Transcriptomics in Toxicogenomics, Part I : Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

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Kinaret , P A S , Serra , A , Federico , A , Kohonen , P , Nymark , P , Liampa , I , Ha , M K , Choi , J-S , Jagiello , K , Sanabria , N , Melagraki , G , Cattelani , L , Fratello , M , Sarimveis , H , Afantitis , A , Yoon , T-H , Gulumian , M , Grafström , R , Puzyn , T & Greco , D 2020 , ' Transcriptomics in Toxicogenomics, Part I : Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects ' , Nanomaterials , vol. 10 , no. 4 , 750 . https://doi.org/10.3390/nano10040750

Title: Transcriptomics in Toxicogenomics, Part I : Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects
Author: Kinaret, Pia Anneli Sofia; Serra, Angela; Federico, Antonio; Kohonen, Pekka; Nymark, Penny; Liampa, Irene; Ha, My Kieu; Choi, Jang-Sik; Jagiello, Karolina; Sanabria, Natasha; Melagraki, Georgia; Cattelani, Luca; Fratello, Michele; Sarimveis, Haralambos; Afantitis, Antreas; Yoon, Tae-Hyun; Gulumian, Mary; Grafström, Roland; Puzyn, Tomasz; Greco, Dario
Other contributor: University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
Date: 2020-04
Language: eng
Number of pages: 23
Belongs to series: Nanomaterials
ISSN: 2079-4991
DOI: https://doi.org/10.3390/nano10040750
URI: http://hdl.handle.net/10138/320336
Abstract: The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.
Subject: transcriptomics
toxicogenomics (TGx)
high throughput
microarrays
sequencing experimental design
engineered nanomaterials (ENM)
toxicology
alternative risk assessment
WALLED CARBON NANOTUBES
GENE-EXPRESSION
RNA-SEQ
PULMONARY INFLAMMATION
CONNECTIVITY MAP
MICROARRAY EXPERIMENTS
TIO2 NANOPARTICLES
RISK-ASSESSMENT
MESSENGER-RNA
SAMPLE-SIZE
1182 Biochemistry, cell and molecular biology
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