Multi-omics approaches for understanding environmental exposure and human health

Koh, Eun Jung; Hwang, Seung Yong

doi:10.1007/s13273-019-0001-4

Cited by 34 publications

(21 citation statements)

References 32 publications

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“…The presented results suggest that BPA does not exert a powerful cytotoxic effect, but it causes changes in the normal transcriptome profile, which is a potential cause of disease. Additionally, multi-dimensional epigenomic analysis could provide the insights to understand the adverse outcome pathway by the chemical exposure [ 50 ]. A previous study demonstrated the effect of the environmental chemical, methylparaben, on the transcriptome profiling of human non-small cell lung carcinoma cells [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells

Kim¹,

Kim²,

Park³

et al. 2021

Genes

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Bisphenol A (BPA) is a xenoestrogen chemical commonly used to manufacture polycarbonate plastics and epoxy resin and might affect various human organs. However, the cellular effects of BPA on the eyes have not been widely investigated. This study aimed to investigate the cellular cytotoxicity by BPA exposure on human retinoblastoma cells. BPA did not show cytotoxic effects, such as apoptosis, alterations to cell viability and cell cycle regulation. Comparative analysis of the transcriptome and proteome profiles were investigated after long-term exposure of Y79 cells to low doses of BPA. Transcriptome analysis using RNA-seq revealed that mRNA expression of the post-transcriptional regulation-associated gene sets was significantly upregulated in the BPA-treated group. Cell cycle regulation-associated gene sets were significantly downregulated by exposure to BPA. Interestingly, RNA-seq analysis at the transcript level indicated that alternative splicing events, particularly retained introns, were noticeably altered by low-dose BPA treatment. Additionally, proteome profiling using MALDI-TOF-MS identified a total of nine differentially expressed proteins. These results suggest that alternative splicing events and altered gene/protein expression patterns are critical phenomena affected by long-term low-dose BPA exposure. This represents a novel marker for the detection of various diseases associated with environmental pollutants such as BPA.

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Section: Discussionmentioning

confidence: 99%

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells

Kim¹,

Kim²,

Park³

et al. 2021

Genes

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“…Because of the accelerated development of technologies and signi cant decrease in costs, omics studies to understand bio-molecular alterations caused by speci c stimulations or conditions have become widely performed [6]. It is important to guarantee the quality of the starting materials when determining the mechanisms or causality of bio-molecular phenomena.…”

Section: Discussionmentioning

confidence: 99%

Evaluating Alteration of Blood Transcriptome Affected by Storage Conditions Using RNA Sequencing

Koh¹,

Yu²,

Kim³

et al. 2020

Preprint

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BackgroundWhole blood is one of the most widely utilized human samples in biological research and is useful for analysing the mechanisms of diverse bio-molecular phenomena. However, owing to its fluidic properties, whole blood is relatively unstable in the frozen state compared to other biopsy samples. Because RNA is structurally unstable, sample damage can severely affect RNA quality, thereby reducing its usability. This study aimed to assess the quality of RNA prepared from blood stored at different temperatures and times prior to freezing, as well as the effect of freezer storage time. ResultsThe quality of the RNA derived from different blood samples was assessed by determining the RNA integrity number and RNA sequencing to identify genes (|fold-change (FC)| > 1.5, p-value < 0.05, false discovery rate (FDR) < 0.05) that were differentially expressed between the differently prepared RNA samples. We found that improper sample handling critically influenced both RNA quality and gene expression patterns. In particular, storing blood at room temperature over 12 h before freezing led to RNA degradation. Differential gene expression analysis revealed that expression of the CXCR1 gene was substantially reduced when using impaired RNA. ConclusionsThis study emphasizes the importance of proper sample management for obtaining reliable downstream application outcomes and suggests the CXCR1 gene as a candidate screening marker for RNA damage caused by improper sample handling.

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“…Besides, the use of these multi-omics approaches may also be of great help to achieve a holistic view of the whole biological picture. These multi-omics studies are suitable for the confirmation of the causal relationship and association between environmental exposure and pathogenesis, by assessing multiple aspects following the omics cascade: mutations in the DNA sequence may induce changes in the degree of epigenetic regulation, which might alter gene expression and, consequently, protein expression, leading eventually to a metabolomics effect [150].…”

Section: Gene Expression Assessmentmentioning

confidence: 99%

Interaction of Environmental Pollutants with Microplastics: A Critical Review of Sorption Factors, Bioaccumulation and Ecotoxicological Effects

Menéndez-Pedriza

Jaumot

2020

Toxics

178

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Microplastics have become one of the leading environmental threats due to their persistence, ubiquity and intrinsic toxic potential. The potential harm that microplastics impose on ecosystems varies from direct effects (i.e., entanglement and ingestion) to their ability to sorb a diversity of environmental pollutants (e.g., heavy metals, persistent organic compounds or pharmaceuticals). Therefore, the toxicological assessment of the combined effects of microplastics and sorbed pollutants can produce in biota is one of the hottest topics on the environmental toxicology field. This review aims to clarify the main impacts that this interaction could have on ecosystems by (1) highlighting the principal factors that influence the microplastics sorption capacities; (2) discussing the potential scenarios in which microplastics may have an essential role on the bioaccumulation and transfer of chemicals; and (3) reviewing the recently published studies describing toxicological effects caused by the combination of microplastics and their sorbed chemicals. Finally, a discussion regarding the need for a new generation of toxicological studies is presented.

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Multi-omics approaches for understanding environmental exposure and human health

Cited by 34 publications

References 32 publications

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells

Evaluating Alteration of Blood Transcriptome Affected by Storage Conditions Using RNA Sequencing

Interaction of Environmental Pollutants with Microplastics: A Critical Review of Sorption Factors, Bioaccumulation and Ecotoxicological Effects

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