Research funded by grants
COVID-19 virus hijacks lipid metabolism in the body to cause disease
The coronavirus that causes COVID-19 establishes infection by rewiring how cells make and process lipids, or fats, according to researchers funded in part by NIEHS. They also found that preventing cells from making certain fats stopped several coronavirus strains from proliferating.
Fats called triacylglycerols (TAGs) — the most abundant fats in animal cells — increased most substantially in response to infection. Further investigation showed a dramatic increase in TAG-related lipid droplets, which store fats, in cells expressing certain viral proteins. The researchers noted that those proteins may play a direct role in stimulating TAG production.
The team also evaluated the ability of fat-targeting compounds, such as weight-loss drugs, to stop infection. Drugs that inhibited pathways involved in TAG synthesis and breakdown successfully blocked viral proliferation. They were also effective against four coronavirus variants of concern, in addition to the original strain.
The array of lipid changes that occurred after infection indicates that SARS-CoV-2 affects fat metabolism in diverse ways, through multiple molecular mechanisms, according to the authors.
Citation: Farley SE, Kyle JE, Leier HC, Bramer LM, Weinstein JB, Bates TA, Lee JY, Metz TO, Schultz C, Tafesse FG. 2022. A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants. Nat Commun 13(1):3487. (Synopsis)
Exposure to PFOS linked to liver cancer
In a first-of-its-kind study, NIEHS-funded researchers revealed that exposure to high levels of perfluorooctane sulfonic acid (PFOS) may increase risk of nonviral hepatocellular carcinoma (HCC) in humans. These findings confirm previous studies in animals linking HCC and exposure to PFOS, which is part of a class of chemicals known as per- and polyfluoroalkyl substances.
The team measured pre-diagnostic plasma PFAS and conducted metabolomics in 50 incident HCC cases and 50 individually matched controls from the Multiethnic Cohort Study.
High PFOS levels, those greater than 55 micrograms per liter, were associated with 4.5-fold increased risk of HCC. PFOS exposure was associated with alterations in amino acid and glycan biosynthesis pathways, which were also associated with HCC risk. The team identified four metabolites linking PFOS exposure with HCC — glucose, butyric acid, alpha-ketoisovaleric acid, and the bile acid 7 alpha-hydroxy-3-oxo-4-cholestenoate.
Although larger studies are needed to confirm the findings, the authors note that this is the first human evidence that exposure to high levels of PFOS may alter metabolism in ways that contribute to HCC risk.
Citation: Goodrich JA, Walker D, Lin X, Wang H, Lim T, McConnell R, Conti DV, Chatzi L, Setiawan VW. 2022. Exposure to perfluoroalkyl substances and risk of hepatocellular carcinoma in a multiethnic cohort. JHEP Rep 4(10):100550. (Synopsis)
Unraveling how DDT exposure contributes to Alzheimer’s disease risk
NIEHS-funded researchers revealed a mechanism linking DDT pesticide exposure to Alzheimer’s disease.
In those with Alzheimer’s disease, protein pieces called amyloid beta accumulate in the brain. The team previously showed that people whose blood contained higher levels of a certain DDT metabolite, or breakdown product, had an increased risk of developing the condition.
Building on that work, the researchers conducted cell and animal studies to explore whether DDT contributed to amyloid beta aggregation. Specifically, they treated fruit flies, human-derived cells, and mice with levels of DDT within the range that Americans encountered in the 1960s and 1970s.
The team found that DDT enhanced amyloid beta production. Specifically, DDT exposure increased the amount of messenger RNA — a molecule that carries instructions for making proteins — associated with APP, a gene that encodes the protein that cleaves into amyloid beta.
The researchers also learned that they could stop amyloid beta production by treating cells with tetrodotoxin, a compound that blocks sodium channels, which are structures that help brain cells communicate.
Citation: Eid A, Mhatre-Winters I, Sammoura FM, Edler MK, von Stein R, Hossain MM, Han Y, Lisci M, Carney K, Konsolaki M, Hart RP, Bennett JW, Richardson JR. 2022. Effects of DDT on amyloid precursor protein levels and amyloid beta pathology: mechanistic links to Alzheimer's disease risk. Environ Health Perspect 130(8):87005. (Synopsis)
Tropical cyclones linked to rise in U.S. deaths
Over the last three decades, tropical cyclones in the U.S. were associated with higher death rates in subsequent months, according to an NIEHS-funded study. This is the first study to evaluate cause-specific mortality risks from tropical cyclones in the entire U.S. population.
The study included data on deaths in U.S. counties that experienced at least one tropical cyclone between 1988 and 2018, as well as data from the Social Vulnerability Index, which combines 15 factors that weaken a community’s ability to respond to a disaster, such as poverty and lack of access to transportation.
Residents of 1,206 counties experienced at least one tropical cyclone during the study. In the month following a cyclone, each additional cyclone day was associated with higher county-level death rates for several causes of death, including injuries; infectious and parasitic diseases; respiratory diseases; cardiovascular diseases; and neuropsychiatric conditions. For hurricanes, injury-related deaths increased by 33.4% in the month the storm hit.
The authors observed overall higher death rates in individuals aged 65 years or older, in injury-related deaths for females compared with males, and in the most socially vulnerable counties.
Citation: Parks RM, Benavides J, Anderson GB, Nethery RC, Navas-Acien A, Dominici F, Ezzati M, Kioumourtzoglou MA. 2022. Association of tropical cyclones with county-level mortality in the US. JAMA 327(10):946–955. (Synopsis)
Classifying genetic variants to better understand cancer risk, treatment
Researchers developed a framework for classifying variants in the gene RAD51C, which codes for a protein involved in DNA repair and tumor suppression.
The researchers mined several gene databases to select 56 RAD51C variants for analysis. Next, they applied three commonly used algorithms to predict how each variant would affect RAD51C protein function. The tools suggested that nearly two-thirds of the variants would have a damaging effect on DNA repair.
To test the accuracy of the algorithms, the team introduced 20 of the variants into human mammary cells. Only 10 correlated with deficient repair, suggesting that the prediction tools are limited. The researchers also investigated how structural changes in proteins produced by the 56 variants affected their function in yeast cells. More than half were defective at forming protein complexes critical to DNA repair.
Next, the team created a structural diagram showing that many of the harmful variants occurred in the Walker A motif, a genetic region that is highly conserved, or similar, across various organisms. Further investigation showed that cancer patients with certain variants in the motif responded well to treatment.
According to the authors, the study could inform assessments of similar DNA repair genes involved in susceptibility to environmental stressors.
Citation: Prakash R, Rawal Y, Sullivan MR, Grundy MK, Bret H, Mihalevic MJ, Rein HL, Baird JM, Darrah K, Zhang F, Wang R, Traina TA, Radke MR, Kaufmann SH, Swisher EM, Guérois R, Modesti M, Sung P, Jasin M, Bernstein KA. 2022. Homologous recombination-deficient mutation cluster in tumor suppressor RAD51C identified by comprehensive analysis of cancer variants. Proc Natl Acad Sci U S A 119(38):e2202727119. (Synopsis)
Leveraging deep learning to predict abdominal age, prevent disease
NIEHS-funded researchers developed a new approach to leverage machine learning to predict biological abdominal age from magnetic resonance images (MRIs) of the liver and pancreas. Unlike chronological age, biological age can be altered by lifestyle habits and our environment. By predicting abdominal age and identifying risk factors for accelerated aging, the team hoped to reveal clues to delay the onset of age-related diseases, such as fatty liver disease and type 2 diabetes.
The team built an abdominal age predictor by training a sophisticated machine learning method on 45,552 liver MRIs and 36,784 pancreas MRIs collected from UK Biobank participants aged 37-82 years old. The researchers reported that abdominal age is a complex trait involving genetics, clinical attributes, disease, and environmental and socioeconomic factors.
For example, predictions were driven by anatomical features in both liver and pancreas as well as their surrounding organs and tissues. They also identified that the gene EFEMP1, markers related to poor liver and metabolic function, and poor general health were associated with increased abdominal aging, as were sedentary behavior, diet, and smoking. The opposite was true for higher socioeconomic status.
According to the authors, their approach can be used to assess abdominal aging or the effectiveness of rejuvenating therapies.
Citation: Le Goallec A, Diai S, Collin S, Prost JB, Vincent T, Patel CJ. 2022. Using deep learning to predict abdominal age from liver and pancreas magnetic resonance images. Nat Commun 13(1):1979. (Synopsis)
Cytokine aids mouse lung repair following exposure to agricultural dust
NIEHS-funded researchers identified a novel role for the cytokine IL-22 in lung repair following exposure in mice to agricultural dust.
The study included 6-8–week-old mice missing the IL-22 gene, called knockout mice, and normal mice. The researchers exposed mice to organic dust extracts from hog confinement facilities for three weeks.
In normal mice, IL-22 was expressed in lung epithelium and in lung cells that promote tissue repair. IL-22 expression was accompanied by increases in an IL-22 receptor within the lung epithelium. Compared with normal mice, knockout mice had an enhanced response to dust exposure as evidenced by a higher number of immune cells moving into the lung and greater tissue damage.
The researchers also assessed expression of IL-22 in a human white blood cell line, finding that IL-22 increased following dust exposure. IL-22 was localized in the Golgi and released following exposure. This suggests that cells package IL-22 in the Golgi and only release it in the presence of an inflammatory insult.
These study results support a protective role for IL-22 following agricultural dust exposure. Findings may inform development of therapeutics that could benefit patients with environmentally induced lung disease, said the authors.
Citation: Ulu A, Sveiven S, Bilg A, Velazquez JV, Diaz M, Mukherjee M, Yuil-Valdes AG, Kota S, Burr A, Najera A, Nordgren TM. 2022. IL-22 regulates inflammatory responses to agricultural dust-induced airway inflammation. Toxicol Appl Pharmacol 446:116044. (Synopsis)
Nanoparticles inhaled during pregnancy can cross the rodent placenta, exposing fetus
Inhaled nanoparticles (NPs) can travel from a pregnant mother’s lungs and cross the placenta to potentially expose the fetus, according to an NIEHS-funded study in rats. NPs are used in many commercial products, including sunscreens, cosmetics, and pharmaceuticals.
Researchers exposed rats to air with titanium dioxide nanoparticles throughout pregnancy. Then they measured concentrations of titanium in maternal, placental, and fetal tissues. They also visualized NP accumulation in placental cells.
Titanium was detected in various organs and tissues of exposed mothers, including the liver, kidney, uterus, placenta, spleen, heart, blood, pancreas, and ovaries. Fetuses of exposed rats had significantly higher titanium in the umbilical cord and heart compared with controls. In exposed rats, there was on average 40.6 parts per billion (ppb) titanium measured on the maternal side of the placenta and 36.3 ppb on the fetal side, indicating that titanium accumulated similarly in both zones.
According to the authors, results suggest that inhaled NPs can be distributed throughout the body to other tissues and organs, including the placenta, in both mothers and their developing offspring.
Citation: D'Errico JN, Doherty C, Reyes George JJ, Buckley B, Stapleton PA. 2022. Maternal, placental, and fetal distribution of titanium after repeated titanium dioxide nanoparticle inhalation through pregnancy. Placenta 121:99–108. (Synopsis)
Factors related to decreased kidney function in migrant farm workers revealed
NIEHS-funded researchers reported lower kidney function in farm workers, particularly among those working in fields with conventional farming practices. The researchers examined factors that may play a role in chronic kidney disease of unknown origin, a condition linked to diverse and complex environmental influences.
Researchers enrolled more than 100 migrant and seasonal farm workers in Northern Mexico and randomly assigned them to work in certified organic or conventional farming areas. These field categories were used as a proxy for pesticide exposure. The scientists also enrolled 50 office workers within the same region to serve as a reference group.
Pre-harvest, all participants had normal kidney function. By late harvest, the team found significantly lower kidney function among farm workers while no changes were detected in office workers. In particular, the authors reported that dehydration and heat strain were associated with worse kidney function. Farm workers in conventional fields had lower kidney function compared to those working in organic fields.
According to the team, these findings reveal that pesticide exposure should be considered in combination with heat strain and dehydration in the development of kidney disease.
Citation: Lopez-Galvez N, Wagoner R, Canales RA, Ernst K, Burgess JL, de Zapien J, Rosales C, Beamer P. 2021. Longitudinal assessment of kidney function in migrant farm workers. Environ Res. 202:111686. (Synopsis)
Air pollution affects children’s brain structure
Exposure to fine particulate matter (PM2.5) in childhood can change the architecture of the brain, according to an NIEHS-funded study. This study was the first to document links between exposure to air pollution at levels below regulatory standards and white matter connectivity in children across the U.S. White matter connectivity is critical for communication between cognitive and emotional regions of the brain.
Researchers identified strong associations between PM2.5 levels and differences in white matter structure and diffusivity. Diffusivity is used to examine structural integrity and variations in the space between cells and cerebrospinal fluid. PM2.5 increased a type of diffusion that indicates changes in the cellular composition of white matter tracts in brain regions important in attention, emotional processing, and memory. Some regions were affected only in the left side of the brain, which controls language and logic, and others were affected in both sides of the brain.
Because most of the study population had PM2.5 exposures below regulatory levels set by the U.S. Environmental Protection Agency, the team suggested further improvements in air quality are needed to protect the developing brain.
Citation: Burnor E, Cserbik D, Cotter DL, Palmer CE, Ahmadi H, Eckel SP, Berhane K, McConnell R, Chen JC, Schwartz J, Jackson R, Herting MM. 2021. Association of outdoor ambient fine particulate matter with intracellular white matter microstructural properties among children. JAMA Netw Open 4(12):e2138300. (Synopsis)
New mechanistic model predicts liver toxicity
Researchers developed a new model for predicting whether chemicals are toxic to the liver. The tool also identified a cellular pathway that might be involved in the process.
Traditional models are time-consuming and expensive. To build their model, the team gathered data from reference drug lists on hundreds of chemicals known to cause liver toxicity and others with no known liver effects. They refined their tool by separating the chemicals into two groups: those that activate a specific cellular pathway in the liver that causes oxidative stress — a sign of injury — and those that do not. The team also incorporated information about chemical structural features that are involved in triggering oxidative stress.
The researchers validated the model by exposing human liver cells to 16 chemicals either implicated in oxidative stress or not, and then compared their experimental results with the model’s predictions for those compounds. Next, they entered five chemicals previously shown to cause liver toxicity and seven nontoxic chemicals into the model. Overall, the model successfully predicted the liver toxicity potential for most chemicals tested.
According to the team, this novel strategy can be used to develop additional models that consider other pathways involved in liver toxicity.
Citation: Jia X, Wen X, Russo DP, Aleksunes LM, Zhu H. 2022. Mechanism-driven modeling of chemical hepatotoxicity using structural alerts and an in vitro screening assay. J Hazard Mater 436:129193. (Synopsis)
Silicone wristbands highlight chemical exposures following Hurricane Harvey
An NIEHS-funded study was the first to reveal higher personal chemical exposures immediately following Hurricane Harvey compared with an estimated baseline. Hurricane Harvey caused flood-related damage to chemical plants, oil refineries, and hazardous waste sites.
Silicone wristband personal sampling devices were given to nearly 100 participants within 45 days of the hurricane and again one year later in the Houston metropolitan area. Because personal exposure data before the hurricane were not available, data collected a year later were used to estimate baseline for comparison.
Exposure levels were generally higher immediately following Hurricane Harvey compared with the one-year follow-up. In total, 188 volatile organic compounds were detected, 29 of which were detected in at least 30% of the study population. Of those 29 chemicals, 23 were found in significantly higher concentrations post-Hurricane Harvey compared with a year later. Similarly, 51 polycyclic aromatic hydrocarbons were detected, 31 of which were detected in at least 30% of the study population. Of those, 12 were found at statistically higher concentrations immediately following the hurricane compared with the follow-up.
According to the team, this study successfully demonstrated the use of a post-disaster timepoint to act as an estimated baseline and documented increased personal chemical exposures after Hurricane Harvey among Houston residents.
Citation: Samon SM, Rohlman D, Tidwell LG, Hoffman PD, Oluyomi AO, Anderson KA. 2022. Associating increased chemical exposure to Hurricane Harvey in a longitudinal panel using silicone wristbands. Int J Environ Res Public Health 19(11):6670. (Synopsis)
Data mining study sheds light on factors contributing to preterm birth disparities
NIEHS-funded researchers used a data mining approach to identify a diverse set of chemicals that may contribute to disparities in preterm birth among different populations.
The study included 19 chemicals observed at higher levels in the blood or urine of Black women compared with white women. The researchers obtained chemical-gene interactions from the Comparative Toxicogenomics Database and a list of genes involved in preterm birth from the Preterm Birth Database. They examined chemicals for enrichment with preterm birth genes and identified biological pathways affected by these genes.
All 19 chemicals were associated with enriched expression of genes involved in preterm birth. Exposure levels for several chemicals were at least 1.5-fold higher in Black women compared with white women. These chemicals, which included methyl mercury, methylparaben, propylparaben, diethyl phthalate, DDE, and bisphenol S, also had a higher degree of enrichment with preterm birth genes. The chemicals affected genes involved in pathways relevant to preterm birth, such as inflammation, aging, and estradiol response. Most chemicals impacted genes involved in all three pathways.
Study results suggest that exposure to an array of chemicals contributes to racial disparities in preterm birth and that multiple chemicals drive these effects.
Citation: Harris SM, Colacino J, Buxton M, Croxton L, Nguyen V, Loch-Caruso R, Bakulski KM. 2022. A data mining approach reveals chemicals detected at higher levels in non-Hispanic Black women target preterm birth genes and pathways. Reprod Sci; doi:10.1007/s43032-022-00870-w [Online 2 Feb 2022]. (Synopsis)
Pine needles work as passive samplers for PFAS
NIEHS-funded researchers showed that pine needles can be used as a tool to monitor the presence and distribution of per- and polyfluoroalkyl substances (PFAS) over time. The pine needle’s waxy coating traps PFAS and other airborne pollutants, providing a record of contamination.
The study included 60 pine needle samples from six North Carolina counties. For historical comparison, the researchers examined 15 archived samples, dating back to the 1960s, collected from the same counties.
More than 70 different PFAS were identified in the pine needles. The types of PFAS detected in samples correlated with known changes in PFAS use over time. For example, samples from the past three decades had an increasing number of newer PFAS, such as GenX, compared with samples collected before the newer substances had emerged. The pine needles, taken at varying distances from contamination sources such as airports, firefighter training sites, and chemical plants, revealed where specific PFAS were being used.
According to the researchers, study results showed that using pine needles in combination with non-targeted multidimensional analyses is a viable method for monitoring the distribution of diverse PFAS.
Citation: Kirkwood KI, Fleming J, Nguyen H, Reif DM, Baker ES, Belcher SM. 2022. Utilizing pine needles to temporally and spatially profile per- and polyfluoroalkyl substances (PFAS). Environ Sci Technol 56(6):3441-3451. (Synopsis)
Air pollution exposure affects populations disproportionately
Certain racial and ethnic groups and low-income populations in the U.S. are exposed to higher levels of fine particulate matter air pollution (PM2.5) compared with other groups, according to an NIEHS-funded study.
Areas where white and Native American populations were overrepresented were consistently exposed to lower average PM2.5 than areas where Black, Asian, and Hispanic or Latino populations were overrepresented. For example, in 2016, the average PM2.5 concentration for the Black population was 13.7% higher than that of the white population and 36.3% higher than that of the Native American population. As the Black population increased in an area, so did PM2.5, with a steep increase for areas where more than 85% of the population was Black. Similar trends held for Hispanic and Latino populations, whereas the opposite was true for areas with high-density white populations.
According to the authors, study results highlighted the importance of targeted air pollution reduction strategies to provide all people protection from environmental hazards.
Citation: Jbaily A, Zhou X, Liu J, Lee TH, Kamareddine L, Verguet S, Dominici F. 2022. Air pollution exposure disparities across US population and income groups. Nature 601(7892):228–233. (Synopsis)
Polymerase delta proofreading ensures fidelity during DNA replication
By investigating DNA replication processes in the yeast Saccharomyces cerevisiae, NIEHS scientists have demonstrated how nucleotide selectivity, proofreading, and mismatch repair (MMR) cooperate to achieve symmetrical error rates between the leading and lagging strands in an intrinsically asymmetrical process. The work provides some insight into the origins and signatures of mutations in cancers with polymerase defects.
During replication, the correct nucleotides are selectively incorporated by polymerases (Pol) alpha, delta, and epsilon. Pols delta and epsilon also possess exonucleolytic activities capable of proofreading wrongly incorporated nucleotides. This study demonstrated that Pol delta not only proofreads errors in cis, or intrinsic proofreading, but also proofreads errors made by Pol delta and epsilon in trans, or extrinsic proofreading.
A series of yeast strains were used to conduct mutation accumulation experiments across the genome, with some modified to contain mutations that abolish proofreading and MMR. This study showed that replication error rates were balanced between the two strands. MMR was more efficient on the lagging strands. This imbalance was countered by the more efficient proofreading on the leading strands conferred by both intrinsic proofreading by Pol epsilon and extrinsic proofreading by Pol delta. The research highlighted the previously underappreciated processes of extrinsic proofreading.
Citation: Zhou ZX, Lujan SA, Burkholder AB, St Charles J, Dahl J, Farrell CE, Williams JS, Kunkel TA. 2021. How asymmetric DNA replication achieves symmetrical fidelity. Nat Struct Mol Biol 28(12):1020–1028. (Synopsis)
Studying regulatory genes may lead to targeted cancer treatments
NIEHS researchers investigated how dexamethasone (Dex), a synthetic anti-inflammatory hormone, regulates transcription of the gene DNA-damage-inducible transcript 4 (DDIT4) at four specific glucocorticoid receptor (GR) sites.
Using cultured human breast cancer cells and the gene editing technique known as CRISPR, the researchers individually deleted four GR binding sites (GBSs) within the DDIT4 super enhancer, which is a regulatory region of the genome that increases the transcription of target genes. The scientists sought to determine how the GBSs contribute to Dex induction of DDIT4 transcription and how they function as parts of the super enhancer. ChIP-seq showed that GR binding at the GBSs within the super enhancer was not uniform and highlighted the role chromatin plays in the transcriptional response. Each binding site is uniquely required to promote or suppress DDIT4 expression.
A variety of hormone-dependent cancer types — including breast, skin, lung, and colon cancers — have been found to occur when the transcription of DDIT4 is dysregulated. The higher the levels of DDIT4, the worse the prognosis. However, Dex treatment reorganizes the enhancer landscape in breast cancer cells. By targeting individual regulatory elements within the hormone responsive DDIT4 super enhancer, DDIT4 can be modulated.
Citation: Hoffman JA, Trotter KW, Day CR, Ward JM, Inoue K, Rodriguez J, Archer TK. 2022. Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response. Mol Cell 82(4):803–815.e5. (Synopsis)
Diabetes during pregnancy poses lifetime risk of type 2 diabetes
Developing diabetes during pregnancy, especially multiple pregnancies, increases the risk of subsequent type 2 diabetes for decades, according to NIEHS researchers and their collaborators.
Gestational diabetes mellitus is characterized by high blood sugar levels during pregnancy in women who never had diabetes when they were not pregnant. Approximately 6% of pregnancies are complicated by gestational diabetes mellitus, which strongly predicts the later development of type 2 diabetes. It has not been clear how long this risk lasts, or whether it depends on the number of affected pregnancies.
To address these questions, the researchers analyzed the reproductive and medical histories of a nationwide sample of 50,884 women participating in the Sister Study. One or more past pregnancies affected by gestational diabetes mellitus predicted an elevated risk of type 2 diabetes. Although this risk declined somewhat with time, it increased steeply with multiple affected pregnancies, and remained elevated for more than 35 years.
The results suggest that women with a history of gestational diabetes mellitus should be screened regularly for type 2 diabetes, even late in life. Personalized lifestyle interventions targeting these individuals may be effective at preventing or delaying the development of type 2 diabetes.
Citation: Diaz-Santana MV, O'Brien KM, Park YM, Sandler DP, Weinberg CR. 2022. Persistence of risk for type 2 diabetes after gestational diabetes mellitus. Diabetes Care; doi:10.2337/dc21-1430 [Online 1 February 2022]. (Synopsis)
Seeing the cell-state forest for the trees
A new computational approach takes inspiration from forests to visualize both discrete and continuous cell transitions, according to NIEHS researchers and their collaborators.
A major controversy in developmental biology is whether cell types and cell states are continuous, discrete, or a mixture of the two. Unfortunately, models for studying cellular progression are not optimized for visualizing both disjointed and continuous transitions between states.
To address this challenge, the researchers outlined a novel data-driven framework called dynamic spanning forest mixtures (DSFMix). This powerful tool uses decision trees to build a forest for visualizing and characterizing complex developmental processes that unfold over time. DSFMix input consists of single-cell data collected at different time points, representing distinct stages of development, and its output is a mixture of discrete and continuous cell lineages. This approach can also be used to investigate relationships between the components of larger biological systems, such as the human body.
The researchers applied DSFMix to a range of biological processes, including the development of sperm and stem cells, the effects of hormones on gene activity, and immune responses to coronavirus disease. According to the authors, further refinement of decision tree–based algorithms could improve our mechanistic understanding of developmental biology at single-cell resolution.
Citation: Anchang B, Mendez-Giraldez R, Xu X, Archer TK, Chen Q, Hu G, Plevritis SK, Motsinger-Reif AA, Li JL. 2022. Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures. Brief Bioinform; doi:10.1093/bib/bbac017 [Online 22 February 2022]. (Synopsis)
Scientists assess the epigenetics of lung function across ancestries
A large-scale, multi-ancestry study by NIEHS researchers and their collaborators provides a comprehensive evaluation 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 modifications that can alter gene expression without affecting the underlying DNA sequence), are influenced by genetics and the environment and may contribute. Epigenome-wide studies have revealed some 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 bases. But replication has been limited, most research focused on European populations, and no large-scale multi-ancestry study had been published.
To overcome these limitations, the researchers conducted epigenome-wide analyses of blood DNA methylation and lung function in 17,503 adults from European, African, and Hispanic/Latino ancestries. Lung function was related 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 individuals of African ancestry. Some implicated genes are targets of approved or investigational drugs.
These findings can be leveraged for understanding mechanisms that regulate lung function, developing diagnostic and prognostic biomarkers of respiratory disease, and identifying potential targets for preventative and therapeutic strategies.
Citation: 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. Pulmonary 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]. (Synopsis)
How coronaviruses evade immune sensors
A new study shows how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, degrades viral molecules to avoid detection by host defense systems, according to NIEHS researchers and their collaborators.
SARS-CoV-2 has infected millions of people worldwide and led to the ongoing pandemic. Despite the rapid development of effective vaccines, new treatments are urgently needed due to emerging SARS-CoV-2 variants and the prevalence of breakthrough infections among those already vaccinated.
One promising antiviral target is a non-structural protein called Nsp15. Coronaviruses produce and deploy this enzyme to cleave viral RNA molecules, preferentially targeting the nucleoside uridine, thereby evading detection by host immune sensors. Yet Nsp15 remains one of the most understudied non-structural proteins, and it has not been clear how the enzyme recognizes and processes double-stranded RNA.
To address this knowledge gap, the researchers used cryogenic electron microscopy to solve the structures of SARS-CoV-2 bound to double-stranded RNA. The results showed that Nsp15 processes double-stranded RNA using a unique base-flipping mechanism. Specifically, the engaged uridine flips out from the double-stranded RNA helix and is positioned in the active site for cleavage. According to the authors, this work reveals multiple RNA-protein interfaces that could be targeted for structure-based drug design.
Citation: Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE. 2022. Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease. Nucleic Acids Res 50(14):8290–8301. (Synopsis)
Avoiding phthalates could prevent preterm births
Phthalate exposure during pregnancy may be a preventable risk factor for preterm delivery, according to NIEHS researchers and their collaborators.
Phthalates are synthetic chemicals used in everyday consumer products such as personal care items and food processing and packaging. As a result, phthalate exposure is widespread among pregnant individuals. But the evidence has been mixed regarding the potential link between phthalate exposure and preterm birth, which affects approximately 10% of pregnancies in the United States and represents a leading cause of neonatal mortality and illness.
To address this issue, the researchers analyzed 11 phthalate metabolites in urine samples collected from 6,045 pregnant women who participated in 16 studies in the U.S. during the past four decades. According to the authors, the study represents the largest prospective investigation of phthalate exposure in pregnancy and preterm birth.
Higher concentrations for several prevalent phthalates were associated with greater odds of delivering preterm. In particular, an increased risk was posed by mono-N-butyl phthalate, mono-isobutyl phthalate, mono(2-ethyl-5-carboxypentyl) phthalate, and mono(3-carboxypropyl) phthalate.
Additional analyses suggested that hypothetical interventions to reduce exposure to multiple phthalates could produce a significant decrease in preterm births. As noted by the authors, these findings highlight the need for public health and policy measures to reduce phthalate exposures among pregnant individuals.
Citation: Welch BM, Keil AP, Buckley JP, Calafat AM, Christenbury KE, Engel SM, O'Brien KM, Rosen EM, James-Todd T, Zota AR, Ferguson KK, Pooled Phthalate Exposure and Preterm Birth Study Group; Alshawabkeh AN, Cordero JF, Meeker JD, Barrett ES, Bush NR, Nguyen RHN, Sathyanarayana S, Swan SH, Cantonwine DE, McElrath TF, Aalborg J, Dabelea D, Starling AP, Hauser R, Messerlian C, Zhang Y, Bradman A, Eskenazi B, Harley KG, Holland N, Bloom MS, Newman RB, Wenzel AG, Braun JM, Lanphear BP, Yolton K, Factor-Litvak P, Herbstman JB, Rauh VA, Drobnis EZ, Sparks AE, Redmon JB, Wang C, Binder AM, Michels KB, Baird DD, Jukic AMZ, Weinberg CR, Wilcox AJ, Rich DQ, Weinberger B, Padmanabhan V, Watkins DJ, Hertz-Picciotto I, Schmidt RJ. 2022. Associations between prenatal urinary biomarkers of phthalate exposure and preterm birth: a pooled study of 16 US cohorts. JAMA Pediatr 11:e222252. (Synopsis)
Two hormones ensure normal testis formation in mice
The proper maintenance of testis structures in mouse embryos depends on hormones called anti-Müllerian hormone (AMH) and activin B, according to NIEHS scientists and their collaborators.
The researchers discovered that these two hormones act together to maintain the identity of Sertoli cells. These testicular cells are known to play a critical role in testis formation and sperm production. The appearance of Sertoli cells in the embryonic testis is thought to be controlled exclusively by transcription factors within the cells. To their surprise, the group in the Reproductive and Developmental Biology Laboratory found that AMH and activin B, both are hormones and not transcription factors, were necessary to maintain the testis program in Sertoli cells.
The absence of these Sertoli cell-derived hormones led to partial sex reversal and resulted in the formation of ovotestes — gonads with features of both testes and ovaries. The ovotestes remained to adulthood and produced both sperm and egg cells, an intriguing phenomenon mostly found in non-mammalian species such as fish.
According to the authors, the findings could explain so-called freemartin effects in pregnant sheep and cows carrying XY and XX twins, which were described by Greek scholar Marcus Terentius Varro in 27 BC. In these cases, the XX twin develops testis structures under the influence of an XY twin. Specifically, AMH and activin B produced by the XY embryo might act as freemartin factors that can masculinize the fetal ovary of the XX twin, rendering the XX twin infertile. In addition, the study may also provide insight into the mechanisms behind disorders of sex development in humans.
Citation: Rodriguez KF, Brown PR, Amato CM, Nicol B, Liu CF, Xu X, Yao HH. 2022. Somatic cell fate maintenance in mouse fetal testes via autocrine/paracrine action of AMH and activin B. Nat Commun 13(1):4130. (Synopsis)
Shining light on neural circuitry of motivated behavior
Brain cells that play an important role in promoting vigilance also affect feeding behavior in mice and possibly help animals focus their efforts to finding and eating snacks, according to NIEHS researchers and their collaborators.
The ability of the brain to integrate internal physiological drives, such as hunger and satiety, with an ever-changing environment is essential for survival. It is well known that noradrenergic neurons of the locus coeruleus (LC-NE) play a key role in modulating diverse physiological and behavioral states, including arousal, sensory processing, stress, and attention. Yet relatively little is known about the involvement of these cells in the regulation of feeding and the integration of internally driven motivational states.
Using a combination of methods in mice, the researchers found that LC-NE activity was suppressed during food consumption. The magnitude of this neural response decreased as mice ate more pellets, suggesting that LC responses to food were influenced by the level of fullness. The responses of these cells to flashes of light were also attenuated in sated mice.
Taken together, the findings suggest that LC-NE neurons affect feeding by integrating both environmental cues and internal drives. According to the authors, the results demonstrate that fasting enhances LC-NE responses to sensory stimuli, potentially supporting food-seeking and self-preservation activities during foraging.
Citation: Sciolino NR, Hsiang M, Mazzone CM, Wilson LR, Plummer NW, Amin J, Smith KG, McGee CA, Fry SA, Yang CX, Powell JM, Bruchas MR, Kravitz AV, Cushman JD, Krashes MJ, Cui G, Jensen P. 2022. Natural locus coeruleus dynamics during feeding. Sci Adv 8(33):eabn9134. (Synopsis)
A constellation of Twinkle structures may have a clinical impact
3D structures of a protein called Twinkle could shed light on mitochondrial diseases in humans, according to NIEHS researchers and their collaborators.
Twinkle is a mammalian enzyme that is vital for the replication and integrity of mitochondrial DNA. More than 90 Twinkle variants have been linked to disorders that are typically characterized by neuromuscular dysfunction. Despite its biological and clinical importance, there had been no atomic models of the enzyme. The lack of high-resolution structural knowledge has hampered a thorough understanding of the molecular mechanisms of Twinkle and associated mitochondrial diseases.
To address this knowledge gap, the researchers used cryo-electron microscopy to determine the full-length structure of the human Twinkle W315L disease variant. They pinpointed the locations of mutations associated with inherited mitochondrial disease, outlining a framework for accurately mapping nearly all clinically identified Twinkle variants.
In addition, the results provide insight into the dynamic movement and molecular consequences of the W315L variant. Taken together, the findings offer a structural basis for the dysfunctional mitochondrial DNA replication that is observed in patients. According to the authors, this study provides a platform for the development of targeted therapies for the treatment of Twinkle-associated mitochondrial diseases.
Citation: Riccio AA, Bouvette J, Perera L, Longley MJ, Krahn JM, Williams JG, Dutcher R, Borgnia MJ, Copeland WC. 2022. Structural insight and characterization of human Twinkle helicase in mitochondrial disease. Proc Natl Acad Sci U S A 119(32):e2207459119. (Synopsis)
Hair straighteners and relaxers linked to uterine cancer
The use of hair straightening and relaxing products is positively associated with uterine cancer incidence, according to NIEHS researchers and their collaborators.
Hair products may contain hazardous chemicals with endocrine-disrupting and carcinogenic properties. Previous studies have found that hair product use is associated with a higher risk of hormone-sensitive cancers, including breast and ovarian cancer, but the relationship with uterine cancer is unclear.
To address this knowledge gap, the researchers examined the association between various hair products and uterine cancer incidence among 33, 947 women aged 35-74 years. The use of straightening and relaxing products in 12 months prior to enrollment was associated with higher rates of uterine cancer. The association was stronger for frequent use (i.e., more than four times in the past 12 months). Notably, the burden of this exposure falls predominately on Black women because of the higher prevalence of straightener and relaxer use. The use of other hair products, including dyes and permanents or body waves, was not associated with uterine cancer.
According to the authors, this study provides the first epidemiologic evidence of a relationship between the use of straightening and relaxing products and uterine cancer. Given the widespread use of hair products and the rising incidence of uterine cancer, more research is needed to confirm this novel finding and to identify specific chemicals driving this observed association.
Citation: Chang CJ, O'Brien KM, Keil AP, Gaston SA, Jackson CL, Sandler DP, White AJ. 2022. Use of straighteners and other hair products and incident uterine cancer. J Natl Cancer Inst; doi:10.1093/jnci/djac165 [Online 17 October 2022]. (Synopsis)
Environmental exposures may surpass polygenic scores for predicting type 2 diabetes
Questionnaire-based polyexposure assessments outperform polygenic scores for the classification of type 2 diabetes, according to NIEHS researchers and their collaborators.
Genome-wide association studies have revealed numerous risk loci for type 2 diabetes, and polygenic scores are well established as predictive of disease risk. The impact of cumulative environmental exposures, or the exposome, is less well understood, and most studies have examined individual exposures rather than mixtures and polyexposure effects. Moreover, studies examining environmental risk factors have included only individuals with European ancestry, limiting the applicability of results.
To assess the effects of environmental factors on type 2 diabetes, the researchers analyzed survey data for 9,414 participants who provided information about genetic, environmental, and health outcomes as part of the NIEHS Personalized Environment and Genes Study. In addition, whole-genome sequencing data were available for 4,737 participants. The results revealed 76 significant associations with type 2 diabetes, including novel risk factors such as asbestos and coal dust exposure. The polyexposure assessment, which considered 13 environmental variables, outperformed polygenic scores for the classification of type 2 diabetes.
By implementing robust modeling approaches, the researchers provided support for adding environmental risk factors into decision support frameworks for public health interventions and, eventually, personalized medicine. The ancestry-based differences in predictive scores also highlight the need for studies that include diverse populations.
Citation: Akhtari FS, Lloyd D, Burkholder A, Tong X, House JS, Lee EY, Buse J, Schurman SH, Fargo DC, Schmitt CP, Hall J, Motsinger-Reif AA. Questionnaire-based polyexposure assessment outperforms polygenic scores for classification of Type 2 diabetes in a multiancestry cohort. Diabetes Care; doi:10.2337/dc22-0295 [Online 16 November 2022]. (Synopsis)
Division of Translational Toxicology research
Automated tool makes data extraction easy
A semi-automated data-extraction tool called Dextr has great potential to enhance the speed and accuracy of conducting literature reviews, according to researchers from the NIEHS Division of Translational Toxicology (formerly called the Division of the National Toxicology Program).
Data extraction is a time- and resource-intensive step in the analysis of scientific literature. Machine-learning methods for automating this process have been explored to address this challenge. Previous approaches have had limited utility, particularly in the field of environmental health sciences.
To address this need, the researchers developed a data-extraction tool that combines machine-learning models with an effective user interface to enable oversight and user verification. This powerful, flexible, web-based approach supports sophisticated features and capabilities when applied to scientific articles. Unlike other workflows, it supports extraction of complex concepts such as multiple experiments, exposures, or doses, allowing users to connect elements within a study.
Dextr performed as well as, or better than, manual extraction of environmental health animal studies. The tool reduced the time required for data extraction by 47% and achieved similar precision and recall for entities such as species, strain, and sex. According to the researchers, Dextr could reduce the workload and resources required for systematic literature reviews in various fields without compromising necessary rigor and transparency.
Citation: Walker VR, Schmitt CP, Wolfe MS, Nowak AJ, Kulesza K, Williams AR, Shin R, Cohen J, Burch D, Stout MD, Shipkowski KA, Rooney AA. 2022. Evaluation of a semi-automated data extraction tool for public health literature-based reviews: Dextr. Environ Int 159:107025. (Synopsis)
Oral vanadium toxicity studied in rodent model
Two vanadium compounds show different absorption, distribution, metabolism, and excretion properties in male and female rats, according to researchers.
Vanadium is a naturally occurring element that is present in a variety of minerals, coal, and crude oils. Low levels of vanadium are detected in many foods and in drinking water, suggesting that there is a potential for human exposure. Although vanadium is an environmental contaminant, little is known about its impact on human health.
To assess vanadium toxicity, the researchers exposed rats to drinking water containing vanadyl sulfate or sodium metavanadate, representing two prevalent oxidation states of vanadium in the environment. Exposure started before birth and lasted for three months after weaning. Vanadium concentration in blood and urine increased with the exposure concentration for both compounds. Compared with males, females had higher levels of vanadium in their blood after vanadyl sulfate exposure, and higher levels in blood and urine after exposure to sodium metavanadate. Animals exposed to sodium metavanadate had up to three-fold higher vanadium levels in blood and urine compared with vanadyl sulfate-exposed animals.
According to the authors, the results will aid in the interpretation of animal data regarding vanadium toxicity and help to determine the relevance of animal toxicity findings to human health.
Citation: Waidyanatha S, Weber FX, Fallacara DM, Harrington JM, Levine K, Robinson VG, Sparrow BR, Stout MD, Fernando R, Hooth MJ, Xie G, Roberts GK. 2022. Systemic exposure and urinary excretion of vanadium following perinatal subchronic exposure to vanadyl sulfate and sodium metavanadate via drinking water. Toxicol Lett 360:53–61. (Synopsis)
Zebrafish screening protocols affect toxicity outcomes
A quantitative assessment of sources of variability in the design of zebrafish experiments could set the groundwork for global efforts to harmonize protocols, according to researchers.
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 vastly, complicating the use of zebrafish screening for regulatory decisions.
To investigate this issue, researchers analyzed zebrafish toxicity data from three independent laboratories using the same set of 87 compounds. They estimated the concentrations that elicited death, developmental toxicity, and impairment of movement responses.
For laboratories that used similar assay protocol parameters, the concordance reached as high as 86% for developmental toxicity results and as high as 68% for neurological toxicity results. By contrast, the concordance dropped for laboratories that used different protocol parameters. Strikingly, the concentration required to produce developmental and neurological toxicity ranged, on average, up to four-fold and six-fold, respectively.
Factors that potentially contributed to this variability included the fish strain, whether the outermost membrane surrounding the embryo had been removed, the exposure scenario and volume, and behavioral testing time. According to the authors, the findings may guide ongoing efforts to incorporate zebrafish as a complementary model for drug development and toxicity testing.
Citation: Hsieh JH, Behl M, Parham F, Ryan K. 2022. Exploring the influence of experimental design on toxicity outcomes in zebrafish embryo tests. Toxicol Sci; doi:10.1093/toxsci/kfac053 [Online 27 May 2022]. (Synopsis)
Assessing the combined effects of multiple exposures through geospatial modeling
A novel geospatial modeling approach demonstrates how risk of exposure to environmental chemical mixtures can be quantified via a common molecular target, according to NIEHS researchers and their collaborators.
In the real world, individuals are exposed to multiple chemicals from sources that vary over space and time. But traditional risk assessments based on animal studies typically use a chemical-by-chemical approach. For chemicals with no existing data, new toxicology methods based on in vitro high-throughput assays can more readily provide mechanistic chemical hazard information than animal studies, according to the scientists.
The researchers established a workflow to assess the joint action of 41 modeled ambient chemical exposures in the air. They integrated human exposures with hazard data from curated high-throughput assays to identify counties where exposure to the local chemical mixture may perturb a common biological target. Specifically, the authors presented a proof-of-concept example using perturbation of a gene called CYP1A1. This perturbation could affect the activation of concurrent exposures to other chemicals and the risks such chemicals pose to individuals in certain counties.
This workflow demonstrates how new toxicology methods can be used to predict early-stage biological perturbations that could lead to adverse health outcomes resulting from exposure to chemical mixtures. This method will help support the development of models to better predict how chemicals affect biological responses.
Citation: Eccles KM, Karmaus AL, Kleinstreuer NC, Parham F, Rider CV, Wambaugh JF, Messier KP. 2022. A geospatial modeling approach to quantifying the risk of exposure to environmental chemical mixtures via a common molecular target. Sci Total Environ 158905. (Synopsis)
Study shows how cadmium affects heart development
2D and 3D model systems provide valuable insights into cellular events and molecular mechanisms associated with cadmium-induced congenital heart disease, according to researchers from the NIEHS Division of Translational Toxicology.
Maternal exposure to cadmium is a significant risk factor for congenital heart disease. But the cellular and molecular mechanisms by which cadmium affects heart development in humans are not well defined, in part due to the lack of appropriate in vitro models.
To address this knowledge gap, the researchers evaluated the effects of cadmium on the different stages of cardiac development. They used an in vitro model of early embryo development as well as a 2D model of heart muscle cell differentiation and a 3D cardiac organoid model that resembles early human fetal hearts.
The results showed that cadmium exposure inhibited the ability of human embryonic stem cells to develop into mature heart muscle cells. This, in turn, impaired cardiac organoid contractions. In addition, the results revealed an early window of sensitivity during heart development, which could mean a possibly lower risk associated with later cadmium exposure.
Together, these findings provided valuable insights into cadmium-induced congenital heart disease and cardiovascular disease. Moreover, the study established a platform for investigating cardiac function and for high-throughput screening of environmental toxicants that could affect heart development.
Citation: Wu X, Chen Y, Luz A, Hu G, Tokar EJ. 2022. Cardiac development in the presence of cadmium: an in vitro study using human embryonic stem cells and cardiac organoids. Environ Health Perspect 130(11):117002. (Synopsis)