Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment
Recent efforts have posited the utility of transcriptomic-based approaches to understand chemical-related perturbations in the context of human health risk assessment. Epigenetic modification (e.g., DNA methylation) can influence gene expression changes and is known to occur as a molecular response...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-06-01
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| Series: | Environment International |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0160412022002057 |
| _version_ | 1811231704574066688 |
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| author | Stephanie Kim Shana M. White Elizabeth G. Radke Jeffry L. Dean |
| author_facet | Stephanie Kim Shana M. White Elizabeth G. Radke Jeffry L. Dean |
| author_sort | Stephanie Kim |
| collection | DOAJ |
| description | Recent efforts have posited the utility of transcriptomic-based approaches to understand chemical-related perturbations in the context of human health risk assessment. Epigenetic modification (e.g., DNA methylation) can influence gene expression changes and is known to occur as a molecular response to some chemical exposures. Characterization of these methylation events is critical to understand the molecular consequences of chemical exposures. In this context, a novel workflow was developed to interrogate publicly available epidemiological transcriptomic and methylomic data to identify relevant pathway level changes in response to chemical exposure, using inorganic arsenic as a case study. Gene Set Enrichment Analysis (GSEA) was used to identify causal methylation events that result in concomitant downstream transcriptional deregulation. This analysis demonstrated an unequal distribution of differentially methylated regions across the human genome. After mapping these events to known genes, significant enrichment of a subset of these pathways suggested that arsenic-mediated methylation may be both specific and non-specific. Parallel GSEA performed on matched transcriptomic samples determined that a substantially reduced subset of these pathways are enriched and that not all chemically-induced methylation results in a downstream alteration in gene expression. The resulting pathways were found to be representative of well-established molecular events known to occur in response to arsenic exposure. The harmonization of enriched transcriptional patterns with those identified from the methylomic platform promoted the characterization of plausibly causal molecular signaling events. The workflow described here enables significant gene and methylation-specific pathways to be identified from whole blood samples of individuals exposed to environmentally relevant chemical levels. As future efforts solidify specific causal relationships between these molecular events and relevant apical endpoints, this novel workflow could aid risk assessments by identifying molecular targets serving as biomarkers of hazard, informing mechanistic understanding, and characterizing dose ranges that promote relevant molecular/epigenetic signaling events occuring in response to chemical exposures. |
| first_indexed | 2024-04-12T10:49:19Z |
| format | Article |
| id | doaj.art-d24352cda8074f86b3d3b1ad02dd7e3b |
| institution | Directory Open Access Journal |
| issn | 0160-4120 |
| language | English |
| last_indexed | 2024-04-12T10:49:19Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Environment International |
| spelling | doaj.art-d24352cda8074f86b3d3b1ad02dd7e3b2022-12-22T03:36:18ZengElsevierEnvironment International0160-41202022-06-01164107278Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessmentStephanie Kim0Shana M. White1Elizabeth G. Radke2Jeffry L. Dean3Superfund and Emergency Management Division, Region 2, U.S. Environmental Protection Agency, NY, USAChemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USAChemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, D.C., USAChemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA; Corresponding author.Recent efforts have posited the utility of transcriptomic-based approaches to understand chemical-related perturbations in the context of human health risk assessment. Epigenetic modification (e.g., DNA methylation) can influence gene expression changes and is known to occur as a molecular response to some chemical exposures. Characterization of these methylation events is critical to understand the molecular consequences of chemical exposures. In this context, a novel workflow was developed to interrogate publicly available epidemiological transcriptomic and methylomic data to identify relevant pathway level changes in response to chemical exposure, using inorganic arsenic as a case study. Gene Set Enrichment Analysis (GSEA) was used to identify causal methylation events that result in concomitant downstream transcriptional deregulation. This analysis demonstrated an unequal distribution of differentially methylated regions across the human genome. After mapping these events to known genes, significant enrichment of a subset of these pathways suggested that arsenic-mediated methylation may be both specific and non-specific. Parallel GSEA performed on matched transcriptomic samples determined that a substantially reduced subset of these pathways are enriched and that not all chemically-induced methylation results in a downstream alteration in gene expression. The resulting pathways were found to be representative of well-established molecular events known to occur in response to arsenic exposure. The harmonization of enriched transcriptional patterns with those identified from the methylomic platform promoted the characterization of plausibly causal molecular signaling events. The workflow described here enables significant gene and methylation-specific pathways to be identified from whole blood samples of individuals exposed to environmentally relevant chemical levels. As future efforts solidify specific causal relationships between these molecular events and relevant apical endpoints, this novel workflow could aid risk assessments by identifying molecular targets serving as biomarkers of hazard, informing mechanistic understanding, and characterizing dose ranges that promote relevant molecular/epigenetic signaling events occuring in response to chemical exposures.http://www.sciencedirect.com/science/article/pii/S0160412022002057Environmental epidemiologyRisk assessmentTranscriptomicsMethylomicsBenchmark dose modeling (BMD)Gene Set Enrichment Analysis (GSEA) |
| spellingShingle | Stephanie Kim Shana M. White Elizabeth G. Radke Jeffry L. Dean Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment Environment International Environmental epidemiology Risk assessment Transcriptomics Methylomics Benchmark dose modeling (BMD) Gene Set Enrichment Analysis (GSEA) |
| title | Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment |
| title_full | Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment |
| title_fullStr | Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment |
| title_full_unstemmed | Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment |
| title_short | Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment |
| title_sort | harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment |
| topic | Environmental epidemiology Risk assessment Transcriptomics Methylomics Benchmark dose modeling (BMD) Gene Set Enrichment Analysis (GSEA) |
| url | http://www.sciencedirect.com/science/article/pii/S0160412022002057 |
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