<p>Toxicogenomic analysis of publicly available transcriptomic data can predict food, drugs, and chemical-induced asthma</p>

Abstract

Background: With the increasing incidence of asthma, more attention is focused on the diverse and complex nutritional and environmental triggers of asthma exacerbations. Currently, there are no established risk assessment tools to evaluate asthma triggering potentials of most of the nutritional and environmental triggers encountered by asthmatic patients.Purpose The objective of this study is to devise a reliable workflow, capable of estimating the toxicogenomic effect of such factors on key player genes in asthma pathogenesis.MethodsGene expression extracted from publicly available datasets of asthmatic bronchial epithelium were subjected to a comprehensive analysis of differential gene expression to identify significant genes involved in asthma development and progression. The identified genes were subjected to Gene Set Enrichment Analysis using a total of 31,826 gene sets related to chemical, toxins, and drugs to identify common agents that share similar asthma-related targets genes and signaling pathways.ResultsOur analysis identified 225 differentially expressed genes between severe asthmatic and healthy bronchial epithelium. Gene Set Enrichment Analysis of the identified genes showed that they are involved in response to toxic substances and organic cyclic compounds and are targeted by 41 specific diets, plants products, and plants related toxins (eg adenine, arachidonic acid, baicalein, caffeic acid, corilagin, curcumin, ellagic acid, luteolin, microcystin-RR, phytoestrogens, protoporphyrin IX, purpurogallin, rottlerin, and salazinic acid). Moreover, the identified chemicals share interesting inflammation-related pathways like NF-κB.ConclusionOur analysis was able to explain and predict the toxicity in terms of stimulating the differentially expressed genes between severe asthmatic and healthy epithelium. Such an approach can pave the way to generate a cost-effective and reliable source for asthma-specific toxigenic reports thus allowing the asthmatic patients, physicians, and medical researchers to be aware of the potential triggering factors with fatal consequences.

In silico Analysis of Publicly Available Transcriptomics Data Identifies Putative Prognostic and Therapeutic Molecular Targets for Papillary Thyroid Carcinoma

“…The significantly activated pathways in different types of PTC samples were selected based on p < 0.05 and FDR < 0.25 as previously described. 10 , 12 The selected pathways were further processed to identify differentially enriched genes between the normal versus non-aggressive and normal versus metastatic PTC cases. This was followed by reducing the set of available genes by identifying the frequency of gene occurrence across differentially activated cellular pathways.…”

As We Drink and Breathe: Adverse Health Effects of Microcystins and Other Harmful Algal Bloom Toxins in the Liver, Gut, Lungs and Beyond

“…Specific genes involved in asthma development and progression were identified, and an analysis showed that they were involved in a response to toxic substances which were targeted by plant products and plant-related toxins. Among these toxins was microcystin, showing that those with asthma may have increased susceptibility to microcystin [ 50 ]. As for the cardiovascular system, exposure to microcystins has also resulted in pathophysiological changes such as declines in stroke volume, cardiac output, heart rate/blood pressure, and oxygen consumption.…”

The Role of Systems Biology in Deciphering Asthma Heterogeneity

“…The use of systems biology and multi-omics to analyze the response of all genes to such chemical exposures can be examined to understand the potential hazards of such irritants and toxicants [ 39 ]. It has been shown that by using the in silico gene expression data and linking it to toxicogenomic data, differentially expressed genes can be used to explain and predict the effect of toxicity on an asthmatic epithelium [ 40 ].…”