Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment

Synergic effect of arsenic exposure related methylation changes in three cohorts exposed to levels of this toxicant

PURPOSE

The results of studies assessing impact of arsenic exposure on methylome are to large extent inconsistent. To contribute to understanding of effect of arsenic exposure on methylome of the exposed cells, we assess the impact of low-level arsenic exposure on methylome of blood cells in three cohorts of exposed individuals.

METHODS

The Infinium MethylationEPIC array (Illumina Inc.) was used for genome-wide methylation profiling and robust linear regression to identify arsenic-related methylation changes in blood cells from healthy individuals with a 12-year cancer-free follow-up and breast cancer patients, sampled on average 4.29 years before diagnosis, as well as methylomics data from cord blood samples of Biomarkers of Exposure to Arsenic cohort.

RESULTS

Our analysis identified a 2,453 arsenic-associated methylation changes in blood from healthy individuals, 9,662 in breast cancer patients and 6,745 in cord blood samples. Similarly to previous studies methylation changes that we identified in each cohort, overlapped only to some extent. However, molecular processes linked to identified methylation changes were very similar in each of the cohorts. And included pathways that could be clearly associated with the adverse effects of arsenic exposure and specifically cancer in the cohort of cancer patients. Moreover, the genomic regions harboring identified in each cohort methylation changes were similar and predominantly included regions participating in regulation of gene transcription.

CONCLUSION

Overall, our findings show that specificity of arsenic related methylation changes is low but the impact of these changes on cell physiology is very similar across three cohorts we studded.

Quantitative relationships of FAM50B and PTCHD3 methylation with reduced intelligence quotients in school aged children exposed to lead: Evidence from epidemiological and in vitro studies

At present, the application of DNA methylation (DNAm) biomarkers in environmental health risk assessment (EHRA) is more challenging due to the unclearly quantitative relationship between them. We aimed to explore the role of FAM50B and PTCHD3 at the level of signaling pathways, and establish the quantitative relationship between them and children's intelligence quotients (IQs). DNAm of target regions was measured in multiple cell models and was compared with the human population data. Then the dose-response relationships of lead exposure with neurotoxicity and DNAm were established by benchmark dose (BMD) model, followed by potential signaling pathway screening. Results showed that there was a quantitative linear relationship between children's IQs and FAM50B/PTCHD3 DNAm (DNAm between 51.40 % - 78.78 % and 31.41 % - 74.19 % for FAM50B and PTCHD3, respectively), and this relationship was more significant when children's IQs > 90. The receiver operating characteristic (ROC) and calibration curves showed that FAM50B/PTCHD3 DNAm had a satisfying accuracy and consistency in predicting children's IQs, which was confirmed by sensitivity analysis of gender and CpG site grouping data. In cell experiments, there was also a quantitative linear relationship between FAM50B DNAm and reactive oxygen species (ROS) production, which was mediated by PI3K-AKT signaling pathway. In addition, the lead BMD of ROS was close to that of FAM50B DNAm, suggesting that FAM50B DNAm was a suitable biomarker for the risk assessments of adverse outcomes induced by lead. Taken collectively, these results suggest that FAM50B/PTCHD3 can be applied to EHRA and the prevention/intervention of adverse effects of lead on children's IQs.

Locomotion and brain gene expression exhibit sex-specific non-monotonic dose-response to HFPO-DA during Drosophila melanogaster lifespan

BACKGROUND

Legacy per- and polyfluoroalkyl substances (PFAS), known for their environmental persistence and bio-accumulative properties, have been phased out in the U.S. due to public health concerns. A newer polymerization aid used in the manufacture of some fluoropolymers, hexafluoropropylene oxide-dimer acid (HFPO-DA), has lower reported bioaccumulation and toxicity, but is a potential neurotoxicant implicated in dopaminergic neurodegeneration.

OBJECTIVE

We investigated HFPO-DA's bio-accumulative potential and sex-specific effects on lifespan, locomotion, and brain gene expression in fruit flies.

METHODS

We quantified bioaccumulation of HFPO-DA in fruit flies exposed to 8.7×10⁴µg/L of HFPO-DA in the fly media for 14 days via UHPLC-MS. Long-term effect on lifespan was determined by exposing both sexes to 8.7×10² - 8.7×10⁵µg/L of HFPO-DA in media. Locomotion was measured following 3, 7, and 14 days of exposures at 8.7×10¹ - 8.7×10⁵µg/L of HFPO-DA in media, and high-throughput 3'-end RNA-sequencing was used to quantify gene expression in fly brains across the same time points.

RESULTS

Bioaccumulation of HFPO-DA in fruit flies was not detected. HFPO-DA-induced effects on lifespan, locomotion, and brain gene expression, and lowest adverse effect level (LOAEL) showed sexually dimorphic patterns. Locomotion scores significantly decreased in at least one dose at all time points for females and only at 3-day exposure for males, while brain gene expression exhibited non-monotonic dose-response. Differentially expressed genes correlated to locomotion scores revealed sex-specific numbers of positively and negatively correlated genes per functional category.

CONCLUSION

Although HFPO-DA effects on locomotion and survival were significant at doses higher than the US EPA reference dose, the brain transcriptomic profiling reveals sex-specific changes and neurological molecular targets; gene enrichments highlight disproportionately affected categories, including immune response: female-specific co-upregulation suggests potential neuroinflammation. Consistent sex-specific exposure effects necessitate blocking for sex in experimental design during HFPO-DA risk assessment.

Physiological and transcriptomic effects of hexafluoropropylene oxide dimer acid in Caenorhabditis elegans during development

Per- and polyfluoroalkyl substances (PFAS) are chemicals resistant to degradation. While such a feature is desirable in consumer and industrial products, some PFAS, including perfluorooctanoic acid (PFOA), are toxic and bioaccumulate. Hexafluoropropylene oxide dimer acid (HFPO-DA), an emerging PFAS developed to replace PFOA, has not been extensively studied. To evaluate the potential toxicity of HFPO-DA with a cost- and time-efficient approach, we exposed C. elegans larvae for 48 h to 4 × 10^-9-4 g/L HFPO-DA in liquid media and measured developmental, behavioral, locomotor, and transcriptional effects at various exposure levels. Worms exposed to 1.5-4 g/L HFPO-DA were developmentally delayed, and progeny production was significantly delayed (p < 0.05) in worms exposed to 2-4 g/L HFPO-DA. Statistically significant differential gene expression was identified in all fourteen HFPO-DA exposure groups ranging from 1.25 × 10^-5 to 4 g/L, except for 6.25 × 10^-5 g/L. Among 10298 analyzed genes, 2624 differentially expressed genes (DEGs) were identified in the developmentally delayed 4 g/L group only, and 78 genes were differentially expressed in at least one of the thirteen groups testing 1.25 × 10^-5-2 g/L HFPO-DA exposures. Genes encoding for detoxification enzymes including cytochrome P450 and UDP glucuronosyltransferases were upregulated in 0.25-4 g/L acute exposure groups. DEGs were also identified in lower exposure level groups, though they did not share biological functions except for six ribosomal protein-coding genes. While our transcriptional data is inconclusive to infer mechanisms of toxicity, the significant gene expression differences at 1.25 × 10^-5 g/L, the lowest concentration tested for transcriptional changes, calls for further targeted analyses of low-dose HFPO-DA exposure effects.