CNT materials, we systematically reviewed existing studies with in vitro toxicological data to propose exact doses that yield toxic effects, summarize studied cell types for a more thorough comparison, the impact of incubation time, and applied toxicity tests. Using several criteria and different scientific databases, we identified and analyzed nearly 200 original publications forming a "golden core" of the field to propose safe doses of the material based on a statistical analysis of retrieved data. We also differentiated the impact of various forms of CNTs: on a substrate and in the form of dispersion because in both cases, some studies demonstrated good biocompatibility of CNTs. We revealed that CNTs located on a substrate had negligible impact, i.e., 90% of studies report good viability and cell behavior similar to control, therefore CNTs could be considered as a prospective conductive substrate for cell cultivation. In the case of dispersions, our analysis revealed mean values of dose/incubation time to be 4-5 μg mL-1 h-1, which suggested the material to be a suitable candidate for further studies to get a more in-depth understanding of its properties in biointerfaces and offer CNTs as a promising platform for fundamental studies in targeted drug delivery, chemotherapy, tissue engineering, biosensing fields, etc. We hope that the present systematic review will shed light on the current knowledge about CNT toxicity, indicate "dark" spots and offer possible directions for the subsequent studies based on the demonstrated here tabulated and statistical data of doses, cell models, toxicity tests, viability, etc.

TiO2 nanosheets promote the transformation of vascular smooth muscle cells into foam cells in vitro and in vivo through the up-regulation of nuclear factor kappa B subunit 2

Titanium dioxide (TiO₂) nanomaterials have been shown to promote atherosclerosis through endothelial dysfunction. This study investigated the toxicity of TiO₂ nanosheets (NSs) to vascular smooth muscle cells (VSMCs), one of the pivotal cells involved in all stages of atherosclerosis. Only a high concentration of TiO₂ NSs (128 μg/mL) modestly induced cytotoxicity by decreasing thiols. RNA-sequencing data revealed that 64 μg/mL TiO₂ NSs significantly down-regulated 94 genes and up-regulated 174 genes, respectively. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to SMC function and lipid metabolism were altered. TiO₂ NSs increased nuclear factor kappa B subunit 2 (NFKB2), which led to a decrease in VSMC marker actin alpha 2, smooth muscle (ACTA2). On the other hand, macrophage marker CD36 and fatty acid synthase (FASN) proteins were increased. Additionally, TiO₂ NSs induced inflammatory cytokines and lipid accumulation, and these effects were curtailed by NFKB inhibitor - triptolide. Furthermore, repeated TiO₂ NS injection (5 mg/kg BW, once a day for 5 continuous days) into ICR mice led to increased NFKB2, CD36 and FASN, with a decreased ACTA2. Our results suggested that TiO₂ NSs promoted the transformation of VSMCs into foam cells through the up-regulation of NFKB2.

Intravenous administration of three multiwalled carbon nanotubes to female rats and their effect on urinary biochemical profile

This study was conducted to investigate the influence of outer diameter (OD) and length (L) of multiwalled carbon nanotubes (MWCNTs) on biodistribution and the perturbation of endogenous metabolite profiles. Three different-sized carboxylated MWCNTs (NIEHS-12-2: L 0.5-2 μm, OD 10-20 nm, NIEHS-13-2: L 0.5-2 μm, OD 30-50 nm, and NIEHS-14-2: L 10-30 μm, OD 10-20 nm) in water were administered to female Sprague-Dawley rats as a single intravenous dose of 1 mg/kg MWCNTs. Biodistribution in liver, lung, spleen, and lymph nodes was evaluated in tissue sections at 1 and 7 days' post-dosing using enhanced darkfield microscopy and hyperspectral imaging. Nuclear magnetic resonance (NMR) analysis was used for biochemical profiling and pathway mapping of endogenous metabolites in urine collected at 24-h intervals prior to dosing, at Day 1 and Day 7. At Day 1 and Day 7, all three MWCNTs were observed in liver. NIEHS-12-2 was observed in spleen, whereas NIEHS-13-2 and NIEHS-14-2 were not. All three MWCNTs were observed in lymph nodes and lung at Day 7. The urinary biochemical profile showed the highest positive fold change (FC) at Day 7 for the metabolites acetate, alanine, and lactate, whereas 1-methylnicotinamide, 2-oxoglutarate, and hippurate had some of the lowest FCs for all three MWCNTs. This study demonstrates that the observed tissue location of MWCNTs is size dependent. Overlaps in the perturbation of endogenous metabolite profiles were found regardless of their size, and the biochemical responses were more profound at Day 7 compared with Day 1, indicating a delayed biological response to MWCNTs.

Genotoxicity of multi-walled carbon nanotube reference materials in mammalian cells and animals

Carbon nanotubes (CNTs) were the first nanomaterials to be evaluated by the International Agency for Research on Cancer (IARC). The categorization as possibly carcinogenic agent to humans was only applicable to multi-walled carbon nanotubes called MWCNT-7. Other types of CNTs were not classifiable because of missing data and it was not possible to pinpoint unique CNT characteristics that cause cancer. Importantly, the European Commission's Joint Research Centre (JRC) has established a repository of industrially manufactured nanomaterials that encompasses at least four well-characterized MWCNTs called NM-400 to NM-403 (original JRC code). This review summarizes the genotoxic effects of these JRC materials and MWCNT-7. The review consists of 36 publications with results on cell culture experiments (22 publications), animal models (9 publications) or both (5 publications). As compared to the publications in the IARC monograph on CNTs, the current database represents a significant increase as there is only an overlap of 8 publications. However, the results come mainly from cell cultures and/or measurements of DNA strand breaks by the comet assay and the micronucleus assay (82 out of 97 outcomes). A meta-analysis of cell culture studies on DNA strand breaks showed a genotoxic response by MWCNT-7, less consistent effect by NM-400 and NM-402, and least consistent effect by NM-401 and NM-403. Results from other in vitro tests indicate strongest evidence of genotoxicity for MWCNT-7. There are too few observations from animal models and humans to make general conclusions about genotoxicity.

Comparison of multi-walled carbon nanotubes and halloysite nanotubes on lipid profiles in human umbilical vein endothelial cells

Tubular nanomaterials (NMs), such as multi-walled carbon nanotubes (MWCNTs) and halloysite nanotubes (HNTs), may be used in biomedicine, but previous studies showed that MWCNTs induced toxicity to endothelial cells (ECs). However, the influence of tubular NMs on EC lipid profiles has gained little attention, probably because ECs are not traditionally considered to be involved in regulating lipid homeostasis. This study compared the different effects of MWCNTs and HNTs on lipid profile changes in human umbilical vein ECs (HUVECs). The results showed that MWCNTs but not HNTs of the same mass concentrations induced cytotoxicity, ultrastuctural changes and intracellular thiol depletion. Meanwhile, only MWCNTs promoted lipid accumulation due to the induction of ER stress leading to up-regulation of fatty acid synthase (FASN). Interestingly, lipidomics results showed that the main lipid classes induced by MWCNTs but not HNTs were ceramide (Cer) and phosphatidylinositol (PI), with most of the lipid classes unaltered or even decreased after NM exposure. Then, extra Cer and PI were added to explore the implications of increase of these lipids. Adding Cer promoted the cytotoxicity of MWCNTs to HUVECs, indicating the lipotoxic role of Cer. Whereas adding PI partially increased intracellular NO and decreased interleukin-6 (IL-6) release due to MWCNT exposure, indicating the signaling role of PI. These results indicated novel roles of lipid dysfunction in NM-induced toxicity to ECs, even though ECs are not the professional cells for controlling lipid homeostasis.

Long-Term Exposure to Nanosized TiO2 Triggers Stress Responses and Cell Death Pathways in Pulmonary Epithelial Cells

There is little in vitro data available on long-term effects of TiO₂ exposure. Such data are important for improving the understanding of underlying mechanisms of adverse health effects of TiO₂. Here, we exposed pulmonary epithelial cells to two doses (0.96 and 1.92 µg/cm²) of TiO₂ for 13 weeks and effects on cell cycle and cell death mechanisms, i.e., apoptosis and autophagy were determined after 4, 8 and 13 weeks of exposure. Changes in telomere length, cellular protein levels and lipid classes were also analyzed at 13 weeks of exposure. We observed that the TiO₂ exposure increased the fraction of cells in G1-phase and reduced the fraction of cells in G2-phase, which was accompanied by an increase in the fraction of late apoptotic/necrotic cells. This corresponded with an induced expression of key apoptotic proteins i.e., BAD and BAX, and an accumulation of several lipid classes involved in cellular stress and apoptosis. These findings were further supported by quantitative proteome profiling data showing an increase in proteins involved in cell stress and genomic maintenance pathways following TiO₂ exposure. Altogether, we suggest that cell stress response and cell death pathways may be important molecular events in long-term health effects of TiO₂.

Investigating biological effects of multidimensional carboxylated carbon-based nanomaterials on human lung A549 cells revealed via non-targeted metabolomics approach

The biological responses of multidimensional carboxylated carbon-based nanomaterials (c-CBNs), including carboxylated graphene, carbon nanotube, and fullerene, on human lung A549 cells were investigated by using metabolomics technology. The structure and components of c-CBNs were characterized, and their biological effects were evaluated through cell apoptosis and viability analysis. Additionally, the metabolomics analysis of the nanomaterial-cell interaction system was performed using the established platform combining liquid chromatography-mass spectrometry (LC-MS) with the bioinformatics system. Results revealed that all tested c-CBNs demonstrated some biological effects in our cell model. However, significant metabolomic alterations induced by c-CBNs were also observed mainly in amino acids, organic acids, glycerophospholipids, and glycerolipids. Further, under the tested concentrations, the multiple dimensions of c-CBNs played a major role in determining the metabolic process in various interaction modes. This study provides an advanced alternative for evaluating metabolic effects of multidimensional nanomaterials through metabolomics technology considering the association between dimension and metabolic characteristics.

Multi-walled carbon nanotubes (MWCNTs) transformed THP-1 macrophages into foam cells: Impact of pulmonary surfactant component dipalmitoylphosphatidylcholine

Pulmonary surfactant or its components can function as barriers toward nanomaterials (NMs) entering pulmonary systems. However, since pulmonary surfactant mainly consists of lipids, it may be necessary to investigate the effects of co-exposure to NMs and pulmonary surfactant or its components on lipid metabolism and related signaling pathways. Recently we found that multi-walled carbon nanotubes (MWCNTs) transformed THP-1 macrophages into lipid-laden foam cells via ER stress pathway. Here this study further investigated the impact of pulmonary surfactant component dipalmitoylphosphatidylcholine (DPPC) on this process. Up to 64 μg/mL hydroxylated or carboxylated MWCNTs induced lipid accumulation and IL-6 release in THP-1 macrophages, accompanying with increased oxidative stress and p-chop proteins (biomarker for ER stress). Incubation with 100 μg/mL DPPC led to MWCNT surface coating but did not significantly alter MWCNT internalization, lipid burden or IL-6 release. However, lipidomics indicated that DPPC altered lipid profliles in MWCNT-exposed cells. DPPC also led to a higher level of de novo lipogenesis regulator FASN in cells exposed to hydroxylated MWCNTs, as well as a higher level of p-chop and scavenger receptor MSR1 in cells exposed to carboxylated MWCNTs. Combined, DPPC did not significantly affect MWCNT-induced lipid accumulation but altered lipid components and ER stress in macrophages.

Phospholipids modifications in human hepatoma cell lines (HepG2) exposed to silver and iron oxide nanoparticles

Metallic nanoparticles such as silver (Ag NPs) and iron oxide (Fe₃O₄ NPs) nanoparticles are high production volume materials due to their applications in various consumer products, and in nanomedicine. However, their inherent toxicities to human cells remain a challenge. The present study was aimed at combining lipidomics data with common phenotypically-based toxicological assays to gain better understanding into cellular response to Ag NPs and Fe₃O₄ NPs exposure. HepG2 cells were exposed to different concentrations (3.125, 6.25, 12.5, 25, 50 and 100 µg/ml) of the nanoparticles for 24 h, after which they were assayed for toxic effects using toxicological assays like cytotoxicity, mutagenicity, apoptosis and oxidative stress. The cell membrane phospholipid profile of the cells was also performed using shotgun tandem mass spectrometry. The results showed that nanoparticles exposure resulted in concentration-dependent cytotoxicity as well as reduced cytokinesis-block proliferation index (CBPI). Also, there was an increase in the production of ROS and superoxide anions in exposed cells compared to the negative control. The lipidomics data revealed that nanoparticles exposure caused a modulation of the phospholipidome of the cells. A total of 155 lipid species were identified, out of which the fold changes of 23 were significant. The high number of differentially changed phosphatidylcholine species could be an indication that inflammation is one of the major mechanisms of toxicity of the nanoparticles to the cells.

Distinct autophagy-apoptosis related pathways activated by Multi-walled (NM 400) and Single-walled carbon nanotubes (NIST-SRM2483) in human bronchial epithelial (16HBE14o-) cells

Given the recent development in the field of particle and fibre toxicology, parallels have been drawn between Carbon nanotubes (CNTs) and asbestos. It is now established that both multi-walled (MWCNTs) and single-walled (SWCNTs) carbon nanotubes might contribute to pulmonary disease. Although multiple mechanisms might be involved in CNT induced pathogenesis, systematic understanding of the relationship between different CNT exposure (MWCNT vs SWCNT) and autophagy/ apoptosis/ necrosis, in human lung epithelial cells remains limited. In this study, we demonstrate that exposure to MWCNT (NM-400), but not SWCNT (NIST-SRM2483), leads to an autophagic response after acute exposure (24 h). MWCNT exposure was characterized by an increase in anti-apoptotic BCL2, downregulation of executor Caspase-3/7 and increase in expression of genes from the autophagy machinery. For SWCNT exposure however, we observed an overexpression of executor Caspase-3/7 and upregulation of pro-apoptotic BAX; enrichment for processes like cornification, apoptotic process, cell differentiation from proteomic analysis. These results clearly indicate a major difference in the pathways initiated by the CNTs, in vitro. While the present study design provides mechanistic understanding after an acute exposure for the tested CNTs, we believe that the information obtained here would have relevance in better understanding of CNT toxicity and pathogenesis in general.

Biological monitoring of workers exposed to engineered nanomaterials

As the number of nanomaterial workers increase there is need to consider whether biomonitoring of exposure should be used as a routine risk management tool. Currently, no biomonitoring of nanomaterials is mandated by authoritative or regulatory agencies. However, there is a growing knowledge base to support such biomonitoring, but further research is needed as are investigations of priorities for biomonitoring. That research should be focused on validation of biomarkers of exposure and effect. Some biomarkers of effect are generally nonspecific. These biomarkers need further interpretation before they should be used. Overall biomonitoring of nanomaterial workers may be important to supplement risk assessment and risk management efforts.