Simultaneous transcriptome and proteome analysis of EA.hy926 cells under stress conditions induced by nanomaterials Piotr Komorowski , 1,2,3 Malgorzata Siatkowska, 1 Tomasz Wasiak, 1 Katarzyna Dzialoszy nska, 1,2 Sylwia Kotarba, 4 Kinga Kądziola, 1 Nina Bartoszek, 1 Paulina Sokolowska, 1 Marcin Elgalal, 1,5 Anna Sobol-Pacyniak, 6,7 Krzysztof Makowski, 2,8 Bogdan Walkowiak 1,2,3,8 1 Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Lodz, Poland 2 Department of Biophysics, Institute of Materials Science, Lodz University of Technology, Lodz, Poland 3 BioTechMed Advanced Technology Centre, Lodz, Poland 4 Biosensor and Organic Electronics Laboratory, Bionanopark Ltd., Lodz, Poland 5 Department of Diagnostic Imaging, Radiation and Isotope Therapy, Medical University of Lodz, Lodz, Poland 6 Department of Internal Medicine and Diabetology, Medical University of Lodz, Lodz, Poland 7 Norbert Barlicki Memorial Teaching Hospital No. 1, Lodz, Poland 8 Industrial Biotechnology Laboratory, Bionanopark Ltd, Lodz, Poland Received 21 January 2018; revised 7 June 2018; accepted 27 June 2018 Published online 00 Month 2018 in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/jbm.b.34195 Abstract: Today, the extensive and constantly growing number of applications in the field of nanotechnology poses a lot of ques- tions about the potential toxicity of nanomaterials (NMs) toward cells of different origins. In our work we employed the tools of molecular biology to evaluate changes that occur in human endo- thelial cells at the transcriptomic and proteomic level, following 24 h of exposure to three different classes of NMs. Using microar- ray technology, we demonstrated that 24 h of exposure to silver nanoparticles (SNPs), multiwalled carbon nanotubes (MWCNTs) and polyamidoamine dendrimers (PAMAMs) leads to changes in 299, 1271, and 431 genes, respectively, influencing specific molecular pathways. The 2D-DIGE and mass spectrometry analy- sis revealed that differentially expressed proteins were involved in numerous cellular processes, for example, cytoskeletal reorga- nization, cell growth and proliferation, or response to stress. Both, transcriptome and proteome alterations indicate reorganization of mechanism regulating cell functioning. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res B Part B: Appl Biomater, 00B: 000–000, 2018. Key Words: silver nanoparticles (SNPs), multi-walled carbon nanotubes (MWCNTs), polyamidoamine dendrimers (PAMAMs), transcriptomics, proteomics How to cite this article: Komorowski P, Siatkowska M, Wasiak T, Działoszy nska K, Kotarba S, Kądzioła K, Bartoszek N, Sokołowska P, Elgalal M, Sobol-Pacyniak A, Makowski K, Walkowiak B. 2018. Simultaneous transcriptome and proteome analysis of EA.hy926 cells under stress conditions induced by nanomaterials. J Biomed Mater Res B Part B. 2018:000B:1–11. INTRODUCTION In recent years, there have been many novel achievements in the field of nanotechnology. The vast number of diverse nano-scale materials such as nanotubes (NTs), nanoparticles (NPs), or quantum dots (QDs) have found their applications in industry, electronics, pharmacy, biomedical engineering, medicine, and many others. 1–6 Due to the great potential of nanomaterials (NMs) in overcoming problems faced by their bulk counterparts, at present they are of great interest to sci- entists, in particular with respect to the treatment and diag- nosis of various types of diseases. Unfortunately, the increasing risk of exposure to these nanoparticles due to ever-growing number of their applications, poses the all- important question—are these materials absolutely safe? According to present state of knowledge it is still uncertain whether NPs are safe for humans and what potential repercussions can have for living cells. Once they enter the biological milieu, they interact with a variety of biomolecules such as proteins, lipids, nucleic acids, and others. This, in turn can lead to alterations of the physico-chemical charac- teristics of NPs and their ultimate reactivity. 7,8 An increasing number of studies have shown the phenomenon of cellular uptake of NPs. The main routes of this uptake are related to phagocytosis, clathrin- or caveolae-dependent endocytosis, or micropinocytosis. 7,9 As a consequence of internalization, NPs can invoke a cytotoxic or genotoxic effect in the cell, 9,10 change certain signaling pathways or alter gene or protein expression. 11,12 The present work focused on three commer- cially available NMs: silver nanoparticles (SNPs), multi- walled carbon nanotubes (MWCNTs), and polyamidoamine dendrimers of 4th generation (PAMAMs). Nanosilver, due to its antibacterial properties is used in wound healing and Additional Supporting Information may be found in the online version of this article. Correspondence: Piotr Komorowski; e-mail: p.komorowski@bionanopark.pl © 2018 WILEY PERIODICALS, INC. 1