An ancestral molecular response to nanomaterial particulates

G. del Giudice; A. Serra; L. A. Saarimäki; K. Kotsis; I. Rouse; S. A. Colibaba; K. Jagiello; A. Mikolajczyk; M. Fratello; A. G. Papadiamantis; N. Sanabria; M. E. Annala; J. Morikka; P.A.S. Kinaret; E. Voyiatzis; G. Melagraki; A. Afantitis; K. Tämm; T. Puzyn; M. Gulumian; V. Lobaskin; I. Lynch; A. Federico; D. Greco

doi:10.1038/s41565-023-01393-4

An ancestral molecular response to nanomaterial particulates

G. del Giudice, A. Serra, L. A. Saarimäki, K. Kotsis, I. Rouse, S. A. Colibaba, K. Jagiello, A. Mikolajczyk, M. Fratello, A. G. Papadiamantis, N. Sanabria, M. E. Annala, J. Morikka, P.A.S. Kinaret, E. Voyiatzis, G. Melagraki, A. Afantitis, K. Tämm, T. Puzyn, M. GulumianV. Lobaskin, I. Lynch, A. Federico, D. Greco^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

The 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.

Original language	English
Journal	Nature Nanotechnology
Early online date	8 May 2023
DOIs	https://doi.org/10.1038/s41565-023-01393-4
Publication status	E-pub ahead of print - 8 May 2023

Bibliographical note

Funding Information:
This study was supported by the Academy of Finland project UNICAST NANO (322761) (D.G.), European Research Council (ERC) programme, Consolidator project ARCHIMEDES (101043848) (D.G), EU Horizon 2020 project NanoSolveIT (814572) (D.G) and NanoInformaTIX (814426) (D.G). A.S. and A.F. were supported by the Tampere Institute for Advanced Study. K.J. was supported by the National Science Center, Poland (TransNano project, grant number UMO-2020/37/B/ST5/01894). A.M. was supported by European Union’s Horizon 2020 research and innovation programme (DIAGONAL Project, grant number 953152 and NanoInformaTIX project, grant number 814426). K.K. and V.L. were supported by Science Foundation Ireland (Bio-Interface project, Grant No. 16/IA/4506). D.G. thanks the principal investigators of the research cluster of Cell and Molecular Physiology (CMP) of the faculty of Medicine and Health Technology (MET) of Tampere University for the insightful discussion.

Publisher Copyright:
© 2023, The Author(s).

ASJC Scopus subject areas

Bioengineering
Atomic and Molecular Physics, and Optics
Biomedical Engineering
General Materials Science
Condensed Matter Physics
Electrical and Electronic Engineering

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del Giudice, G., Serra, A., Saarimäki, L. A., Kotsis, K., Rouse, I., Colibaba, S. A., Jagiello, K., Mikolajczyk, A., Fratello, M., Papadiamantis, A. G., Sanabria, N., Annala, M. E., Morikka, J., Kinaret, P. A. S., Voyiatzis, E., Melagraki, G., Afantitis, A., Tämm, K., Puzyn, T., ... Greco, D. (2023). An ancestral molecular response to nanomaterial particulates. Nature Nanotechnology. Advance online publication. https://doi.org/10.1038/s41565-023-01393-4

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title = "An ancestral molecular response to nanomaterial particulates",

abstract = "The 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.",

author = "{del Giudice}, G. and A. Serra and Saarim{\"a}ki, {L. A.} and K. Kotsis and I. Rouse and Colibaba, {S. A.} and K. Jagiello and A. Mikolajczyk and M. Fratello and Papadiamantis, {A. G.} and N. Sanabria and Annala, {M. E.} and J. Morikka and P.A.S. Kinaret and E. Voyiatzis and G. Melagraki and A. Afantitis and K. T{\"a}mm and T. Puzyn and M. Gulumian and V. Lobaskin and I. Lynch and A. Federico and D. Greco",

note = "Funding Information: This study was supported by the Academy of Finland project UNICAST NANO (322761) (D.G.), European Research Council (ERC) programme, Consolidator project ARCHIMEDES (101043848) (D.G), EU Horizon 2020 project NanoSolveIT (814572) (D.G) and NanoInformaTIX (814426) (D.G). A.S. and A.F. were supported by the Tampere Institute for Advanced Study. K.J. was supported by the National Science Center, Poland (TransNano project, grant number UMO-2020/37/B/ST5/01894). A.M. was supported by European Union{\textquoteright}s Horizon 2020 research and innovation programme (DIAGONAL Project, grant number 953152 and NanoInformaTIX project, grant number 814426). K.K. and V.L. were supported by Science Foundation Ireland (Bio-Interface project, Grant No. 16/IA/4506). D.G. thanks the principal investigators of the research cluster of Cell and Molecular Physiology (CMP) of the faculty of Medicine and Health Technology (MET) of Tampere University for the insightful discussion. Publisher Copyright: {\textcopyright} 2023, The Author(s).",

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del Giudice, G, Serra, A, Saarimäki, LA, Kotsis, K, Rouse, I, Colibaba, SA, Jagiello, K, Mikolajczyk, A, Fratello, M, Papadiamantis, AG, Sanabria, N, Annala, ME, Morikka, J, Kinaret, PAS, Voyiatzis, E, Melagraki, G, Afantitis, A, Tämm, K, Puzyn, T, Gulumian, M, Lobaskin, V, Lynch, I, Federico, A & Greco, D 2023, 'An ancestral molecular response to nanomaterial particulates', Nature Nanotechnology. https://doi.org/10.1038/s41565-023-01393-4

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AU - Colibaba, S. A.

AU - Jagiello, K.

AU - Mikolajczyk, A.

AU - Fratello, M.

AU - Papadiamantis, A. G.

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AU - Annala, M. E.

AU - Morikka, J.

AU - Kinaret, P.A.S.

AU - Voyiatzis, E.

AU - Melagraki, G.

AU - Afantitis, A.

AU - Tämm, K.

AU - Puzyn, T.

AU - Gulumian, M.

AU - Lobaskin, V.

AU - Lynch, I.

AU - Federico, A.

AU - Greco, D.

N1 - Funding Information: This study was supported by the Academy of Finland project UNICAST NANO (322761) (D.G.), European Research Council (ERC) programme, Consolidator project ARCHIMEDES (101043848) (D.G), EU Horizon 2020 project NanoSolveIT (814572) (D.G) and NanoInformaTIX (814426) (D.G). A.S. and A.F. were supported by the Tampere Institute for Advanced Study. K.J. was supported by the National Science Center, Poland (TransNano project, grant number UMO-2020/37/B/ST5/01894). A.M. was supported by European Union’s Horizon 2020 research and innovation programme (DIAGONAL Project, grant number 953152 and NanoInformaTIX project, grant number 814426). K.K. and V.L. were supported by Science Foundation Ireland (Bio-Interface project, Grant No. 16/IA/4506). D.G. thanks the principal investigators of the research cluster of Cell and Molecular Physiology (CMP) of the faculty of Medicine and Health Technology (MET) of Tampere University for the insightful discussion. Publisher Copyright: © 2023, The Author(s).

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AB - The 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.

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An ancestral molecular response to nanomaterial particulates

Abstract

Bibliographical note

ASJC Scopus subject areas

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