Papers of the Month
By Victoria Placentra, Prashant Rai, Saniya Rattan, Nancy Urbano, Qing Xu
Perinatal boric acid exposure causes growth restriction in rats
Researchers from the Division of the National Toxicology Program studied the effects of gestational and postnatal boron exposure on developing rat pups. The researchers were the first to show that pups exposed to an oxidized form of boron commonly found in the environment called boric acid gained significantly less weight during postnatal development.
Boron is essential for development, but excess exposure can have detrimental effects. Humans are exposed to boron primarily through diet and drinking water. Some infants are potentially exposed when drinking water is used to reconstitute formula. The scientists performed the research because no previous studies had assessed the potential for boron-mediated toxicity during early postnatal development.
Pregnant rats were exposed to varying concentrations of boric acid once daily by oral gavage dosing, a technique that administered it directly to the stomach. Food intake, body weight, boron blood plasma levels, and any signs of morbidity were evaluated during gestation. After birth, the pups received boric acid at the same concentration as their mothers, and the same parameters were monitored in the pups for the next 28 days. The researchers found the pups that received the highest dose of boric acid had a 23% reduction in weight gain. (VP)
Citation: Watson ATD, Sutherland VL, Cunny H, Miller-Pinsler L, Furr J, Hebert C, Collins B, Waidyanatha S, Smith L, Vinke T, Aillon K, Xie G, Shockley KR, McIntyre BS. 2020. Postnatal effects of gestational and lactational gavage exposure to boric acid in the developing Sprague Dawley rat. Toxicol Sci; doi:10.1093/toxsci/kfaa061 [Online 11 May 2020].
Differential DNA methylation found in adult asthma
NIEHS researchers and their collaborators have identified changes in DNA methylation — the attachment of methyl tags to DNA — in adult asthma. As the largest epigenome-wide association study (EWAS) of adult asthma, the research provides new insights into the molecular mechanisms and pathogenesis of this respiratory disease.
Asthma is a common chronic disorder that causes inflammation in the airways and recurrent attacks of labored breathing. The disorder can be classified as non-atopic or atopic depending on whether allergen-specific antibodies are present or not. The pathogenesis of asthma likely varies by atopy status, but no previous EWAS of adult asthma has evaluated the disorder in this way.
This study recruited more than 2,000 adult farmers and their spouses enrolled in the Agricultural Lung Heath Study. Using DNA from blood and a comprehensive bead-based methylation assay, the researchers observed that the patterns of DNA methylation were altered in participants with atopic or non-atopic asthma compare to the controls, with more changes found in the participants with atopic asthma. The findings were replicated in asthma-relevant tissues. Identified changes implicated genes related to the nervous system for non-atopic asthma, and inflammation for atopic asthma. Results may contribute to discovery of novel drug targets for asthma. (QX)
Citation: Hoang TT, Sikdar S, Xu CJ, Lee MK, Cardwell J, Forno E, Imboden M, Jeong A, Madore AM, Qi C, Wang T, Bennett BD, Ward JM, Parks CG, Beane-Freeman LE, King D, Motsinger-Reif A, Umbach DM, Wyss AB, Schwartz DA, Celedon JC, Laprise C, Ober C, Probst-Hensch N, Yang IV, Koppelman GH, London SJ. 2020. Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study. Eur Respir J; doi: 10.1183/13993003.00217-2020 [Online 7 May 2020].
Tankyrase required for normal embryo development in mice
A protein called tankyrase serves a critical role in mammalian embryonic genome activation (EGA), according to NIEHS researchers and their collaborators. By utilizing an in vitro culture system, the researchers identified and characterized tankyrase, a factor that is directly responsible for allowing EGA to occur. The characterization of tankyrase during the oocyte-to-embryo transition fills a critical gap in knowledge of how factors are activated in mammalian oocytes and early embryos and may lead to improved strategies for treating infertility.
Using a mouse model, the scientists depleted tankyrase from the embryos and observed that they could not perform EGA and stopped developing. They also found that tankyrase is necessary for gene transcription, protein translation, DNA damage repair, and modulation of beta-catenin in the early embryo. Prior studies determined that tankyrase is involved in regulating pathways that are disrupted during tumorigenesis. This study finds a new role for tankyrase during normal development, revealing an essential function of this protein during the oocyte-to-embryo transition. (SR)
Citation: Gambini A, Stein P, Savy V, Grow EJ, Papas BN, Zhang Y, Kenan AC, Padilla-Banks E, Cairns BR, Williams CJ. 2020. Developmentally programmed tankyrase activity upregulates beta-catenin and licenses progression of embryonic genome activation. Dev Cell 53(5):545–560.e7. [Story]
Ubiquitin regulates removal of TOP2 DNA-protein crosslinks via TDP2
Ubiquitin (Ub) stimulates the removal of topoisomerase 2¬¬–DNA-protein crosslinks (TOP2-DPCs) by tyrosyl-DNA phosphodiesterase 2 (TDP2), according to NIEHS researchers and their collaborators in Spain. The team also reported that TDP2 single nucleotide polymorphisms can disrupt the TDP2-Ub interface. Since TDP2 works with a protein called ZATT to remove dangerous DNA-protein crosslinks, the work is important for understanding how cells handle this type of DNA damage.
Using X-ray crystallography and small angle X-ray scattering analysis, the scientists examined how Ub-dependent links and TDP2 function as they relate to DNA repair and other cellular pathways. Previous studies hypothesized that TDP2 interacts with K48-Ub chains to promote recruitment to TOP2-DPCs that are repaired using a proteasome-mediated TOP2 degradation pathway. However, the authors showed that TDP2 preferentially binds to K63-linked Ub3 and associates with K27 and K63 poly-Ub chains. Results showed that K63-linked Ub3 regulates TDP2 activity and interactions with TOP2 and ZATT via the TDP2 UBA (Ubiquitin associated) domain.
The study also defined the molecular architecture of the human TDP2-UBA:UBA complex at the ultra-high resolution of 0.85 angstroms. The data were later compared to the architectural structure of the complex in C. elegans, which uncovered some species to species differences in TOP2-DPC repair. (NU)
Citation: Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA, Cortes-Ledesma F, Williams RS. 2020. Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2. Nucleic Acids Res 48(11):6310–6325.
Webtool predicts signal interference during high-throughput screening
A team of scientists at NIEHS, including the Division of the National Toxicology Program, has created a user-friendly webtool called Interpred to predict possible chemical interferences on experimental readouts used during high-throughput screening. Interpred allows users to understand chemical properties that may interfere and help select appropriate assay conditions for study design.
The majority of toxicological or functional screening of chemicals is based on light spectrum readouts, such as luminescence and fluorescence. However, chemicals themselves can interact with the light spectrum and could cause up to 5-10% of false positive signals. Using machine learning techniques on approximately 800,000 chemicals from the Distributed Structure-Searchable Toxicity (DSSTox) Database, the Interpred webserver can predict the probability that any new chemical will interfere with the spectral readouts in different cellular conditions.
Interpred analysis of the DSSTox database predicted that most interfering chemicals inhibited luminescence and blue light fluorescence, which was associated with the presence of specific structural features in the chemicals. As a webtool, Interpred could provide valuable insights into specific chemical structures driving false signals in common screening methods of chemical libraries. (PR)
Citation: Borrel A, Mansouri K, Nolte S, Saddler T, Conway M, Schmitt C, Kleinstreuer NC. 2020. InterPred: A webtool to predict chemical autofluoresence and luminescence interference. Nucleic Acids Res; doi: 10.1093/nar/gkaa378 [Online 18 May 2020].