Network Analysis Reveals Similar Transcriptomic Responses to Intrinsic Properties of Carbon Nanomaterials in Vitro and in Vivo

Abstract

Understanding the complex molecular alterations related to engineered nanomaterial (ENM) exposure is essential for carrying out toxicity assessment. Current experimental paradigms rely on both in vitro and in vivo exposure setups that often are difficult to compare, resulting in questioning the real efficacy of cell models to mimic more complex exposure scenarios at the organism level. Here, we have systematically investigated transcriptomic responses of the THP-1 macrophage cell line and lung tissues of mice, after exposure to several carbon nanomaterials (CNMs). Under the assumption that the CNM exposure related molecular alterations are mixtures of signals related to their intrinsic properties, we inferred networks of responding genes, whose expression levels are coordinately altered in response to specific CNM intrinsic properties. We observed only a minute overlap between the sets of intrinsic property-correlated genes at different exposure scenarios, suggesting specific transcriptional programs working in different exposure scenarios. However, when the effects of the CNM were investigated at the level of significantly altered molecular functions, a broader picture of substantial commonality emerged. Our results imply that in vitro exposures can efficiently recapitulate the complex molecular functions altered in vivo. In this study, altered molecular pathways in response to specific CNM intrinsic properties have been systematically characterized from transcriptomic data generated from multiple exposure setups. Our computational approach to the analysis of network response modules further revealed similarities between in vitro and in vivo exposures that could not be detected by traditional analysis of transcriptomics data. Our analytical strategy also opens a possibility to look for pathways of toxicity and understanding the molecular and cellular responses identified across predefined biological themes.

Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture damage

“…For determination of gene expression profiles, mRNA isolation, quality control, amplification, hybridization, scanning, and data preprocessing/normalization were carried out for all 129 samples as described previously, with slight modifications. Briefly, raw data files were imported into R and preprocessed with the methods available in the Limma package .…”

Conventional and novel “omics”‐based approaches to the study of carbon nanotubes pulmonary toxicity

“…In fact, although most of the altered pathways that were identified are shared between the two experimental models, the specific genes that are involved are different (Poulsen et al, 2013). Moreover, although differences in gene expression exist between in vivo and in vitro exposure to CNT, in vitro exposures can efficiently recapitulate the significantly altered molecular functions in vivo (Kinaret et al, 2017).…”

Multi-omics analysis of ten carbon nanomaterials effects highlights cell type specific patterns of molecular regulation and adaptation

“…In addition to a variety of in vitro end point assessments, OMICS approaches allow for comparison of different in vitro systems as well as better correspondence to in vivo exposure scenarios (Kinaret et al, 2017b;Drasler et al, 2017). Combination of different OMICS methods can inform more thoroughly about ENMs MOA, which could be further used in ENM grouping approaches, as suggested by Riebeling et al (2017).…”

“…We and others already showed that ENMs are able to exert toxic effects on the respiratory system, by using animal exposure models (Kinaret et al, 2017a;Rydman et al, 2015;Rydman et al, 2014). Apart from the pathological responses, ENMs MOA has been investigated in different tissues (Kinaret et al, 2017b;Fröhlich, 2017;Costa and Fadeel, 2016), by analyzing the molecular perturbations that these materials are able to induce on the normal transcriptional program of exposed cells and tissues.…”

“…We recently demonstrated that carbon based nanomaterials have distinct transcriptional MOA between in vivo and in vitro experimental settings and that commonalities are to be found by using comprehensive gene network models (Kinaret et al, 2017b).…”