Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition

Abstract

BackgroundSubtle DNA methylation alterations mediated by carbon nanotubes (CNTs) exposure might contribute to pathogenesis and disease susceptibility. It is known that both multi-walled carbon nanotubes (MWCNTs) and single-walled carbon nanotubes (SWCNTs) interact with nucleus. Such, nuclear-CNT interaction may affect the DNA methylation effects.In order to understand the epigenetic toxicity, in particular DNA methylation alterations, of SWCNTs and short MWCNTs, we performed global/genome-wide, gene-specific DNA methylation and RNA-expression analyses after exposing human bronchial epithelial cells (16HBE14o- cell line). In addition, the presence of CNTs on/in the cell nucleus was evaluated in a label-free way using femtosecond pulsed laser microscopy.ResultsGenerally, a higher number of SWCNTs, compared to MWCNTs, was deposited at both the cellular and nuclear level after exposure. Nonetheless, both CNT types were in physical contact with the nuclei. While particle type dependency was noticed for the identified genome-wide and gene-specific alterations, no global DNA methylation alteration on 5-methylcytosine (5-mC) sites was observed for both CNTs. After exposure to MWCNTs, 2398 genes were hypomethylated (at gene promoters), and after exposure to SWCNTs, 589 CpG sites (located on 501 genes) were either hypo- (N = 493 CpG sites) or hypermethylated (N = 96 CpG sites).Cells exposed to MWCNTs exhibited a better correlation between gene promoter methylation and gene expression alterations. Differentially methylated and expressed genes induced changes (MWCNTs > SWCNTs) at different cellular pathways, such as p53 signalling, DNA damage repair and cell cycle. On the other hand, SWCNT exposure showed hypermethylation on functionally important genes, such as SKI proto-oncogene (SKI), glutathione S-transferase pi 1 (GTSP1) and shroom family member 2 (SHROOM2) and neurofibromatosis type I (NF1), which the latter is both hypermethylated and downregulated.ConclusionAfter exposure to both types of CNTs, epigenetic alterations may contribute to toxic or repair response. Moreover, our results suggest that the observed differences in the epigenetic response depend on particle type and differential CNT-nucleus interactions.Electronic supplementary materialThe online version of this article (10.1186/s12989-018-0244-6) contains supplementary material, which is available to authorized users.

DNA Methylation Profiles in a Group of Workers Occupationally Exposed to Nanoparticles

“…Hypermethylation, following exposure to all carbon NPs, was reported for this hypotriploid cancer cell line [4]. The epigenetic effects of exposure to MWCNTs and SWCNTs were also studied in bronchial epithelial cells (16HBE14o-), where no global DNA methylation alteration on 5-mC was observed, but a detailed array screening revealed hypo-and/or hypermethylation, in particular on CpG sites [5]. The same array analysis also revealed minor effects of TiO 2 and MWCNTs exposure in human bronchial epithelial lung cells (BEAS-2B), where the altered CpG sites were mainly located in low-density regions and very frequently on the X chromosome [6].…”

“…This is particularly evident when the levels of hypermethylated and hypomethylated CpG loci are balanced, as, for example, in a study focused on the effect of exposure to SWCNTs and MWCNTs. In this study, detailed array screening using Human Methylation 450K BeadChip revealed specific differences [5]. This state-of-the-art methylation assay is whole-genome bisulfite sequencing (WGBS), which provides complete information on site-specific differences.…”

No excessive mutations in transcription activator-like effector nuclease-mediated α-1,3-galactosyltransferase knockout Yucatan miniature pigs

“…When we compared the fold-changes of the genes commonly differentially expressed in GGTA1 knockout pigs, most showed similar directions of change (up-or down-regulation) compared to the wild-type pig ( Figure 3C). Literature mining revealed that several differentially expressed genes in GGTA1 knockout pigs are associated with DNA methylation in gene regulation, including family with sequence similarity 50, member B (FAM50B) [23,24], cytochrome C, somatic [25], SHROOM2 [26], protein tyrosine phosphatase, non-receptor type 13 (PTPN13) [27], and LDL receptor-related protein 12 (LRP12) [28]. Other differentially expressed genes are known to be involved in respiratory diseases, such as lung cancer, including FAM50B [24], ATPase phospholipid transporting 11C [29], WWC family member 3 [30][31][32], PTPN13 [27], RAS protein activator-like 2 [33], tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta [34,35], and LRP12 [28].…”

Single-walled and multi-walled carbon nanotubes induce sequence-specific epigenetic alterations in 16 HBE cells

“…Aberrant methylation signatures associated with altered gene expression and dysregulation of key pathways have been observed in cancer [ 18 – 21 ]. In this context, some recent studies [ 22 – 26 ] including that by our group [ 17 , 27 – 29 ] have identified epigenetic changes as one of the potential players in CNT-induced patho-physiological response. In our previous study in human monocytes (THP-1) [ 28 ] and bronchial epithelial cells (16-HBE) [ 29 ], we observed differential methylation of genes in PI3K-AKT-mTOR pathway, JAK-STAT pathway, MAPK pathway, cell cycle, VEGF pathways.…”

“…In this context, some recent studies [ 22 – 26 ] including that by our group [ 17 , 27 – 29 ] have identified epigenetic changes as one of the potential players in CNT-induced patho-physiological response. In our previous study in human monocytes (THP-1) [ 28 ] and bronchial epithelial cells (16-HBE) [ 29 ], we observed differential methylation of genes in PI3K-AKT-mTOR pathway, JAK-STAT pathway, MAPK pathway, cell cycle, VEGF pathways. The epigenetic changes in pathways from our study were in agreement with that reported by other studies using other endpoints [ 8 , 10 , 11 ].…”