{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T08:06:28Z","timestamp":1791273988575,"version":"4.1.0"},"reference-count":68,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2014,8,28]],"date-time":"2014-08-28T00:00:00Z","timestamp":1409184000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJERPH"],"abstract":"<jats:p>Silica (SiO2) nanoparticles (NPs) have found extensive applications in industrial manufacturing, biomedical and biotechnological fields. Therefore, the increasing exposure to such ultrafine particles requires studies to characterize their potential cytotoxic  effects in order to provide exhaustive information to assess the impact of nanomaterials on human health. The understanding of the biological processes involved in the development and maintenance of a variety of pathologies is improved by genome-wide approaches,  and in this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. In this work we show how the use of a combination of  gene-by-gene and gene set analyses can enhance the interpretation of results of in vitro treatment of A549 cells with Ludox\u00ae colloidal amorphous silica nanoparticles.  By gene-by-gene and gene set analyses, we evidenced a specific cell response in relation to NPs size and elapsed time after treatment, with the smaller NPs (SM30) having higher impact on inflammatory and apoptosis processes than the bigger ones. Apoptotic process appeared to be activated by the up-regulation of the initiator genes TNFa and IL1b and by ATM. Moreover, our analyses evidenced that cell treatment with Ludox\u00d2 silica nanoparticles activated the matrix metalloproteinase genes MMP1, MMP10 and MMP9. The information derived from this study can be informative about the cytotoxicity of Ludox\u00ae and other similar colloidal amorphous silica NPs prepared by solution processes.<\/jats:p>","DOI":"10.3390\/ijerph110908867","type":"journal-article","created":{"date-parts":[[2014,8,28]],"date-time":"2014-08-28T10:37:35Z","timestamp":1409222255000},"page":"8867-8890","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Altered Gene Transcription in Human Cells Treated with Ludox\u00ae Silica Nanoparticles"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4372-7889","authenticated-orcid":false,"given":"Caterina","family":"Fede","sequence":"first","affiliation":[{"name":"Department of Biology, University of Padova, Via G. Colombo 3, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caterina","family":"Millino","sequence":"additional","affiliation":[{"name":"Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative\u2014CRIBI Biotechnology Centre, University of Padova, Via U. Bassi 58\/B, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beniamina","family":"Pacchioni","sequence":"additional","affiliation":[{"name":"Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative\u2014CRIBI Biotechnology Centre, University of Padova, Via U. Bassi 58\/B, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Celegato","sequence":"additional","affiliation":[{"name":"Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative\u2014CRIBI Biotechnology Centre, University of Padova, Via U. Bassi 58\/B, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiara","family":"Compagnin","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Via G. Colombo 3, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Martini","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Via G. Colombo 3, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Selvestrel","sequence":"additional","affiliation":[{"name":"Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrizio","family":"Mancin","sequence":"additional","affiliation":[{"name":"Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Celotti","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Via G. Colombo 3, Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerolamo","family":"Lanfranchi","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Via G. 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