Papers of the Month
By Kelley Christensen and Janelle Weaver
DNTP study spotlights the hidden harm of crude oil refinement
Inhalation of a hazardous compound produced during crude oil refining causes wide-ranging health problems in rodents, according to researchers from the NIEHS Division of the National Toxicology Program.
Ethyltoluenes are isolated during crude oil refinement for use in gasoline and commercial products. Exposure to these environmental contaminants, which are widespread in the air, can occur both occupationally and in the general population. However, critical toxicity data have been lacking.
To address this knowledge gap, the researchers explored the hazardous effects of the potent molecule 2-ethyltoluene (2-ET) in rats and mice. Inhalation of 2-ET for two weeks decreased survival and body weight and damaged the nasal tissue related to the sense of smell.
Pregnant rats exposed to higher concentrations of 2-ET produced fewer pups per litter, suggesting that the chemical may harm reproduction. In addition, their offspring showed liver damage and major decreases in body weight.
According to the authors, more research is needed to understand how 2-ET exposure causes toxicity and to clarify the relevance of these findings to humans. Although there are some estimates of ethyltoluenes in the environment, internal measures of human exposure have not been well documented. (JW)
Citation: Huang MC, Willson CJ, Jaligama S, Baker GL, Singer AW, Cao Y, Pierfelice J, Mutlu E, Burback B, Xie G, Malarkey DE, Sparrow B, Ryan K, Stout M, Roberts GK. 2021. Whole-body inhalation exposure to 2-ethyltoluene for two weeks produced nasal lesions in rats and mice. Inhal Toxicol 33(9-14):334–346.
Nonpersistent chemical mixtures affected fetal growth
A collaborative group led by an NIEHS researcher found that prenatal exposure to a mixture of phthalates, bisphenols, and organophosphate pesticides was associated with lower fetal weight during pregnancy and lower weight at birth.
The scientists used the Generation R study, a population-based cohort in the Netherlands. They analyzed urinary concentrations of 11 phthalate, three bisphenol, and five dialkylphosphate metabolites provided during the pregnancies of 776 women. These measurements were taken at less than 18, 18-25, and greater than 25 weeks of pregnancy. The research team used ultrasound, measures of head circumference, estimated fetal weight, and femur length to calculate effects of exposure.
Using novel methods developed at NIEHS, the team estimated the joint impact of all investigated chemicals as a mixture, which is a more realistic case than past research into single chemical exposures. The chemicals studied are commonly found in beauty products, food packaging, and in food itself.
The researchers found that higher exposure to the mixture was associated with lower estimated fetal weight during the mid-pregnancy period and eventually lower birth weight. Even low levels of exposure may influence fetal growth during early pregnancy. This work suggests that interventions during pregnancy to reduce multiple chemicals could prevent fetal development issues. (KC)
Citation: van den Dries MA, Keil AP, Tiemeier H, Pronk A, Spaan S, Santos S, Asimakopoulos AG, Kannan K, Gaillard R, Guxens M, Trasande L, Jaddoe VWV, Ferguson KK.. 2021. Prenatal exposure to nonpersistent chemical mixtures and fetal growth: a population-based study. Environ Health Perspect 129(11):117008.
RNA-binding protein TtpA controls ameba post-transcription processes
NIEHS researchers and their collaborators have determined that the RNA binding protein TtpA in the ameba Dictyostelium discoideum co-regulates the expression of several related proteins following mRNA transcription.
TtpA is a member of the tristetraprolin (TTP) family, a group of zinc finger proteins that promote mRNA decay. It is found in all vertebrates and the ameba. TtpA signals for the removal of adenylate from the polyA tails of mRNA, leading to mRNA degradation.
Using the cloned and sequenced cDNA for TtpA from the wild-type D. discoideum, the researchers conducted CRISPR-Cas mutagenesis to create null mutants, in which a number of mRNA targets of TtpA were upregulated compared with their wild-type counterparts. The null mutants included those with mutations in the tandem zinc finger domain, which is found in all members of this protein family and is responsible for mRNA binding. The scientists performed RNA-Seq, NanoString mRNA quantification, 3’-UTR analyses, northern and western blotting, and structure modeling.
Because of their parallel behavior in the null mutants and during cellular differentiation, the researchers proposed that TtpA controls a regulon — a group of genes controlled as a unit — and that its primary activity is to manage mRNA deadenylation and decay following transcription. (KC)
Citation: Bai W, Wells ML, Lai WS, Hicks SN, Burkholder AB, Perera L, Kimmel AR, Blackshear PJ. 2021. A post-transcriptional regulon controlled by TtpA, the single tristetraprolin family member expressed in Dictyostelium discoideum. Nucleic Acids Res 49(20):11920–11937.
Genetic algorithm detects inherited disease risk
NIEHS scientists developed an algorithm to use family studies to identify epistasis. Epistasis is said to operate when distinct genetic variants act jointly to modify a trait.
Genetic Algorithm for Detecting Genetic Epistasis using Triads or Siblings (GADGETS) uses guided random searches among sets of single nucleotide polymorphisms (SNPs) to find sets that are jointly and preferentially transmitted to affected offspring, suggesting epistasis. GADGETS incorporates data from either parents-affected child triads or affected-unaffected sibling pairs.
The researchers simulated data for 10,000 SNPs, where two epistatic sets — each involving at most five SNPs — influenced risk. GADGETS searched through the staggering number of possible combinations and found the interacting sets. It also outperformed existing methods for family data.
Next, the scientists reanalyzed data from families in which a baby was born with an oral cleft, which is a birth defect. It is plausible that epistasis contributes to this highly heritable condition because in pre-modern times, most newborns with a cleft would die, implying there must have been strong genetic selection against any single causative SNP. GADGETS was able to nominate potentially epistatic SNP sets associated with clefting. (KC)
Citation: Nodzenski M, Shi M, Krahn JM, Wise AS, Li Y, Li L, Umbach DM, Weinberg CR. 2021. GADGETS: A genetic algorithm for detecting epistasis using nuclear families. Bioinformatics; doi: 10.1093/bioinformatics/btab766 [Online 12 November 2021].
Bivalent chromatin offers protective function against cancer
Although it was previously hypothesized that bivalent chromatin primes certain genes for rapid activation during embryonic development, NIEHS researchers have found that it protects genes from aberrant DNA methylation and irreversible gene silencing.
Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Despite the presence of activation-associated H3K4me3, bivalently marked gene promoters are transcriptionally inactive. The researchers report that loss of bivalency and H3K4me3, in particular, makes bivalently marked genes more susceptible to abnormal DNA methylation during aging and in diseases such as cancer. They scientists further suggest that aging-associated hypermethylation of genes that are bivalently marked in embryonic stem cells can serve as a biomarker for carcinogenesis in older people. Bivalency may thus represent a regulatory mechanism to maintain epigenetic plasticity during normal development by protecting reversibly repressed genes from irreversible silencing.
For this study, the researchers used publicly available National Institutes of Health Roadmap Epigenomics project data, which are drawn from a diverse collection of human tissues and progenitor cells, and human DNA methylation data from 14 solid epithelial cancer types, generated by The Cancer Genome Atlas network. (KC)
Citation: Kumar D, Cinghu S, Oldfield AJ, Yang P, Jothi R. 2021. Decoding the function of bivalent chromatin in development and cancer. Genome Res 31(12):2170–2184.
(Kelley Christensen is a contract writer and editor for the NIEHS Office of Communications and Public Liaison [OCPL]. Janelle Weaver, Ph.D., is a contract writer for OCPL.)