Environmental Factor – July 2022: Intramural Articles of the Month

DNTP study shows zebrafish screening protocols affect toxicity outcomes

A quantitative assessment of sources of variability in the design of zebrafish experiments could lay the groundwork for global efforts to harmonize protocols, according to researchers from the NIEHS Division of the National Toxicology Program (DNTP).

Zebrafish embryos have been widely used as toxicity screening tools due to advantages such as transparency and rapid development. But data obtained from independent laboratories can vary widely, complicating the use of zebrafish screening for regulatory decisions.

To investigate this problem, DNTP researchers analyzed zebrafish toxicity data from three independent laboratories using the same set of 87 compounds. They estimated the concentrations that caused death, developmental toxicity, and impaired movement responses.

For labs that used similar testing protocol parameters, agreement was 86% for developmental toxicity results and 68% for neurological toxicity results. In contrast, agreement dropped for labs that used different protocol parameters. Strikingly, the concentration required to produce developmental and neurological toxicity varied, on average, up to four and six times, respectively.

Factors that potentially contributed to this variability included fish strain, whether the outermost membrane surrounding the embryo had been removed, exposure scenario and volume, and duration of behavioral testing. According to the authors, the findings could guide ongoing efforts to incorporate zebrafish as a complementary model for drug development and toxicity testing.

Quote: Hsieh JH, Behl M, Parham F, Ryan K. 2022. Exploring the influence of experimental design on toxicity outcomes in zebrafish embryo testing. Toxicol Sci; doi:10.1093/toxsci/kfac053 [Online 27 May 2022].

Early biomarkers can predict lung disease in premature babies

Molecular biomarkers present at birth are linked to the later development of a chronic respiratory disease called bronchopulmonary dysplasia (BPD), according to NIEHS researchers and their collaborators.

Borderline personality disorder primarily affects infants born before 30 weeks of gestational age with a birth weight of less than 1000 grams and who receive more than four weeks of therapeutic oxygen supplementation in the neonatal intensive care unit. The condition is characterized by impaired lung development that persists into later life. Cases have increased and therapeutic options for prevention and treatment are limited. Moreover, the mechanisms that lead to the disease are not fully understood.

To fill this knowledge gap, the researchers took umbilical cord blood samples from 107 preterm infants, 14 of whom developed borderline personality disorder. They analyzed epigenetic patterns – chemical changes that could affect gene activity in the absence of changes in the underlying DNA sequence. The results revealed a higher number of epigenetic mutations that altered DNA methylation, as well as differences in gene activity, in newborns who later developed borderline personality disorder compared to those who did not. haven’t done it.

Specifically, BPD risk was associated with altered cord blood DNA methylation profiles in genes involved in lung and alveolar development, and hematopoiesis. Taken together, the findings shed light on the biological pathways involved in BPD and suggest several potential epigenetic biomarkers that may indicate higher susceptibility to BPD at birth. Co-first authors Xuting Wang, Ph.D., and Hye-Youn Cho, Ph.D., of the Environmental Epigenomics and Disease Group, say further studies are needed to determine whether CpG sites (regions where DNA methylation occurs) that they have identified will prove to be clinically relevant.

Quote: Wang X, Cho HY, Campbell MR, Panduri V, Coviello S, Caballero MT, Sambandan D, Kleeberger SR, Polack FP, Ofman G, Bell DA. 2022. Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants: findings from the discovery-BPD program. Clin Epigenetics 14(1):57.

Scientists assess epigenetics of lung function across ancestors

A large-scale, multi-ancestry study by NIEHS researchers and their collaborators provides a comprehensive assessment of epigenome-wide DNA methylation in relation to lung function.

Lung function is affected by both genetics and environmental exposures. Large genome-wide association studies have identified more than 300 loci related to lung function, but much of the variability remains unexplained. Epigenetic marks, such as methylation (chemical changes that can alter gene expression without affecting the underlying DNA sequence), are influenced by and can contribute to genetics and the environment. Epigenome-wide studies have revealed certain associations between lung function and cytosine-phosphate-guanine (CpG) sites, which are regions where a cytosine nucleotide is followed by a guanine nucleotide in the linear sequence of basics. But replication has been limited, with most research focusing on European populations and no large-scale multi-ancestry studies published.

To overcome these limitations, the researchers performed epigenome-wide analyzes of blood DNA methylation and lung function in 17,503 adults of European, African, and Hispanic/Latino ancestry. Lung function was linked to DNA methylation at 1,267 CpG sites spanning 1,042 genes. The vast majority of these genes had never been implicated in lung function. Although most signals were consistent across ancestries, some were potentially unique to people of African descent. Some of the genes involved are targets for approved or experimental drugs.

These results can be exploited to understand the mechanisms that regulate lung function, develop diagnostic and prognostic biomarkers of respiratory diseases and identify potential targets for preventive and therapeutic strategies.

Quote: Lee M, Huan T, McCartney DL, Chittoor G, de Vries M, Lahousse L, Nguyen JN, Brody JA, Castillo-Fernandez J, Terzikhan N, Qi C, Joehanes R, Min JL, Smilnak GJ, Shaw JR, Yang CX , Colicino E, Hoang TT, Bermingham ML, Xu H, Justice AE, Xu CJ, Rich SS, Cox SR, Vonk JM, Prokić I, Sotoodehnia N, Tsai PC, Schwartz JD, Leung JM, Sikdar S, Walker RM, Harris SE, van der Plaat DA, Van Den Berg DJ, Bartz TM, Spector TD, Vokonas PS, Marioni RE, Taylor AM, Liu Y, Barr RG, Lange LA, Baccarelli AA, Obeidat M, Fornage M, Wang T, Ward JM , Motsinger-Reif AA, Hemani G, Koppelman GH, Bell JT, Gharib SA, Brusselle G, Boezen HM, North KE, Levy D, Evans KL, Dupuis J, Breeze CE, Manichaikul A, London SJ; BIOS Consortium, GoDMC. 2022. Lung function and blood DNA methylation: a multi-ancestry epigenome-wide association meta-analysis. Am J Respir Crit Care Med; doi:10.1164/rccm.202108-1907OC [Online 10 May 2022].

Prenatal exposure to phthalates may predispose children to obesity

According to NIEHS researchers and their collaborators, endocrine disruptors called phthalates are linked to both lower fatness and lower birth weight, and higher fatness during childhood.

Phthalates are ubiquitous in the environment, personal care products, food and beverage packaging materials, and vinyl products. Prenatal exposure to phthalates has been associated with lower birth weight, but also higher childhood weight. Yet, few studies have examined prenatal exposure to phthalates in relation to weight or BMI measured from the prenatal period through childhood. This pattern of association could be important because lower birth weight combined with rapid weight gain in early life is a risk factor for later cardiometabolic disease.

To address this knowledge gap, the researchers analyzed a panel of phthalate metabolites in urine collected from 780 pregnant women during two visits to four sites in the United States. Prenatal exposure to several phthalates was linked to lower birth weight, but not during childhood. In addition, prenatal exposure to certain phthalates was associated with a low weight-for-height ratio at birth, as well as a high body mass index between three and six years of age. According to the authors, continued investigation into the role of these environmental exposures is warranted, given the high rates of childhood obesity in the United States.

Quote: Ferguson KK, Bommarito PA, Arogbokun O, Rosen EM, Keil AP, Zhao S, Barrett ES, Nguyen RHN, Bush NR, Trasande L, McElrath TF, Swan SH, Sathyanarayana S. 2022. Prenatal Exposure to Phthalates and Childhood Weight and Fatty in utero is 6 years old. Environ Health Perspect 130(4):47006.

Structural snapshots illuminate the choreography of catalysis

According to the NIEHS researchers and their collaborators, the crystal structures of mysterious molecular complexes have provided atomic-level insight into the diversity of mechanisms underlying enzymatic reactions.

Protein tyrosine phosphatases (PTPs) are essential enzymes for many cellular functions. It has not been clear how enzymatic reactions proceed for a subgroup of PTPs that lack the classical version of an important structural element called the WPD loop. Progress towards solving this puzzle requires high-resolution structures of members of this particular group of enzymes interacting with their natural substrates.

To meet this need, the researchers provided crystal complexes for such an outlier of PTP: Arabidopsis thaliana atypical dual specificity phosphatase 1 plants and fungi (ToPFA-DSP1). High-resolution crystal structures revealed the catalytic core of ToPFA-DSP1 interacting with signaling molecules called inositol pyrophosphates (PP-InsPs). By linking individual structural data sets, the researchers elucidated how the WPD loop contributes to catalysis, despite the absence of its typical peptide sequence. In plants, this type of reaction can impact drought tolerance and regulate molecular defenses against larvae and herbivorous pathogens.

Taken together, the results represent a significant extension of the known chemical versatility of the WPD loop, thereby greatly expanding the mechanistic understanding of its important contributions to tailoring reactivity profiles for individual members of the PTP family.

Quote: Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB. A structural exposition of the non-canonical molecular reactivity in the WPD loop of protein tyrosine phosphatase. 2022. Common Nat 13(1):2231.

(Janelle Weaver, Ph.D., is a contract writer for the NIEHS Office of Communications and Public Liaison.)

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