Papers of the Month
By Janelle Weaver and Meklit Daniel
Streamlining toxicity testing in zebrafish
A new data analysis pipeline for assessing developmental toxicity outcomes using zebrafish could make comparing results across laboratories easier, according to researchers from the NIEHS Division of Translational Toxicology.
The embryonic zebrafish is a useful vertebrate model for characterizing the effects of substances on growth and development. In contrast to mammals, zebrafish embryos have a fast reproduction rate and a small, transparent body for microscopic evaluations. However, reported developmental defects in zebrafish may not be directly comparable across laboratories.
To address this limitation, the researchers established the Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) program. The goal is to investigate how differences in experimental protocols can influence chemical-mediated effects on developmental toxicity. As part of the program, three laboratories used a uniform data analysis pipeline to evaluate the same dataset of 42 substances. The researchers translated findings from the different laboratories into the same terminology and used the results to design a database and develop a data analysis pipeline.
According to the researchers, this is the first study to create tools for comparing zebrafish developmental toxicity results at the level of specific altered traits across laboratories. The study could pave the way for broader adoption of the zebrafish model for toxicological screening.
Citation: Hsieh J-H, Nolte S, Hamm JT, Wang Z, Roberts GK, Schmitt CP, Ryan KR. 2023. Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT): developing a data analysis pipeline for the assessment of developmental toxicity with an interlaboratory study. Toxics 11(5):407. (JW)
3D structures shed light on precursor step to protein production
New structural visualization of a protein complex known as TSEN shows how mutations may cause a family of human neurodevelopmental disorders, according to NIEHS researchers and their collaborators.
Before their involvement in protein synthesis, molecules called transfer RNAs (tRNAs) undergo extensive processing and modification. For example, nucleotide sequences known as introns must be removed from the precursor of tRNA (pre-tRNA) before protein production. This process is initiated by the heterotetrameric tRNA splicing endonuclease (TSEN) complex. Mutations within the TSEN complex are associated with a family of neurodevelopmental disorders called pontocerebellar hypoplasia (PCH). Yet, the overall molecular architecture of human TSEN complexes has remained elusive.
To address this knowledge gap, the researchers reported the near-atomic-resolution, cryo-electron microscopy structures of the human TSEN complex bound to intron-containing pre-tRNAs. The study unveiled the arrangement and function of all four subunits and revealed a structural core within the complex that is conserved from archaeal ancestors.
The results also showed that the TSEN54 subunit functions as a pivotal scaffold for the pre-tRNA and the two endonuclease subunits. In addition to providing insights into tRNA recognition and processing, the findings revealed the structural environment of PCH-causing mutations, which suggests that loss of TSEN stability may contribute to neurodevelopmental disease.
Citation: Hayne CK, Butay KJU, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE. 2023. Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Nat Struct Mol Biol 30(6):824–833. (JW)
Assessing gene and protein regulation in children and adults with autoimmune disease
Analysis of gene regulation in patients with an autoimmune disorder called dermatomyositis has revealed potential therapeutic targets, according to NIEHS researchers and their collaborators.
Dermatomyositis in adults and children affects skin and muscle tissues, causing rashes and weakness. Most gene regulation in these patients is described only at the level of transcripts — RNA molecules produced by copying a gene’s DNA sequence — with protein measurements limited to a targeted subset of genes of interest. No studies have previously analyzed transcript and protein expression together.
To address this gap, the researchers assessed transcript and protein regulation using blood samples from 14 adult and 12 juvenile patients with dermatomyositis, as well as healthy control subjects. The researchers discovered that the expression of 1,124 gene loci was altered in patients, with 70 genes shared by adults and children. In adult patients, the key altered pathways featured increased expression of PI3K/AKT, ERK, and p38 MAPK signaling, as well as neutrophil degranulation at both the transcript and protein levels. Other components of these and other signaling pathways were affected in both adult and juvenile patients. Some additional pathways were found that were unique to adult patients with dermatomyositis.
The assessment of transcript and proteomics expression together broadened the identification of up- and down-regulated pathways in patients with this rare autoimmune disease. According to the authors, these key signaling pathways, including those that feed into PI3K/AKT and MAPK signaling and neutrophil degranulation, are potential therapeutic targets that should be further investigated in future studies.
Citation: Ward J, Ambatipudi M, O'Hanlon TP, Smith MA, de Los Reyes M, Schiffenbauer A, Rahman S, Zerrouki K, Miller FW, Sanjuan MA, Li J-L, Casey KA, Rider LG. 2023. Shared and distinctive transcriptomic and proteomic pathways in adult and juvenile dermatomyositis. Arthritis Rheumatol; doi: 10.1002/art.42615. [Online 25 May 2023]. (JW)
Air pollution may affect breast tissue composition, cancer risk
Exposure to fine particulate matter (PM2.5) outdoors may increase the risk for breast cancer by affecting the composition of the normal breast to make it more susceptible to breast cancer, according to NIEHS researchers and their collaborators.
PM2.5 has been related to a higher breast cancer risk in studies that have considered the chemical composition of the pollutant particles. However, the biologic pathways underpinning the association between air pollution and breast cancer remain poorly understood.
To address this gap, the researchers investigated whether residential exposure to PM2.5 was associated with normal breast tissue composition using tissue samples from 3,577 volunteers who donated to the Susan G. Komen Tissue Bank. Breast tissue composition, including the proportion of epithelial, stromal, and adipose tissue, was quantified using machine-learning methods. The scientists estimated residential exposure to overall PM2.5 as well as five specific PM2.5 chemical components — sulfate, nitrate, ammonium, elemental carbon, and organic carbon. They also identified subgroups of participants who were exposed to similar PM2.5 component mixtures.
The researchers observed that among women who were exposed to a PM2.5 mixture with greater proportions of nitrogenous compounds, higher PM2.5 was related to breast tissue characteristics consistent with a higher risk of developing breast cancer. These findings support the possible role of PM2.5 in breast cancer development and breast tissue composition as a potential pathway through which outdoor air pollution affects breast cancer risk.
Citation: Ish JL, Abubakar M, Fan S, Jones RR, Niehoff NM, Henry JE, Gierach GL, White AJ. 2023. Outdoor air pollution and histologic composition of normal breast tissue. Environ Int 176:107984. (MD)
Phthalate exposure may impair fetal growth
Early pregnancy exposure to harmful chemicals called phthalates is linked to reduced fetal growth, according to NIEHS researchers and their collaborators.
Phthalates are a class of synthetic chemicals often used in food packaging, as well as hygiene, personal, and consumer care products, which results in widespread human exposure. These hormone-disrupting chemicals are of particular concern during pregnancy because exposure may affect both maternal and fetal health. Previous studies that examined the consequences of early pregnancy exposure relied on single spot urine measures and did not investigate chemicals introduced to replace phthalates.
To address these limitations, the researchers analyzed data from 254 pregnancies, measuring concentrations of phthalate and replacement biomarkers in two spot urine samples collected at approximately 12 and 14 weeks of gestation. Using ultrasound, they also measured fetal growth throughout all trimesters. Urine concentrations of phthalate biomarkers, but not replacement biomarkers, in early pregnancy were associated with reductions in fetal growth, particularly abdominal and head circumferences.
The results may have important clinical implications given that fetal growth restriction is a major contributor to infant mortality and contributes to health problems and mortality across the lifespan. According to the authors, the findings suggest that early pregnancy exposure to phthalates may pose a substantial burden to population health.
Citation: Stevens DR, Rosen EM, Van Wickle K, McNell EE, Bommarito PA, Calafat AM, Botelho JC, Sinkovskaya E, Przybylska A, Saade G, Abuhamad A, Ferguson KK. 2023. Early pregnancy phthalates and replacements in relation to fetal growth: The Human Placenta and Phthalates Study. Environ Res 15;229:115975. (JW)