An ancestral molecular response to nanomaterial particulates

dc.contributor.authorDel Giudice, G.
dc.contributor.authorSerra, A.
dc.contributor.authorSaarimaki, L.A.
dc.contributor.authorKotsis, K.
dc.contributor.authorRouse, I.
dc.contributor.authorColibaba, S.A.
dc.contributor.authorJagiello, K.
dc.contributor.authorMikolajczyk, A.
dc.contributor.authorFratello, M.
dc.contributor.authorPapadiamantis, A.G.
dc.contributor.authorSanabria, N.
dc.contributor.authorAnnala, M.E.
dc.contributor.authorMorikka, J.
dc.contributor.authorKinaret, P.A.S.
dc.contributor.authorVoyiatzis, E.
dc.contributor.authorMelagraki, G.
dc.contributor.authorAfantitis, A.
dc.contributor.authorTamm, K.
dc.contributor.authorPuzyn, T.
dc.contributor.authorGulumian, M.
dc.contributor.authorLobaskin, V.
dc.contributor.authorLynch, I.
dc.contributor.authorFederico, A.
dc.contributor.authorGreco, D.
dc.date.accessioned2024-09-03T12:24:12Z
dc.date.available2024-09-03T12:24:12Z
dc.date.issued2023-08
dc.descriptionDATA AVAILABILITY : The pre-processed version of the transcriptomic datasets included in the discovery datasets, that is, ENM exposures of human and mouse samples, have been previously deposited at https://zenodo.org/ record/3949890#.YlPUri0RqH0. The original datasets can be accessed at Array Express (https://www.ebi.ac.uk/biostudies/arrayexpress) with the entry code EMTAB6396 and at GEO (https://www.ncbi.nlm.nih. gov/) under accession numbers GSE103101, GSE112780, GSE113088, GSE117056, GSE122197, GSE127773, GSE146708, GSE148705, GSE157266, GSE16727, GSE17676, GSE19487, GSE20692, GSE29042, GSE35193, GSE39330, GSE41041, GSE42066, GSE42067, GSE42068, GSE43515, GSE45322, GSE45598, GSE4567, GSE46998, GSE46999, GSE50176, GSE51186, GSE51417, GSE51421, GSE51636, GSE53700, GSE55286, GSE55349, GSE56324, GSE56325, GSE60797, GSE60798, GSE60799, GSE60800, GSE61366, GSE62253, GSE62769, GSE63552, GSE63806, GSE68036, GSE75429, GSE79766, GSE81564, GSE81565, GSE81566, GSE81567, GSE81568, GSE81569, GSE82062, GSE84982, GSE85711, GSE88786, GSE92563, GSE92900, GSE92987, GSE96720, GSE98236 and GSE99929. Transcriptomic datasets used for the eco-toxicological analysis are freely available at GEO under accession numbers GSE80461, GSE32521, GSE70509, GSE73427, GSE77148, GSE41333 and GSE47662. Transcriptomic datasets of small molecule exposure (Open-TG GATEs) have been downloaded from https://dbarchive.biosciencedbc.jp/en/ open-tggates/download.html in November 2020. Functional data were downloaded from https://www.gsea-msigdb.org/gsea/msigdb/ version 7.2. All the other relevant data and data supporting the findings of this study have been deposited in the online Zenodo repository (https://doi.org/10.5281/zenodo.7674574).en_US
dc.descriptionCODE AVAILABILITY : All the relevant and custom code supporting the findings of this study has been deposited in the online Zenodo repository (https://DOI. org/10.5281/zenodo.7674574) and on Github at https://github.com/ fhaive/metanalysis_toxicogenomic_data.en_US
dc.description.abstractThe varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that impact the transcriptomic response. Analysis identifies deregulation of immune functions as a prominent response across different exposure studies. Looking at the promoter regions of these genes, a set of binding sites for zinc finger transcription factors C2H2, involved in cell stress responses, protein misfolding and chromatin remodelling and immunomodulation, is identified. The model can be used to explain the outcomes of mechanism of action and is observed across a range of species indicating this is a conserved part of the innate immune system.en_US
dc.description.departmentSchool of Health Systems and Public Health (SHSPH)en_US
dc.description.librarianam2024en_US
dc.description.sdgSDG-03:Good heatlh and well-beingen_US
dc.description.sponsorshipThe Academy of Finland project UNICAST NANO; European Research Council (ERC) programme; Consolidator project ARCHIMEDES; EU Horizon 2020 project NanoSolveIT; NanoInformaTIX; the Tampere Institute for Advanced Study; the National Science Center, Poland; European Union’s Horizon 2020 research and innovation programme; and Science Foundation Ireland. Open access funding provided by Tampere University including Tampere University Hospital, Tampere University of Applied Sciences (TUNI).en_US
dc.description.urihttps://www.nature.com/nnano/en_US
dc.identifier.citationDel Giudice, G., Serra, A., Saarimaki, L.A. et al. 2023, 'An ancestral molecular response to nanomaterial particulates', Nature Nanotechnology, vol. 18, pp. 957-966. https://DOI.org/10.1038/s41565-023-01393-4.en_US
dc.identifier.issn1748-3387 (print)
dc.identifier.issn1748-3395 (online)
dc.identifier.other10.1038/s41565-023-01393-4
dc.identifier.urihttp://hdl.handle.net/2263/97995
dc.language.isoenen_US
dc.publisherNature Researchen_US
dc.rights© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.subjectTranscriptomicen_US
dc.subjectNanoparticlesen_US
dc.subjectMechanismen_US
dc.subjectInnate immune systemen_US
dc.subjectSDG-03: Good health and well-beingen_US
dc.titleAn ancestral molecular response to nanomaterial particulatesen_US
dc.typeArticleen_US

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