Dynamics of Cytosine Methylation in the Proximal Promoters of CYP3A4 and CYP3A7 in Pediatric and Prenatal Livers

Abstract

Members of the human CYP3A family of metabolizing enzymes exhibit developmental changes in expression whereby CYP3A7 is expressed in fetal tissues, followed by a transition to expression of CYP3A4 in the first months of life. Despite knowledge about the general pattern of CYP3A activity in human development, the mechanisms that regulate developmental expression remain poorly understood. Epigenetic changes, including cytosine methylation, have been suggested to play a role in the regulation of CYP3A expression. The objective of this study was to investigate changes in cytosine methylation of the CYP3A4 and CYP3A7 genes in human pediatric and prenatal livers. The methylation status of cytosinephospho-guanine dinucleotides was determined in 16 pediatric liver samples using methyl-seq and confirmed by bisulfite sequencing of 48 pediatric and 34 prenatal liver samples. Samples were separated by age into five groups (prenatal, < 1 year of age, 1.8-6 years, 7-11 years, and 12-17 years). Methyl-seq anaylsis revealed that cytosines in the proximal promoter of CYP3A7 are hypomethylated in neonates compared with adolescents (P < 0.001). In contrast, a cytosine 383 base pair upstream of CYP3A4 is hypermethylated in liver samples from neonates compared with adolescents (P = 0.00001). Developmental changes in methylation of cytosines in the proximal promoters of CYP3A4 and CYP3A7 in pediatric livers were confirmed by bisulfite sequencing. In addition, the methylation status of cytosine in the CYP3A4 and CYP3A7 proximal promoters correlated with changes in developmental expression of mRNA for the two enzymes.

Regulation of Hepatic Long Noncoding RNAs by Pregnane X Receptor and Constitutive Androstane Receptor Agonists in Mouse Liver

“…Paradoxically, although 5MeC is considered a genesilencing mark, our observation is consistent with the more recent literature report stating that many actively transcribed gene bodies are marked with 5MeC. This observation correlates with transcriptional activity rather than repression, that the basal function of gene body methylation facilitates the establishment of their constitutive expression, and that cytosine-specific methylation may regulate gene expression (Coleman-Derr and Zilberman, 2012; Vyhlidal et al, 2016). After PXR activation, a moderate number of PCN-regulated lncRNAs (either upregulated or downregulated) had positive enrichment of H3K4me2, and most of these lncRNAs had direct PXR-DNA binding sites.…”

Critical Issues and Optimized Practices in Quantification of Protein Abundance Level to Determine Interindividual Variability in DMET Proteins by LC‐MS/MS Proteomics

“…Moreover, the effect of these population variables on DMET proteins is generally nonmonotonic. For example, unlike the major cytochrome P450 (CYP) and uridine 5′‐diphospho‐glucuronosyltransferase (UGT) enzymes, where an age‐dependent increase is observed in the protein abundance from neonates to adults, CYP3A7 is a predominant fetal liver enzyme, the protein abundance of which is steeply diminished after birth . Some enzymes such as CYP3A4, CYP2B6, and UGT2B17 show gender‐dependent activity.…”

“…For example, unlike the major cytochrome P450 (CYP) and uridine 5 0diphospho-glucuronosyltransferase (UGT) enzymes, where an age-dependent increase is observed in the protein abundance from neonates to adults, 1,2 CYP3A7 is a predominant fetal liver enzyme, the protein abundance of which is steeply diminished after birth. 3 Some enzymes such as CYP3A4, 4 CYP2B6, 5 and UGT2B17 6 show gender-dependent activity. The enzyme activity or abundance of multiple hepatic DMEs is differentially regulated in diseased condition.…”

Challenges and Opportunities for Increasing the Knowledge Base Related to Drug Biotransformation and Pharmacokinetics during Growth and Development

“…The inability to generate conclusive data regarding chromatin structural dynamics and CYP3A7 transcription in prenatal liver was attributed to cellular heterogeneity. Indeed, Vyhlidal et al (2016) observed cytosine methylation in the CYP3A7 proximal promoter to be similar between prenatal and adult liver despite higher CYP3A7 expression in the former; since CYP3A7 is not expressed in hematopoietic stem cells, the predominance of that cell type in human prenatal liver obscures CpG methylation in the parenchymal hepatocytes where CYP3A7 is expressed.…”

“…Two papers provide additional insights into the well-characterized CYP3A7-CYP3A4 developmental transition that occurs between prenatal and postnatal liver. Vyhlidal et al (2016) used methylation-sequencing analysis and confirmatory bisulfite sequencing to compare the methylation state of the CYP3A4 and CYP3A7 proximal promoters. Hypomethylation of CpG dinucleotides in the CYP3A7 proximal promoter of neonatal samples compared with adults, and hypermethylation of cytosine 383 nucleotides upstream of CYP3A4 in neonates relative to adolescent samples is consistent with the CYP3A7-CYP3A4 switch characteristic of the CYP3A locus after birth.…”