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8.4.5 “Omics” Methodologies
Some biomolecules expression, including genes, mRNA transcripts, proteins, and
metabolites, can be affected in an organism after a xenobiotic exposure, providing
information about the specific pathways that have been altered as a consequence of
this exposure. These molecular indicators can serve as biomarkers not only to provide insights into the triggered toxicity mechanisms but also to provide information
about the modulation of the general molecular response of a cell, tissue, or organism
in response, for instance to NMs (Klaper et al. 2014).
Innovative and advanced technology platforms such as genomics, transcriptomics, proteomics, lipidomics, and metabolomics have been lately applied to
investigate mode of action and mechanisms of nanomedicines. “Omics” technologies can also represent a valuable tool to improve the evaluation methods of NMs
toxicity signatures. These approaches allow the simultaneous detection and identification of many different molecules, including their minor parts, presented,
expressed, or altered in a biological system following xenobiotic exposure.
Furthermore, the assessment of the behavior of these molecules can also provide
information about the interactions and interferences of the xenobiotic with biochemical pathways (Azhdarzadeh et al. 2015).
Gene expression can provide a sensitive endpoint for toxicity as it suffers alterations in response to external stimuli, such as NMs. Given genomics and transcriptomics studies, genomics refers to the study of the genome function and structure,
while transcriptomics is the study of transcriptome, namely, the messenger RNA
molecules in biological systems using microarray technology to monitor the global
changes occurring into cells after a xenobiotic exposure. For instance, genomic/
transcriptomic studies on the effect of NMs on gastrointestinal tract have been carried out with whole human genome oligo microarray using human cell-based systems (Fisichella et al. 2012; Bouwmeester et al. 2011).
Gene expression alteration studies are usually complemented by the studies on
the alterations induced on protein, lipid, and metabolic mechanisms and pathways.
Proteomics refers to the large-scale study of proteins, focusing on their structures
and functions. In vitro proteomics provides useful information aiming to identify
toxicity biomarkers for oxidative stress and cell death mechanisms. To study the
impact of nanoformulations on proteome, along with two-dimensional gel electrophoresis (Sturla et al. 2014), advanced mass spectrometry-based techniques, such as
stable isotope label-free quantitative mass spectrometry, have been developed and
applied (Calvano et al. 2014; Bouwmeester et al. 2011; Ng et al. 2015). The cellular
lipid pathways and networks in biological systems are studied through lipidomics.
The analysis of the complete lipid profile within cells, tissues, or organisms after a
xenobiotic exposure is also an important tool in the understanding of the interactions between NMs and biological systems. Making use of different types of mass
spectrometry (Paglia et al. 2015), it is possible to study alterations in lipid compositions and possible lipid modifications induced by oxidative stress (Hinterwirth et al.
2013; Vaz et al. 2015). Physiological changes within cells, tissues, and organisms
8 In Vitro Methodologies for Toxicological Assessment of Drug Delivery Nanocarriers
8.4.5 “Omics” Methodologies
Some biomolecules expression, including genes, mRNA transcripts, proteins, and
metabolites, can be affected in an organism after a xenobiotic exposure, providing
information about the specific pathways that have been altered as a consequence of
this exposure. These molecular indicators can serve as biomarkers not only to provide insights into the triggered toxicity mechanisms but also to provide information
about the modulation of the general molecular response of a cell, tissue, or organism
in response, for instance to NMs (Klaper et al. 2014).
Innovative and advanced technology platforms such as genomics, transcriptomics, proteomics, lipidomics, and metabolomics have been lately applied to
investigate mode of action and mechanisms of nanomedicines. “Omics” technologies can also represent a valuable tool to improve the evaluation methods of NMs
toxicity signatures. These approaches allow the simultaneous detection and identification of many different molecules, including their minor parts, presented,
expressed, or altered in a biological system following xenobiotic exposure.
Furthermore, the assessment of the behavior of these molecules can also provide
information about the interactions and interferences of the xenobiotic with biochemical pathways (Azhdarzadeh et al. 2015).
Gene expression can provide a sensitive endpoint for toxicity as it suffers alterations in response to external stimuli, such as NMs. Given genomics and transcriptomics studies, genomics refers to the study of the genome function and structure,
while transcriptomics is the study of transcriptome, namely, the messenger RNA
molecules in biological systems using microarray technology to monitor the global
changes occurring into cells after a xenobiotic exposure. For instance, genomic/
transcriptomic studies on the effect of NMs on gastrointestinal tract have been carried out with whole human genome oligo microarray using human cell-based systems (Fisichella et al. 2012; Bouwmeester et al. 2011).
Gene expression alteration studies are usually complemented by the studies on
the alterations induced on protein, lipid, and metabolic mechanisms and pathways.
Proteomics refers to the large-scale study of proteins, focusing on their structures
and functions. In vitro proteomics provides useful information aiming to identify
toxicity biomarkers for oxidative stress and cell death mechanisms. To study the
impact of nanoformulations on proteome, along with two-dimensional gel electrophoresis (Sturla et al. 2014), advanced mass spectrometry-based techniques, such as
stable isotope label-free quantitative mass spectrometry, have been developed and
applied (Calvano et al. 2014; Bouwmeester et al. 2011; Ng et al. 2015). The cellular
lipid pathways and networks in biological systems are studied through lipidomics.
The analysis of the complete lipid profile within cells, tissues, or organisms after a
xenobiotic exposure is also an important tool in the understanding of the interactions between NMs and biological systems. Making use of different types of mass
spectrometry (Paglia et al. 2015), it is possible to study alterations in lipid compositions and possible lipid modifications induced by oxidative stress (Hinterwirth et al.
2013; Vaz et al. 2015). Physiological changes within cells, tissues, and organisms
8 In Vitro Methodologies for Toxicological Assessment of Drug Delivery Nanocarriers