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4. Kinome screen of ferroptosis reveals a novel role of ATM in regulating iron metabolism.

Author

Chen, Po-Han, Wu, Jianli, Lin, Chao-Chieh, Pan, Samuel, Bossa, Nathan, Xu, Yitong, Yang, Wen-Hsuan, Mathey-Prevot, Bernard, Chi, Jen-Tsan, and Ding, Chien-Kuang

Subjects
Ataxia Telangiectasia Mutated Proteins, Cation Transport Proteins, Cell Line, Tumor, Cystine, Ferroptosis, Gene Expression Regulation, Humans, Iron, Models, Biological, Piperazines, Protein Kinases, Proteome, RNA, Messenger, Transcription, Genetic
Abstract

Ferroptosis is a specialized iron-dependent cell death that is associated with lethal lipid peroxidation. Modulation of ferroptosis may have therapeutic potential since it has been implicated in various human diseases as well as potential antitumor activities. However, much remains unknown about the underlying mechanisms and genetic determinants of ferroptosis. Given the critical role of kinases in most biological processes and the availability of various kinase inhibitors, we sought to systemically identify kinases essential for ferroptosis. We performed a forward genetic-based kinome screen against ferroptosis in MDA-MB-231 cells triggered by cystine deprivation. This screen identified 34 essential kinases involved in TNFα and NF-kB signaling. Unexpectedly, the DNA damage response serine/threonine kinase ATM (mutated in Ataxia-Telangiectasia) was found to be essential for ferroptosis. The pharmacological or genetic inhibition of ATM consistently rescued multiple cancer cells from ferroptosis triggered by cystine deprivation or erastin. Instead of the canonical DNA damage pathways, ATM inhibition rescued ferroptosis by increasing the expression of iron regulators involved in iron storage (ferritin heavy and light chain, FTH1 and FTL) and export (ferroportin, FPN1). The coordinated changes of these iron regulators during ATM inhibition resulted in a lowering of labile iron and prevented the iron-dependent ferroptosis. Furthermore, we found that ATM inhibition enhanced the nuclear translocation of metal-regulatory transcription factor 1 (MTF1), responsible for regulating expression of Ferritin/FPN1 and ferroptosis protection. Genetic depletion of MTF-1 abolished the regulation of iron-regulatory elements by ATM and resensitized the cells to ferroptosis. Together, we have identified an unexpected ATM-MTF1-Ferritin/FPN1 regulatory axis as novel determinants of ferroptosis through regulating labile iron levels.

Published
2020

10. The role of FAIR nanosafety data and nanoinformatics in achieving the UN Sustainable Development Goals: the NanoCommons experience

Author

Alfaro Serrano, Beatriz, primary, Gheorghe, L. Cristiana, additional, Exner, Thomas, additional, Resch, Susanne, additional, Wolf, Clemens, additional, Himly, Martin, additional, Falk, Andreas, additional, Bossa, Nathan, additional, Vazquez, Socorro, additional, Papadiamantis, Anastasios, additional, Afantitis, Antreas, additional, Melagraki, Georgia, additional, Maier, Dieter, additional, Sarimveis, Haralambos, additional, Willighagen, Egon, additional, Lobaskin, Vladimir, additional, Oldfield, Jon, additional, and Lynch, Iseult, additional

Published
2024
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11. 5 Risk screening tools for engineered nanomaterials

Author

Grieger, Khara, primary, Isigonis, Panagiotis, additional, Franken, Remy, additional, Wigger, Henning, additional, Bossa, Nathan, additional, Janer, Gemma, additional, Rycroft, Taylor, additional, Kennedy, Alan J., additional, and Hansen, Steffen Foss, additional

Published
2021
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12. New frontiers and outlook

Author

Ortiz, Juan M., primary, Salinas-Rodríguez, Sergio G., additional, Bossa, Nathan, additional, Borràs, Eduard, additional, Arévalo, Juan, additional, and Esteve-Núñez, Abraham, additional

Published
2021
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17. Metadata stewardship in nanosafety research: learning from the past, preparing for an “on-the-fly” FAIR future

Author

Exner, Thomas E., primary, Papadiamantis, Anastasios G., additional, Melagraki, Georgia, additional, Amos, Jaleesia D., additional, Bossa, Nathan, additional, Gakis, Georgios P., additional, Charitidis, Costas A., additional, Cornelis, Geert, additional, Costa, Anna L., additional, Doganis, Philip, additional, Farcal, Lucian, additional, Friedrichs, Steffi, additional, Furxhi, Irini, additional, Klaessig, Frederick C., additional, Lobaskin, Vladimir, additional, Maier, Dieter, additional, Rumble, John, additional, Sarimveis, Haralambos, additional, Suarez-Merino, Blanca, additional, Vázquez, Socorro, additional, Wiesner, Mark R., additional, Afantitis, Antreas, additional, and Lynch, Iseult, additional

Published
2023
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23. Risk screening tools for engineered nanomaterials

Author

Grieger, Khara, Isigonis, Panagiotis, Franken, Remy, Wigger, Henning, Bossa, Nathan, Ganer, Janer, Rycroft, Taylor, Kennedy, Alan J., and Hansen, Steffen Foss

Subjects
Nano-enabled products, Risk analysis, Risk screening tools, Decisionmaking, Risk assessment, Risk-benefit, Nanomaterials
Published
2021
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24. D6.1 - A workflow and checklist for experimental design and informatics workflow for risk assessment for use in WP9

Author

Sarimveis, Haralambos, Liampa, Irene, Tsiros, Periklis, Doganis, Philip, Karatzas, Pantelis, Varsou, Dimitra-Danai, Bossa, Nathan, and Lynch, Iseult

Subjects
Informatics, H2020, NanoCommons, Experimental design, Workflows, Risk assessment
Abstract

The development of safe and effective nanomaterials (NMs) is highly important for both industry and regulatory agencies, especially considering their continuously growing economic potential, and their wide range of industrial, consumer, medical, and diagnostic NM applications. The basic methodology for performing risk assessment (RA) for NMs is similar to the philosophy used for conventional chemicals RA, i.e. compare the level of exposure with the hazard assessment. However, exposure and hazard assessments for NMs are more challenging than for conventional chemicals, because of the complex NM structures, which are dynamic as many of their properties are context-dependent (extrinsic), and can be modified or evolve during their life-cycle. In this deliverable (D6.1) we describe a number of computationally oriented tools and methodologies that can be used for exposure modelling, hazard prediction and eventually for RA. Additionally, we present checklists and best practices for the most efficient use of the tools and workflows, as well as optimal combinations of these tools for performing RA for NMs. We report here on the current status of development and integration of existing RA tools into the NanoCommons knowledge infrastructure, and outline the strategy that will be used in the subsequent months of the project for further development, for supporting case studies to demonstrate the utility of the RA tools, and Transnational Access (TA) activities.

Published
2020
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25. Comparative Impact of SiO2 and TiO2 Nanofillers on the Performance of Thin Film Nanocomposite Membranes

Author

Urper-Bayram, Gulsum Melike, Bossa, Nathan, Warsinger, David M, Koyuncu, Ismail, and Wiesner, Mark

Subjects
separation techniques, nanocrystals, nanowires, membranes, morphology, nanoparticles, polyamides
Abstract

Nanoparticle (NP) additions can substantially improve the performance of reverse osmosis and nanofiltration polyamide (PA) membranes. However, the relative impacts of leading additives are poorly understood. In this study, we compare the effects of TiO2 and SiO2 NPs as nanofillers in PA membranes with respect to permeate flux and the rejection of organic matter (OM) and salts. Thin‐film nanocomposite (TFN) PA membranes were fabricated using similarly sized TiO2 15 nm and SiO2 (10 – 20 nm) NPs, introduced at four different NP concentrations (0.01, 0.05, 0.2, and 0.5% w/v). Compared with PA membranes fabricated without NPs, membranes fabricated with nanofillers improved membranes hydrophilicity, membrane porosity, and consequently the permeability. Permeability was increased by 24 and 58% with the addition of TiO2 and SiO2, respectively. Rejection performance and fouling behavior of the membranes were examined with salt (MgSO4 and NaCl) and OM (humic acid [HA] and tannic acid [TA]). The addition of TiO2 and SiO2 nanofillers to the PA membranes improved the permeability of these membranes and also increased the rejection of MgSO4, especially for TiO2 membranes. The addition of TiO2 and SiO2 to the membranes exhibited a higher flux and lower flux decline ratio than the control membrane in OM solution filtration. TFN membranes' HA and TA rejections were at least 77 and 71%, respectively. The surface change properties of NPs appear to play a dominant role in determining their effects as nanofillers in the composite membrane matrix through a balance of changes produced in membrane pore size and membrane hydrophilicity.

Published
2020

26. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Author

Lynch, Iseult, Anreas Afantitis, Exner, Thomas, Himley, Martin, Lobaskin, Vladimir, Doganis, Phillip, Maier, Dieter, Sanabria, Natasha, Rybinska-Fryca, Anna, Gromelski, Maciej, Puzyn, Tomasz, Willighagen, Egon, Johnston, Blair, Gulumian, Mary, Matzke, Marianne, Etxabe, Amaia Green, Bossa, Nathan, Serra, Angela, Liampa, Irene, Harper, Stacey, Tämm, Kaido, Jensen, Alexander CØ, Kohonen, Pekka, Slater, Luke, Tsoumanis, Andreas, Greco, Dario, Winkler, David, Haralambos Sarimveis, and Melagraki, Georgia

Subjects
FOS: Nanotechnology, 100708 Nanomaterials
Abstract

Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analysed issues involved in developing an InChI for NMs (NInChI). The layers needed to captureNMstructures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a “nano” extension to the InChI standard.

Published
2020
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28. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Author

Lynch, Iseult, primary, Afantitis, Antreas, additional, Exner, Thomas, additional, Himly, Martin, additional, Lobaskin, Vladimir, additional, Doganis, Philip, additional, Maier, Dieter, additional, Sanabria, Natasha, additional, Papadiamantis, Anastasios G., additional, Rybinska-Fryca, Anna, additional, Gromelski, Maciej, additional, Puzyn, Tomasz, additional, Willighagen, Egon, additional, Johnston, Blair D., additional, Gulumian, Mary, additional, Matzke, Marianne, additional, Green Etxabe, Amaia, additional, Bossa, Nathan, additional, Serra, Angela, additional, Liampa, Irene, additional, Harper, Stacey, additional, Tämm, Kaido, additional, Jensen, Alexander CØ, additional, Kohonen, Pekka, additional, Slater, Luke, additional, Tsoumanis, Andreas, additional, Greco, Dario, additional, Winkler, David A., additional, Sarimveis, Haralambos, additional, and Melagraki, Georgia, additional

Published
2020
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30. Differential Reactivity of Copper- and Gold-Based Nanomaterials Controls Their Seasonal Biogeochemical Cycling and Fate in a Freshwater Wetland Mesocosm

Author

Avellan, Astrid, primary, Simonin, Marie, additional, Anderson, Steven M., additional, Geitner, Nicholas K., additional, Bossa, Nathan, additional, Spielman-Sun, Eleanor, additional, Bernhardt, Emily S., additional, Castellon, Benjamin T., additional, Colman, Benjamin P., additional, Cooper, Jane L., additional, Ho, Mengchi, additional, Hochella, Michael F., additional, Hsu-Kim, Heileen, additional, Inoue, Sayako, additional, King, Ryan S., additional, Laughton, Stephanie, additional, Matson, Cole W., additional, Perrotta, Brittany G., additional, Richardson, Curtis J., additional, Unrine, Jason M., additional, Wiesner, Mark R., additional, and Lowry, Gregory V., additional

Published
2020
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36. Application and testing of risk screening tools for nanomaterial risk analysis

Author

Grieger, Khara Deanne, Bossa, Nathan, Levis, James W., von Borries, Kerstin Johanna Felicitas, Strader, Phillip, Cuchiara, Maude, Hendren, Christine Ogilvie, Hansen, Steffen Foss, Jones, Jacob L., Grieger, Khara Deanne, Bossa, Nathan, Levis, James W., von Borries, Kerstin Johanna Felicitas, Strader, Phillip, Cuchiara, Maude, Hendren, Christine Ogilvie, Hansen, Steffen Foss, and Jones, Jacob L.

Abstract

The field of engineered nanomaterial (ENM) risk analysis has matured significantly in the past decade. While there is a suite of new, emerging tools to evaluate ENM risks and make decisions regarding these risks, there has not yet been thorough testing of these tools. This analysis applies and tests three risk screening tools (NanoRiskCat, LICARA nanoSCAN, NanoGRID) using a common case study focused on ENMs designed for water treatment technologies, compares results generated, and highlights key lessons learned and best practices for stakeholders involved in developing and/or applying ENM risk screening tools. NanoRiskCat was found to be most useful for providing a visual aid to characterize the potential exposure and health impact profiles of the ENMs, while LICARA nanoSCAN was most useful for providing guidance on proceeding with ENM-enabled innovations. NanoGRID was helpful for characterizing data on potential ENM exposure and hazards and providing detailed guidance for subsequent laboratory-based testing. At the same time, several key challenges were identified during tool application and testing phases, ranging from minor inconveniences to more complex, foundational issues. Key lessons learned and potential best practices gleaned from this analysis include: i) risk screening tools can be used together in a complementary manner; ii) risk managers and other users should be clear on the selection of underlying data and impacts on results; iii) multidisciplinary teams are essential for tool completion; and iv) continued testing and validation of emerging risk analysis tools for ENMs is a continued research need.

Published
2018

37. Comparative impact of SiO2 and TiO2 nanofillers on the performance of thin‐film nanocomposite membranes.

Author

Urper‐Bayram, Gulsum Melike, Bossa, Nathan, Warsinger, David M., Koyuncu, Ismail, and Wiesner, Mark

Subjects
REVERSE osmosis, NANOCOMPOSITE materials, HUMIC acid, MEMBRANE permeability (Biology), ORGANIC compounds, TANNINS
Abstract

Nanoparticle (NP) additions can substantially improve the performance of reverse osmosis and nanofiltration polyamide (PA) membranes. However, the relative impacts of leading additives are poorly understood. In this study, we compare the effects of TiO2 and SiO2 NPs as nanofillers in PA membranes with respect to permeate flux and the rejection of organic matter (OM) and salts. Thin‐film nanocomposite (TFN) PA membranes were fabricated using similarly sized TiO2 15 nm and SiO2 (10 – 20 nm) NPs, introduced at four different NP concentrations (0.01, 0.05, 0.2, and 0.5% w/v). Compared with PA membranes fabricated without NPs, membranes fabricated with nanofillers improved membranes hydrophilicity, membrane porosity, and consequently the permeability. Permeability was increased by 24 and 58% with the addition of TiO2 and SiO2, respectively. Rejection performance and fouling behavior of the membranes were examined with salt (MgSO4 and NaCl) and OM (humic acid [HA] and tannic acid [TA]). The addition of TiO2 and SiO2 nanofillers to the PA membranes improved the permeability of these membranes and also increased the rejection of MgSO4, especially for TiO2 membranes. The addition of TiO2 and SiO2 to the membranes exhibited a higher flux and lower flux decline ratio than the control membrane in OM solution filtration. TFN membranes' HA and TA rejections were at least 77 and 71%, respectively. The surface change properties of NPs appear to play a dominant role in determining their effects as nanofillers in the composite membrane matrix through a balance of changes produced in membrane pore size and membrane hydrophilicity. [ABSTRACT FROM AUTHOR]

Published
2020
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39. Size-Based Differential Transport, Uptake, and Mass Distribution of Ceria (CeO2) Nanoparticles in Wetland Mesocosms

Author

Geitner, Nicholas K., primary, Cooper, Jane L., additional, Avellan, Astrid, additional, Castellon, Benjamin T., additional, Perrotta, Brittany G., additional, Bossa, Nathan, additional, Simonin, Marie, additional, Anderson, Steven M., additional, Inoue, Sayako, additional, Hochella, Michael F., additional, Richardson, Curtis J., additional, Bernhardt, Emily S., additional, Lowry, Gregory V., additional, Ferguson, P. Lee, additional, Matson, Cole W., additional, King, Ryan S., additional, Unrine, Jason M., additional, Wiesner, Mark R., additional, and Hsu-Kim, Heileen, additional

Published
2018
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41. Impacts des produits résiduaires organiques sur la teneur et le comportement des éléments-traces dans les sols. Le point de vue du géochimiste

Author

Doelsch, Emmanuel, Cambier, Philippe, Bravin, Matthieu, Bossa, Nathan, Cazevieille, Patrick, Chataing, Sophie, Chevassus-Rosset, Claire, and Tella, Marie

Subjects
P33 - Chimie et physique du sol, Élément métallique, Résidu, Pollution par l'agriculture, Déchet agricole, Fertilisation, Métal lourd, Matière organique du sol, Toxicité, Matière organique, Propriété physicochimique du sol, Eau du sol, Q70 - Traitement des déchets agricoles, Déchet organique, Utilisation des déchets, Déchet urbain, Cuivre, Biodisponibilité, P02 - Pollution, Modèle mathématique, F04 - Fertilisation
Published
2016

46. Groundwater Chemistry Has a Greater Influence on the Mobility of Nanoparticles Used for Remediation than the Chemical Heterogeneity of Aquifer Media

Author

Micić, Vesna, Bossa, Nathan, Schmid, Doris, Wiesner, Mark R., and Hofmann, Thilo

Abstract

The application of nanoscale zerovalent iron (nano-ZVI) particles for groundwater remediation has spurred research into the influence of the collector heterogeneity on the nano-ZVI mobility. The chemical heterogeneity of surfaces within aquifer media affects their surface charge distribution and their affinity for nano-ZVI. The groundwater chemistry affects the properties of both aquifer surfaces and the nano-ZVI particles. Commercial poly(acrylic acid)-coated nano-ZVI (PAA–nano-ZVI) particles were tested in column experiments using two solution chemistries and silica collectors with different degrees of chemical heterogeneity, achieved by ferrihydrite coating. A porous media filtration model was used to determine the attachment efficiency of PAA–nano-ZVI particles, and the Derjaguin–Landau–Verwey–Overbeek (DLVO) theory was used to describe the interactions between PAA–nano-ZVI particles and the aquifer “collectors”. The mobility of PAA–nano-ZVI particles suspended in ultrapure water depended on the extent of ferrihydrite coating on the collector surfaces. The mobility of PAA–nano-ZVI particles under environmentally relevant conditions was independent of the collector chemical heterogeneity. The size of PAA–nano-ZVI aggregates doubled, inducing gravitational sedimentation and possibly straining as mechanisms of particle deposition. There was no repulsive energy barrier between particles and collectors, and the DLVO theory was unable to explain the observed particle attachment. Our results suggest that the groundwater chemistry has a greater influence on the mobility of PAA–nano-ZVI particles than the collector chemical heterogeneity. A better understanding of polymer adsorption to nanoparticles and its conformation under natural groundwater conditions is needed to further elucidate nanoparticle–collector interactions.

Published
2020
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49. Size-Based Differential Transport, Uptake, and Mass Distribution of Ceria (CeO2) Nanoparticles in Wetland Mesocosms.

Author

Geitner, Nicholas K., Cooper, Jane L., Avellan, Astrid, Castellon, Benjamin T., Perrotta, Brittany G., Bossa, Nathan, Simonin, Marie, Anderson, Steven M., Inoue, Sayako, Hochella Jr., Michael F., Richardson, Curtis J., Bernhardt, Emily S., Lowry, Gregory V., Ferguson, P. Lee, Matson, Cole W., King, Ryan S., Unrine, Jason M., Wiesner, Mark R., and Hsu-Kim, Heileen

Published
2018
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50. Mechanisms limiting the release of TiO2nanomaterials during photocatalytic cement alteration: the role of surface charge and porous network morphologyElectronic supplementary information (ESI) available. See DOI: 10.1039/c8en00700d

Author

Bossa, Nathan, Chaurand, Perrine, Levard, Clément, Vicente, Jérôme, Borschneck, Daniel, Geantet, Christophe, Aguerre-Chariol, Olivier, and Rose, Jérôme

Abstract

Nanomaterials have been widely used in a wide range of manufactured products in order to improve/add new properties. Photocatalytic cement maintains clean and white wall fronts and also provides interesting air pollution-reducing properties due to the photocatalytic activity of incorporated TiO2-NMs. However, despite these environmental benefits, there is evidence of the release of TiO2-NMs during cement use. Therefore, it is crucial to understand the parameters controlling TiO2-NM release. The zeta potentials of TiO2-NMs were investigated from the unaltered core to the cement altered surface using simulated cement pore waters. The mineralogy and chemical composition of the altered layer were investigated using X-ray diffraction (XRD) and micro X-ray fluorescence spectroscopy (micro-XRF). Finally, the pore network morphology was fully analyzed using X-ray computed tomography at both micro and nano-scales (micro and nano-CT) and quantified using 3D morphological software (i-Morph). This study provides evidence that the TiO2-NM release comes from a very thin “active surface layer” (thickness less than 20 μm) where both the cement surface chemistry and the pore network appear to be favorable for the TiO2-NM diffusion. The pore volume connected to the surface with a throat size of ≥1016 nm appears to control and be used as a predictor for TiO2-NM release.

Published
2019
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