Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta

5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.

Inter- and trans-generational impacts of environmental exposures on the germline resolved at the single-cell level

Reproduction is a remarkably intricate process involving the interaction of multiple cell types and organ systems unfolding over long periods of time and that culminates with the production of gametes. The initiation of germ cell development takes place during embryogenesis but only completes decades later in humans. The complexity inherent to reproduction and its study has long hampered our ability to decipher how environmental agents disrupt this process. Single-cell approaches provide an opportunity for a deeper understanding of the action of toxicants on germline function and analyze how the response to their exposure is differentially distributed across tissues and cell types. In addition to single-cell RNA sequencing, other single-cell or nucleus level approaches such as ATAC-sequencing and multi-omics have expanded the strategies that can be implemented in reproductive toxicological studies to include epigenomic and the nuclear transcriptomic data. Here we will discuss the current state of single-cell technologies and how they can best be utilized to advance reproductive toxicological studies. We will then discuss case studies in two model organisms (Caenorhabditis elegans and mouse) studying different environmental exposures (alcohol and e-cigarettes respectively) to highlight the value of single-cell and single-nucleus approaches for reproductive biology and reproductive toxicology.

Lifetime residential data collection protocol for the Adolescent Brain Cognitive Development (ABCD) Study

Understanding the impacts of environmental exposures on health outcomes during development is an important area of research for plenty of reasons. Collecting retrospective and prospective residential history can enrich observational studies through eventual linkages to external sources. Augmenting participant health outcome data with environmental data can better inform on the role of the environment, thereby enhancing prevention and intervention efforts. However, collecting the geospatial information needed for this type of research can be difficult, especially when data are collected directly from participants. Participants' residential histories are unique and often complex. Collecting residential history data often involves capturing precise spatial locations along specific timeframes as well as contending with recall bias and unique, complex living arrangements. When trying to assess lifetime environmental exposures, researchers must consider the many changes in location a person goes through and the timeframes in which these changes occur, ultimately creating a multidimensional and dynamic dataset. Creating data collection protocols that are feasible to administer, result in accurate data, and minimize data missingness is a major challenge to undertake. Here, we provide an overview of the protocol developed to collect the lifetime residential address information of participants in the Adolescent Brain Cognitive Development (ABCD) Study.

Associations of fine particulate matter with incident cardiovascular disease; comparing models using ZIP code-level and individual-level fine particulate matter and confounders

BACKGROUND

PM2.5 has been positively associated with cardiovascular disease (CVD) incidence. Most evidence has come from cohorts and administrative databases. Cohorts typically have extensive information on potential confounders and residential-level exposures. Administrative databases are usually more representative but typically lack information on potential confounders and often only have exposures at coarser geographies (e.g., ZIP code). The weaknesses in both types of studies have been criticized for potentially jeopardizing the validity of their findings for regulatory purposes.

METHODS

We followed 101,870 participants from the US-based Nurses' Health Study (2000-2016) and linked residential-level PM2.5 and individual-level confounders, and ZIP code-level PM2.5 and confounders. We used time-varying Cox proportional hazards models to examine associations with CVD incidence. We specified basic models (adjusted for individual-level age, race and calendar year), individual-level confounder models, and ZIP code-level confounder models.

RESULTS

Residential- and ZIP code-level PM2.5 were strongly correlated (Pearson r = 0.88). For residential-level PM2.5, the hazard ratio (HR, 95 % confidence interval) per 5 μg/m3 increase was 1.06 (1.01, 1.11) in the basic and 1.04 (0.99, 1.10) in the individual-level confounder model. For ZIP code-level PM2.5, the HR per 5 μg/m3 was 1.04 (0.99, 1.08) in the basic and 1.02 (0.97, 1.08) in the ZIP code-level confounder model.

CONCLUSION

We observed suggestive positive, but not statistically significant, associations between long-term PM2.5 and CVD incidence, regardless of the exposure or confounding model. Although differences were small, associations from models with individual-level confounders and residential-level PM2.5 were slightly stronger than associations from models with ZIP code-level confounders and PM2.5.

Integrating traffic pollution dispersion into spatiotemporal NO2 prediction

Accurately predicting ambient NO2 concentrations has great public health importance, as traffic-related air pollution is of major concern in urban areas. In this study, we present a novel approach incorporating traffic contribution to NO2 prediction in a fine-scale spatiotemporal model. We used nationally available traffic estimate dataset in a scalable dispersion model, Research LINE source dispersion model (RLINE). RLINE estimates then served as an additional input for a validated spatiotemporal pollution modeling approach. Our analysis uses measurement data collected by the Multi-Ethnic Study of Atherosclerosis and Air Pollution in the greater Los Angeles area between 2006 and 2009. We predicted road-type-specific annual average daily traffic (AADT) on road segments via national-level spatial regression models with nearest-neighbor Gaussian processes (spNNGP); the spNNGP models were trained based on over half a million point-level traffic volume measurements nationwide. AADT estimates on all highways were combined with meteorological data in RLINE models. We evaluated two strategies to integrate RLINE estimates into spatiotemporal NO2 models: 1) incorporating RLINE estimates as a space-only covariate and, 2) as a spatiotemporal covariate. The results showed that integrating the RLINE estimates as a space-only covariate improved overall cross-validation R2 from 0.83 to 0.84, and root mean squared error (RMSE) from 3.58 to 3.48 ppb. Incorporating the estimates as a spatiotemporal covariate resulted in similar model improvement. The improvement of our spatiotemporal model was more profound in roadside monitors alongside highways, with R2 increasing from 0.56 to 0.66 and RMSE decreasing from 3.52 to 3.11 ppb. The observed improvement indicates that the RLINE estimates enhanced the model's predictive capabilities for roadside NO2 concentration gradients even after considering a comprehensive list of geographic covariates including the distance to roads. Our proposed modeling framework can be generalized to improve high-resolution prediction of NO2 exposure - especially near major roads in the U.S.

The impact of COVID-19 on psychiatric clinical encounters among low-income racially-diverse children

BACKGROUND

There is a lack of longitudinal data to examine the impact of COVID-19 on all types of clinical encounters among United States, underrepresented BIPOC (Black, Indigenous, and people of color), children. This study aims to examine the changes in all the outpatient clinical encounters during the pandemic compared to the baseline, with particular attention to psychiatric encounters and diagnoses.

METHOD

This study analyzed 3-year (January 2019 to December 2021) longitudinal clinical encounter data from 3,394 children in the Boston Birth Cohort, a US urban, predominantly low-income, Black and Hispanic children. Outcomes of interest were completed outpatient clinical encounters and their modalities (telemedicine vs. in person), including psychiatric care and diagnoses, primary care, emergency department (ED), and developmental and behavioral pediatrics (DBP).

RESULTS

The study children's mean (SD) age is 13.9 (4.0) years. Compared to 2019, psychiatric encounters increased by 38% in 2020, most notably for diagnoses of adjustment disorders, depression, and post-traumatic stress disorders (PTSD). In contrast, primary care encounters decreased by 33%, ED encounters decreased by 55%, and DBP care decreased by 16% in 2020. Telemedicine was utilized the most for psychiatric and DBP encounters and the least for primary care encounters in 2020. A remarkable change in 2021 was the return of primary care encounters to the 2019 level, but psychiatric encounters fluctuated with spikes in COVID-19 case numbers.

CONCLUSIONS

Among this sample of US BIPOC children, compared to the 2019 baseline, psychiatric encounters increased by 38% during 2020, most notably for the new diagnoses of adjustment disorder, depression, and PTSD. The 2021 data showed a full recovery of primary care encounters to the baseline level but psychiatric encounters remained sensitive to the pandemic spikes. The long-term impact of the pandemic on children's mental health warrants further investigation.

Association of prenatal chlorpyrifos exposure with sexually dimorphic differences in anogenital distance among Thai farmworker children

Organophosphate (OP) insecticides are some of the most abundantly used insecticides, and prenatal exposures have been linked to adverse maternal and child health outcomes. Anogenital distance (AGD) has emerged as an early marker of androgen activity, and later reproductive outcomes, that is sensitive to alteration by environmental chemicals. Here, we examined associations between prenatal exposure to chlorpyrifos, an OP insecticide, with AGD. Pregnant farmworkers were enrolled in the Study of Asian Women and their Offspring's Development and Environmental Exposures (SAWASDEE; N = 104) between 2017 and 2019 in Northern Thailand. Concentrations of 3,5,6-trichloro-2-pyridinol (TCPy), a specific metabolite of chlorpyrifos, were measured in composited urine samples obtained from each trimester of pregnancy. AGD was measured at 12 months of age. Sex-specific adjusted linear regression models were used to examine associations between average and trimester-specific TCPy levels and AGD. In adjusted models for females and males, increasing TCPy was consistently associated with a modest, non-significant reduction in AGD. Across both strata of sex, associations were greatest in magnitude for trimester 3 (females: β = -2.17, 95 % confidence interval (CI) = -4.99, 0.66; males: β = -3.02, 95 % CI = -6.39, 0.35). In the SAWASDEE study, prenatal chlorpyrifos exposure was not strongly associated with AGD at 12 months of age.

A miniaturized sample preparation method for routine elemental determination in whole blood using volumetric absorptive micro-sampling by ICP-QQQ

Volumetric absorptive micro-sampling (VAMS) has emerged as a simple and safe tool for collecting and storing blood samples in clinical and bioanalytical fields. This study presents a novel method for determining essential and non-essential trace elements (As, Be, Cd, Cs, Cu, Fe, Mg, P, Pb, S, Sb, Se, Tl, V, U) in VAMS-collected blood samples using microwave-assisted digestion with diluted acid as sample preparation method and an inductively coupled plasma triple quadrupole mass spectrometry (ICP-QQQ) as determination technique. While certain elements posed challenges due to VAMS tip background issues (Al, Ti, Cr, Mn, Co, Ni, Sn, Mo, Ba), the method demonstrated high precision and accuracy for the targeted analytes. It was demonstrated that 4.5 mol L-1 HNO3 plus 100 µL H2O2 30% (w/w) was suitable for an efficiency of digestion for further elemental determination using micro-analysis (spending less than 300 µL analytical solution) by ICP-QQQ, given that the residual carbon content (RCC) after the digestion procedure was lower than 5%. All the results higher than limit of quantification (LOQ) were in agreement with reference values for all analytes. Accuracy was assessed through reference material analysis and recovery tests using spiked samples. Moreover, suitable agreements (p > 0.05) between this method (VAMS-M) and the comparative method (liquid sampling method) were obtained for all analytes >LOQ. Furthermore, all results >LOQ showed good precision according to precision requirements (Horwitz equation). In this way, with the use of dilute acid, low dilution factor (30-fold), and excellent digestion efficiency (>95%), the proposed method was able to achieve an excellent detection limit, precision, and accuracy for 15 elements: As, Be, Cd, Cs, Cu, Fe, Mg, P, Pb, S, Sb, Se, Tl, V, and U using ICP-MS/MS, without the need for matrix-matched calibration curves. This research showcases an innovative analytical approach using VAMS for blood samples, offering biosafety, practicality, sensitivity, versatility, and robustness. This method contributes to the advancement of trace element analysis in biomedical research and clinical applications.

Use of human predictive patch test (HPPT) data for the classification of skin sensitization hazard and potency

Since the 1940s, patch tests in healthy volunteers (Human Predictive Patch Tests, HPPTs) have been used to identify chemicals that cause skin sensitization in humans. Recently, we reported the results of a major curation effort to support the development of OECD Guideline 497 on Defined Approaches (DAs) for skin sensitization (OECD in Guideline No. 497: Defined Approaches on Skin Sensitisation, 2021a. https://doi.org/10.1787/b92879a4-en ). In the course of this work, we compiled and published a database of 2277 HPPT results for 1366 unique test substances (Strickland et al. in Arch Toxicol 97:2825-2837, 2023. https://doi.org/10.1007/s00204-023-03530-3 ). Here we report a detailed analysis of the value of HPPT data for classification of chemicals as skin sensitizers under the United Nations' Globally Harmonized System of Classification and Labelling of Chemicals (GHS). As a result, we propose the dose per skin area (DSA) used for classification by the GHS to be replaced by or complemented with a dose descriptor that may better reflect sensitization incidence [e.g., the DSA causing induction of sensitization in one individual (DSA1+) or the DSA leading to an incidence of induction in 5% of the tested individuals (DSA05)]. We also propose standardized concepts and workflows for assessing individual HPPT results, for integrating multiple HPPT results and for using them in concert with Local Lymph Node Assay (LLNA) data in a weight of evidence (WoE) assessment. Overall, our findings show that HPPT results are often not sufficient for deriving unambiguous classifications on their own. However, where they are, the resulting classifications are reliable and reproducible and can be integrated well with those from other skin sensitization data, such as the LLNA.

Fully automated whole brain segmentation from rat MRI scans with a convolutional neural network

BACKGROUND

Whole brain delineation (WBD) is utilized in neuroimaging analysis for data preprocessing and deriving whole brain image metrics. Current automated WBD techniques for analysis of preclinical brain MRI data show limited accuracy when images present with significant neuropathology and anatomical deformations, such as that resulting from organophosphate intoxication (OPI) and Alzheimer's Disease (AD), and inadequate generalizability.

METHODS

A modified 2D U-Net framework was employed for WBD of MRI rodent brains, consisting of 27 convolutional layers, batch normalization, two dropout layers and data augmentation, after training parameter optimization. A total of 265 T2-weighted 7.0 T MRI scans were utilized for the study, including 125 scans of an OPI rat model for neural network training. For testing and validation, 20 OPI rat scans and 120 scans of an AD rat model were utilized. U-Net performance was evaluated using Dice coefficients (DC) and Hausdorff distances (HD) between the U-Net-generated and manually segmented WBDs.

RESULTS

The U-Net achieved a DC (median[range]) of 0.984[0.936-0.990] and HD of 1.69[1.01-6.78] mm for OPI rat model scans, and a DC (mean[range]) of 0.975[0.898-0.991] and HD of 1.49[0.86-3.89] for the AD rat model scans.

COMPARISON WITH EXISTING METHODS

The proposed approach is fully automated and robust across two rat strains and longitudinal brain changes with a computational speed of 8 seconds/scan, overcoming limitations of manual segmentation.

CONCLUSIONS

The modified 2D U-Net provided a fully automated, efficient, and generalizable segmentation approach that achieved high accuracy across two disparate rat models of neurological diseases.

Association between ambient exposure to PM2.5 and upper aerodigestive tract cancer in Los Angeles

Fine particulate matter (PM2.5 ) contains carcinogens similar to those generated by tobacco smoking, which may increase the risks of developing smoking-related cancers, such as upper aerodigestive track (UADT) cancers, for both smokers and never-smokers. Therefore, it is imperative to understand the relation between ambient PM2.5 exposure and risk of UADT cancers. A population-based case-control study involving 565 incident UADT cancer cases and 983 controls was conducted in Los Angeles County from 1999 to 2004. The average residential PM2.5 concentration 1 year before the diagnosis date for cases and the reference date for controls was assessed using a chemical transport model. The association between ambient PM2.5 and the UADT cancers was estimated by unconditional logistic regression, adjusting for confounders at the individual and block-group level. Stratified analyses were conducted by sex, tobacco smoking status and UADT subsites. We also assessed the interaction between PM2.5 and tobacco smoking on UADT cancers. PM2.5 concentrations were associated with an elevated odds of UADT cancers (adjusted odds ratio = 1.21 per interquartile range [4.5 μg/m3 ] increase; 95% confidence interval: 1.02, 1.44). The association between PM2.5 and UADT cancers was similar across UADT subsites, sex and tobacco smoking status. The interaction between PM2.5 and tobacco smoking on UADT cancers was approximately additive on the odds scale. The effect estimate for PM2.5 and UADT cancers was similar among never smokers. Our findings support the hypothesis that exposure to PM2.5 increases the risk of UADT cancers. Improvements in air quality may reduce the risk of UADT cancers.

Infertility treatment is associated with increased risk of postpartum hospitalization due to heart disease

BACKGROUND

Cardiovascular disease is a major cause of maternal mortality, but the extent to which infertility treatment is implicated in heart disease remains unclear.

OBJECTIVE

To evaluate the association between infertility treatment and postpartum heart disease.

METHODS

We designed a retrospective cohort study of patients who delivered in the United States between 2010 and 2018. The primary outcome was hospitalization within 12-month post-delivery due to heart disease (including ischemic heart disease, atherosclerotic heart disease, cardiomyopathy, hypertensive disease, heart failure, and cardiac dysrhythmias). We estimated the rate difference (RD) of hospitalizations among patients who conceived with infertility treatment and those who conceived spontaneously. Associations were expressed as hazard ratios (HRs) and 95% confidence intervals (CIs), derived from Cox proportional hazards regression after adjustment for potential confounders.

RESULTS

Infertility treatment was recorded in 0.9% (n = 287,813) of 31,339,991 deliveries. Rates of heart disease hospitalizations with infertility treatment and with spontaneous conception were 550 and 355 per 100,000, respectively (RD 195, 95% CI: 143-247; adjusted HR 1.99, 95% CI: 1.80-2.20). The most important increase in risk was observed for hypertensive disease (adjusted HR 2.16, 95% CI: 1.92-2.42). This increased risk was apparent as early as 30-day post-delivery (HR 1.61, 95% CI: 1.39-1.86), with progressively increasing risk up to a year.

CONCLUSIONS

Although the absolute risk of postpartum heart disease hospitalization is low, infertility treatment is associated with an increased risk, especially for hypertensive disease. These findings highlight the importance of timely postpartum follow-ups in patients who received infertility treatment.

Predictors of Subspecialty Appointment Scheduling and Completion for Patients Referred From a Pediatric Primary Care Clinic

Failure to complete subspecialty referrals decreases access to subspecialty care and may endanger patient safety. We conducted a retrospective analysis of new patient referrals made to the 14 most common referral departments at Boston Children's Hospital from January 1 to December 31, 2017. The sample included 2031 patient referrals. The mean wait time between referral and appointment date was 39.6 days. In all, 87% of referrals were scheduled and 84% of scheduled appointments attended, thus 73% of the original referrals were completed. In multivariate analysis, younger age, medical complexity, being a non-English speaker, and referral to a surgical subspecialty were associated with a higher likelihood of referral completion. Black and Hispanic/Latino race/ethnicity, living in a Census tract with Social Vulnerability Index (SVI) ≥ 90th percentile, and longer wait times were associated with a lower likelihood of appointment attendance. Future interventions should consider both health care system factors such as appointment wait times and community-level barriers to referral completion.

Epidemiologic and Clinical Clues to the Etiology of Eosinophilic Esophagitis

Despite the rising prevalence and incidence of eosinophilic esophagitis (EoE), the etiology and pathophysiology remain unknown. Studies to date suggest that complex interactions between genetic and environmental risk factors result in the development and presentation of disease. Examining environmental factors both in the early life and later life exposures offers potential clues for the development of EoE, although challenges exist in making causal inferences due to diagnostic delay and access, ascertainment biases, and misclassification of cases. The authors review studies supporting early life factors as etiologic factors in the development of EoE.

Overview and Clinical Applications of Artificial Intelligence and Machine Learning in Cardiac Anesthesiology

Artificial intelligence- (AI) and machine learning (ML)-based applications are becoming increasingly pervasive in the healthcare setting. This has in turn challenged clinicians, hospital administrators, and health policymakers to understand such technologies and develop frameworks for safe and sustained clinical implementation. Within cardiac anesthesiology, challenges and opportunities for AI/ML to support patient care are presented by the vast amounts of electronic health data, which are collected rapidly, interpreted, and acted upon within the periprocedural area. To address such challenges and opportunities, in this article, the authors review 3 recent applications relevant to cardiac anesthesiology, including depth of anesthesia monitoring, operating room resource optimization, and transthoracic/transesophageal echocardiography, as conceptual examples to explore strengths and limitations of AI/ML within healthcare, and characterize this evolving landscape. Through reviewing such applications, the authors introduce basic AI/ML concepts and methodologies, as well as practical considerations and ethical concerns for initiating and maintaining safe clinical implementation of AI/ML-based algorithms for cardiac anesthesia patient care.

Examining the impact of air pollution, climate change, and social determinants of health on asthma and environmental justice

PURPOSE OF REVIEW

In this review, we discuss the current literature examining the impact air pollution and climate change has on asthma onset, control, and exacerbation. This review also addresses the risk of exposure to specific disproportionately affected communities, highlighting health disparities in exposure and asthma outcomes.

RECENT FINDINGS

Recent studies have shifted from highlighting the associations between asthma exacerbations and indoor and outdoor air pollution. Studies are now focused on confirming the association of asthma incidence from these same exposures. Many studies have linked particulate matter to adverse asthma outcomes, however, the pollutant exposures that pose the greatest risk and the effect of natural disasters fueled by climate change are under current study. Some studies have observed that the true burden that pollutant exposures have on asthma outcomes occurs at the intersection of exposure and vulnerability. Future studies in this area will address social determinants of health, societal factors such as redlining and other systemic racism practices.

SUMMARY

Although decades of research support the causal link between gaseous and particulate air pollution and the exacerbation of preexisting asthma, recent studies suggest air pollution can cause incident (new onset) asthma. Studies have started to focus on the underlying drivers of poor outcomes in asthma. Many of the structural impediments to high quality asthma care at the society level (e.g. poverty, redlining, systemic racism) also are risk factors for worsened climate events and air pollution exposure. The individuals in these disproportionately affected groups are doubly affected by worsened exposure and worsened access to care for the resultant asthma exacerbations or incident asthma. More research is needed to understand the specific climate and air pollution mitigation efforts where disproportionately affected communities would derive the most benefit.

Joint effects of air pollution and neighborhood socioeconomic status on cognitive decline - Mediation by depression, high cholesterol levels, and high blood pressure

Air pollution and neighborhood socioeconomic status (N-SES) are associated with adverse cardiovascular health and neuropsychiatric functioning in older adults. This study examines the degree to which the joint effects of air pollution and N-SES on the cognitive decline are mediated by high cholesterol levels, high blood pressure (HBP), and depression. In the Emory Healthy Aging Study, 14,390 participants aged 50+ years from Metro Atlanta, GA, were assessed for subjective cognitive decline using the cognitive function instrument (CFI). Information on the prior diagnosis of high cholesterol, HBP, and depression was collected through the Health History Questionnaire. Participants' census tracts were assigned 3-year average concentrations of 12 air pollutants and 16 N-SES characteristics. We used the unsupervised clustering algorithm Self-Organizing Maps (SOM) to create 6 exposure clusters based on the joint distribution of air pollution and N-SES in each census tract. Linear regression analysis was used to estimate the effects of the SOM cluster indicator on CFI, adjusting for age, race/ethnicity, education, and neighborhood residential stability. The proportion of the association mediated by high cholesterol levels, HBP, and depression was calculated by comparing the total and direct effects of SOM clusters on CFI. Depression mediated up to 87 % of the association between SOM clusters and CFI. For example, participants living in the high N-SES and high air pollution cluster had CFI scores 0.05 (95 %-CI:0.01,0.09) points higher on average compared to those from the high N-SES and low air pollution cluster; after adjusting for depression, this association was attenuated to 0.01 (95 %-CI:-0.04,0.05). HBP mediated up to 8 % of the association between SOM clusters and CFI and high cholesterol up to 5 %. Air pollution and N-SES associated cognitive decline was partially mediated by depression. Only a small portion (<10 %) of the association was mediated by HBP and high cholesterol.

Evaluation of Orthotrichum lyellii moss as a biomonitor of diesel exhaust

Exhaust from diesel combustion engines is an important contributor to urban air pollution and poses significant risk to human health. Diesel exhaust contains a chemical class known as nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) and is enriched in 1-nitropyrene (1-NP), which has the potential to serve as a marker of diesel exhaust. The isomeric nitro-PAHs 2-nitropyrene (2-NP) and 2-nitrofluoranthene (2-NFL) are secondary pollutants arising from photochemical oxidation of pyrene and fluoranthene, respectively. Like other important air toxics, there is not extensive monitoring of nitro-PAHs, leading to gaps in knowledge about relative exposures and urban hotspots. Epiphytic moss absorbs water, nutrients, and pollutants from the atmosphere and may hold potential as an effective biomonitor for nitro-PAHs. In this study we investigate the suitability of Orthotrichum lyellii as a biomonitor of diesel exhaust by analyzing samples of the moss for 1-NP, 2-NP, and 2-NFL in the Seattle, WA metropolitan area. Samples were collected from rural parks, urban parks, residential, and commercial/industrial areas (N = 22 locations) and exhibited increasing concentrations across these land types. Sampling and laboratory method performance varied by nitro-PAH, but was generally good. We observed moderate to moderately strong correlation between 1-NP and select geographic variables, including summer normalized difference vegetation index (NDVI) within 250 m (r = -0.88, R2 = 0.77), percent impervious surface within 50 m (r = 0.83, R2 = 0.70), percent high development land use within 500 m (r = 0.77, R2 = 0.60), and distance to nearest secondary and connecting road (r = -0.75, R2 = 0.56). The relationships between 2-NP and 2-NFL and the geographic variables were generally weaker. Our results suggest O. lyellii is a promising biomonitor of diesel exhaust, specifically for 1-NP. To our knowledge this pilot study is the first to evaluate using moss concentrations of nitro-PAHs as biomonitors of diesel exhaust.

Reproductive and Social Policies, Sociopolitical Stress, and Implications for Maternal and Child Health Equity

PURPOSE OF REVIEW

Although many environmental exposures (e.g., air pollution) are geographically patterned and persist as a result of historic economic policies (e.g., redlining), the impact of reproductive and social policies on maternal and child health remains incompletely understood. Reproductive and social policies are increasingly important for maternal and child health equity, particularly following the 2022 US Supreme Court decision in Dobbs v Jackson Women's Health Organization ("Dobbs decision"), which restricted access to abortion. Here, we summarize the literature from original research studies examining influences of reproductive and social policy on maternal and child health, focusing on impacts on adverse birth outcomes and policies as sources of stress.

RECENT FINDINGS

Several studies suggest that those most impacted by the Dobbs decision are younger, non-white, socioeconomically disadvantaged, and living in states with less access to government safety net programs, all of which are compounded by environmental injustices. Further, studies conducted in the wake of the Dobbs decision find elevated stress levels among women of reproductive age. This may represent one pathway leading to adverse birth outcomes, as epidemiologic studies demonstrate that preterm birth rates increased following the 2016 election, a period of heightened stress. Reproductive and social policies are understudied contributors to adverse outcomes for reproductive-aged women and their children. This has important implications for maternal and child health equity, as those who will be the most impacted by reproductive and social policies already experience the highest rates of adverse birth outcomes and environmental toxicant exposure.

Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase β

N6-(2-deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.

Use and co-use of tobacco and cannabis before, during, and after pregnancy: A longitudinal analysis of waves 1-5 of the Population Assessment of Tobacco and Health (PATH) study

OBJECTIVE

Co-use of tobacco and cannabis may be prevalent in pregnancy, potentially leading to additional adverse health outcomes. Utilizing a national sample of women followed prospectively before, during, and after pregnancy, this study tested whether prepregnancy co-use of tobacco and cannabis (vs. tobacco-only use and cannabis-only use) was associated with greater likelihood of continuing to use tobacco and/or cannabis during pregnancy and postpartum.

METHOD

Data were drawn from Waves 1-5 (2013-2019) of the Population Assessment of Tobacco and Health (PATH) Study. Prepregnancy, pregnancy, and postpartum data were captured and stacked over three intervals (Waves 1-3, 2-4, and 3-5). Participants were N = 686 U.S. women (72% White, 46% age 25-34) who were currently pregnant during the middle wave of an interval. Rates of tobacco-only use, cannabis-only use, and tobacco and cannabis co-use at all three time points were examined.

RESULTS

Generalized estimating equation models demonstrated that pregnant women who reported prepregnancy tobacco and cannabis co-use (vs. tobacco-only or cannabis-only use) were more likely to continue to use tobacco and/or cannabis during pregnancy and relapse in postpartum (p < .05). Among women who endorsed prepregnancy co-use and continued to use tobacco and/or cannabis in pregnancy, about half transitioned to tobacco-only use (45.16%).

CONCLUSIONS

Findings underscore the need for further clinical and empirical focus on dynamic patterns of use/co-use of tobacco and cannabis across the perinatal period, including cessation interventions to reduce tobacco and cannabis use in pregnancy and protect against relapse in postpartum. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Partial-linear single-index transformation models with censored data

In studies with time-to-event outcomes, multiple, inter-correlated, and time-varying covariates are commonly observed. It is of great interest to model their joint effects by allowing a flexible functional form and to delineate their relative contributions to survival risk. A class of semiparametric transformation (ST) models offers flexible specifications of the intensity function and can be a general framework to accommodate nonlinear covariate effects. In this paper, we propose a partial-linear single-index (PLSI) transformation model that reduces the dimensionality of multiple covariates into a single index and provides interpretable estimates of the covariate effects. We develop an iterative algorithm using the regression spline technique to model the nonparametric single-index function for possibly nonlinear joint effects, followed by nonparametric maximum likelihood estimation. We also propose a nonparametric testing procedure to formally examine the linearity of covariate effects. We conduct Monte Carlo simulation studies to compare the PLSI transformation model with the standard ST model and apply it to NYU Langone Health de-identified electronic health record data on COVID-19 hospitalized patients' mortality and a Veteran's Administration lung cancer trial.

Comparative Analysis of the Physiological and Transport Functions of Various Sources of Renal Proximal Tubule Cells Under Static and Fluidic Conditions in PhysioMimix{trade mark, serif} T12 Platform

In vitro models that can faithfully replicate critical aspects of kidney tubule function such as directional drug transport are in high demand in pharmacology and toxicology. Accordingly, development and validation of new models is underway. The objective of this study was to characterize physiological and transport functions of various sources of human renal proximal tubule epithelial cells (RPTECs). We tested TERT1-immortalized RPTEC, including OAT1-, OCT2- or OAT3-overexpressing variants, and primary RPTECs. Cells were cultured on transwell membranes in static (24-well transwells) and fluidic (transwells in PhysioMimix{trade mark, serif} T12 organ-on-chip with 2 mL/s flow) conditions. Barrier formation, transport, and gene expression were evaluated. We show that two commercially available primary RPTECs were not suitable for studies of directional transport on transwells because they formed a substandard barrier even though they exhibited higher expression of transporters, especially under flow. TERT1-parent, -OAT1 and -OAT3 cells formed robust barriers, but were unaffected by flow. TERT1-OAT1 cells exhibited inhibitable para-aminohippurate transport, it was enhanced by flow. However, efficient tenofovir secretion and perfluorooctanoic acid reabsorption by TERT1-OAT1 cells were not modulated by flow. Gene expression showed that TERT1 and TERT1-OAT1 cells were most correlated with human kidney than other cell lines, but that flow did not have noticeable effects. Overall, our data show that addition of flow to in vitro studies of the renal proximal tubule may afford benefits in some aspects of modeling kidney function, but that careful consideration of the impact such adaptations would have on the cost and throughput of the experiments is needed. Significance Statement The topic of reproducibility and robustness of the complex microphysiological systems is looming large in the field of biomedical research; therefore, the uptake of these new models by the end-users is slow. This study systematically compared various RPTEC sources and experimental conditions, aiming to identify the level of model complexity needed for testing renal tubule transport. We demonstrate that while tissue chips may afford some benefits, their throughput and complexity need careful consideration in each context of use.

Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study

BACKGROUND

Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans.

METHODS

We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders.

RESULTS

OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6.

CONCLUSION

In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.

Genetically Regulated Gene Expression in the Brain Associated With Chronic Pain: Relationships With Clinical Traits and Potential for Drug Repurposing

BACKGROUND

Chronic pain is a common, poorly understood condition. Genetic studies including genome-wide association studies have identified many relevant variants, which have yet to be translated into full understanding of chronic pain. Transcriptome-wide association studies using transcriptomic imputation methods such as S-PrediXcan can help bridge this genotype-phenotype gap.

METHODS

We carried out transcriptomic imputation using S-PrediXcan to identify genetically regulated gene expression associated with multisite chronic pain in 13 brain tissues and whole blood. Then, we imputed genetically regulated gene expression for over 31,000 Mount Sinai BioMe participants and performed a phenome-wide association study to investigate clinical relationships in chronic pain-associated gene expression changes.

RESULTS

We identified 95 experiment-wide significant gene-tissue associations (p < 7.97 × 10-7), including 36 unique genes and an additional 134 gene-tissue associations reaching within-tissue significance, including 53 additional unique genes. Of the 89 unique genes in total, 59 were novel for multisite chronic pain and 18 are established drug targets. Chronic pain genetically regulated gene expression for 10 unique genes was significantly associated with cardiac dysrhythmia, metabolic syndrome, disc disorders/dorsopathies, joint/ligament sprain, anemias, and neurologic disorder phecodes. Phenome-wide association study analyses adjusting for mean pain score showed that associations were not driven by mean pain score.

CONCLUSIONS

We carried out the largest transcriptomic imputation study of any chronic pain trait to date. Results highlight potential causal genes in chronic pain development and tissue and direction of effect. Several gene results were also drug targets. Phenome-wide association study results showed significant associations for phecodes including cardiac dysrhythmia and metabolic syndrome, thereby indicating potential shared mechanisms.

A dynamic model of inorganic arsenic-induced carcinogenesis reveals an epigenetic mechanism for epithelial-mesenchymal plasticity

Inorganic arsenic (iAs) causes cancer by initiating dynamic transitions between epithelial and mesenchymal cell phenotypes. These transitions transform normal cells into cancerous cells, and cancerous cells into metastatic cells. Most in vitro models assume that transitions between states are binary and complete, and do not consider the possibility that intermediate, stable cellular states might exist. In this paper, we describe a new, two-hit in vitro model of iAs-induced carcinogenesis that extends to 28 weeks of iAs exposure. Through week 17, the model faithfully recapitulates known and expected phenotypic, genetic, and epigenetic characteristics of iAs-induced carcinogenesis. By 28 weeks, however, exposed cells exhibit stable, intermediate phenotypes and epigenetic properties, and key transcription factor promoters (SNAI1, ZEB1) enter an epigenetically poised or bivalent state. These data suggest that key epigenetic transitions and cellular states exist during iAs-induced epithelial-to-mesenchymal transition (EMT), and that it is important for our in vitro models to encapsulate all aspects of EMT and the mesenchymal-to-epithelial transition (MET). In so doing, and by understanding the epigenetic systems controlling these transitions, we might find new, unexpected opportunities for developing targeted, cell state-specific therapeutics.

Role of UDP-Glycosyltransferase (ugt) Genes in Detoxification and Glycosylation of 1-Hydroxyphenazine (1-HP) in Caenorhabditis elegans

Caenorhabditis elegans is a useful model organism to study the xenobiotic detoxification pathways of various natural and synthetic toxins, but the mechanisms of phase II detoxification are understudied. 1-Hydroxyphenazine (1-HP), a toxin produced by the bacterium Pseudomonas aeruginosa, kills C. elegans. We previously showed that C. elegans detoxifies 1-HP by adding one, two, or three glucose molecules in N2 worms. Our current study evaluates the roles that some UDP-glycosyltransferase (ugt) genes play in 1-HP detoxification. We show that ugt-23 and ugt-49 knockout mutants are more sensitive to 1-HP than reference strains N2 or PD1074. Our data also show that ugt-23 knockout mutants produce reduced amounts of the trisaccharide sugars, while the ugt-49 knockout mutants produce reduced amounts of all 1-HP derivatives except for the glucopyranosyl product compared to the reference strains. We characterized the structure of the trisaccharide sugar phenazines made by C. elegans and showed that one of the sugar modifications contains an N-acetylglucosamine (GlcNAc) in place of glucose. This implies broad specificity regarding UGT function and the role of genes other than ogt-1 in adding GlcNAc, at least in small-molecule detoxification.

Molecular-Level Dysregulation of Insulin Pathways and Inflammatory Processes in Peripheral Blood Mononuclear Cells by Circadian Misalignment

Circadian misalignment due to night work has been associated with an elevated risk for chronic diseases. We investigated the effects of circadian misalignment using shotgun protein profiling of peripheral blood mononuclear cells taken from healthy humans during a constant routine protocol, which was conducted immediately after participants had been subjected to a 3-day simulated night shift schedule or a 3-day simulated day shift schedule. By comparing proteomic profiles between the simulated shift conditions, we identified proteins and pathways that are associated with the effects of circadian misalignment and observed that insulin regulation pathways and inflammation-related proteins displayed markedly different temporal patterns after simulated night shift. Further, by integrating the proteomic profiles with previously assessed metabolomic profiles in a network-based approach, we found key associations between circadian dysregulation of protein-level pathways and metabolites of interest in the context of chronic metabolic diseases. Endogenous circadian rhythms in circulating glucose and insulin differed between the simulated shift conditions. Overall, our results suggest that circadian misalignment is associated with a tug of war between central clock mechanisms controlling insulin secretion and peripheral clock mechanisms regulating insulin sensitivity, which may lead to adverse long-term outcomes such as diabetes and obesity. Our study provides a molecular-level mechanism linking circadian misalignment and adverse long-term health consequences of night work.

Multiple imputation of more than one environmental exposure with nondifferential measurement error

Measurement error is common in environmental epidemiologic studies, but methods for correcting measurement error in regression models with multiple environmental exposures as covariates have not been well investigated. We consider a multiple imputation approach, combining external or internal calibration samples that contain information on both true and error-prone exposures with the main study data of multiple exposures measured with error. We propose a constrained chained equations multiple imputation (CEMI) algorithm that places constraints on the imputation model parameters in the chained equations imputation based on the assumptions of strong nondifferential measurement error. We also extend the constrained CEMI method to accommodate nondetects in the error-prone exposures in the main study data. We estimate the variance of the regression coefficients using the bootstrap with two imputations of each bootstrapped sample. The constrained CEMI method is shown by simulations to outperform existing methods, namely the method that ignores measurement error, classical calibration, and regression prediction, yielding estimated regression coefficients with smaller bias and confidence intervals with coverage close to the nominal level. We apply the proposed method to the Neighborhood Asthma and Allergy Study to investigate the associations between the concentrations of multiple indoor allergens and the fractional exhaled nitric oxide level among asthmatic children in New York City. The constrained CEMI method can be implemented by imposing constraints on the imputation matrix using the mice and bootImpute packages in R.

Early life exposure to secondhand tobacco smoke and eating behaviors at age 12 years

BACKGROUND

Prenatal or early childhood secondhand tobacco smoke (SHS) exposure increases obesity risk. However, the potential mechanisms underlying this association are unclear, but obesogenic eating behaviors are one pathway that components of SHS could perturb. Our aim was to assess associations of prenatal and early childhood SHS exposure with adolescent eating behaviors.

METHODS

Data came from a prospective pregnancy and birth cohort (N = 207, Cincinnati, OH). With multiple informant models, we estimated associations of prenatal (mean of 16 and 26 weeks of gestation maternal serum cotinine concentrations) and early childhood cotinine (average concentration across ages 12, 24, 36, and 48 months) with eating behaviors at age 12 years (Child Eating Behaviors Questionnaire). We tested whether associations differed by exposure periods and adolescent's sex. Models adjusted for maternal and child covariates.

RESULTS

We found no statistically significant associations between cotinine measures and adolescent's eating behaviors. Yet, in females, prenatal cotinine was associated with greater food responsiveness (β: 0.23; 95% CI: 0.08, 0.38) and lower satiety responsiveness (β: -0.14; 95% CI: -0.26, -0.02); in males, prenatal and postnatal cotinine was related to lower food responsiveness (prenatal: β: -0.25; 95% CI: -0.04, -0.06; postnatal: β: -0.36; 95% CI: -0.06, -0.11). No significant effect modification by sex or exposure window was found for other eating behaviors.

CONCLUSION

Prenatal and early childhood SHS exposures were not related to adolescent's eating behavior in this cohort; however, biological sex may modify these associations.

Exemplar Hospital initiation trial to Enhance Treatment Engagement (EXHIT ENTRE): protocol for CTN-0098B a randomized implementation study to support hospitals in caring for patients with opioid use disorder

BACKGROUND

Hospitalizations involving opioid use disorder (OUD) are increasing. Medications for opioid use disorder (MOUD) reduce mortality and acute care utilization. Hospitalization is a reachable moment for initiating MOUD and arranging for ongoing MOUD engagement following hospital discharge. Despite existing quality metrics for MOUD initiation and engagement, few hospitals provide hospital based opioid treatment (HBOT). This protocol describes a cluster-randomized hybrid type-2 implementation study comparing low-intensity and high-intensity implementation support strategies to help community hospitals implement HBOT.

METHODS

Four state implementation hubs with expertise in initiating HBOT programs will provide implementation support to 24 community hospitals (6 hospitals/hub) interested in starting HBOT. Community hospitals will be randomized to 24-months of either a low-intensity intervention (distribution of an HBOT best-practice manual, a lecture series based on the manual, referral to publicly available resources, and on-demand technical assistance) or a high-intensity intervention (the low-intensity intervention plus funding for a hospital HBOT champion and regular practice facilitation sessions with an expert hub). The primary efficacy outcome, adapted from the National Committee on Quality Assurance, is the proportion of patients engaged in MOUD 34-days following hospital discharge. Secondary and exploratory outcomes include acute care utilization, non-fatal overdose, death, MOUD engagement at various time points, hospital length of stay, and discharges against medical advice. Primary, secondary, and exploratory outcomes will be derived from state Medicaid data. Implementation outcomes, barriers, and facilitators are assessed via longitudinal surveys, qualitative interviews, practice facilitation contact logs, and HBOT sustainability metrics. We hypothesize that the proportion of patients receiving care at hospitals randomized to the high-intensity arm will have greater MOUD engagement following hospital discharge.

DISCUSSION

Initiation of MOUD during hospitalization improves MOUD engagement post hospitalization. Few studies, however, have tested different implementation strategies on HBOT uptake, outcome, and sustainability and only one to date has tested implementation of a specific type of HBOT (addiction consultation services). This cluster-randomized study comparing different intensities of HBOT implementation support will inform hospitals and policymakers in identifying effective strategies for promoting HBOT dissemination and adoption in community hospitals.

TRIAL REGISTRATION

NCT04921787.

An adaptive biomolecular condensation response is conserved across environmentally divergent species

Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.

Bioorthogonally activated reactive species for target identification

A target identification platform derived from the bioorthogonal activation of reactive species is described. We explore the reactivity of halogenated enamine N-oxides and report that the previously undisclosed α,γ-halogenated enamine N-oxides can be reduced biooorthogonally by diboron reagents to produce highly electrophilic α,β-unsaturated haloiminium ions suitable for labeling a range of amino acid residues on proteins in a 1,2- or 1,4-fashion. Affinity labeling reagents bearing this motif enable ligand-directed protein modification and afford highly sensitive and selective target identification in unbiased chemoproteomics experiments. Target identification is supported in both cell lysate and live cells.

Assessment of census-tract level socioeconomic position as a modifier of the relationship between short-term PM2.5 exposure and cardiovascular emergency department visits in Missouri

INTRODUCTION

Ambient particulate matter ≤ 2.5 µm in aerodynamic diameter (PM2.5) exposure elevates the risk for cardiovascular disease morbidity (CVDM). The aim of this study is to characterise which area-level measures of socioeconomic position (SEP) modify the relationship between PM2.5 exposure and CVDM in Missouri at the census-tract (CT) level.

METHODS

We use individual level Missouri emergency department (ED) admissions data (n=3 284 956), modelled PM2.5 data, and yearly CT data from 2012 to 2016 to conduct a two-stage analysis. Stage one uses a case-crossover approach with conditional logistic regression to establish the baseline risk of ED visits associated with IQR changes in PM2.5. In the second stage, we use multivariate metaregression to examine how CT-level SEP modifies the relationship between ambient PM2.5 exposure and CVDM.

RESULTS

We find that overall, ambient PM2.5 exposure is associated with increased risk for CVDM. We test effect modification in statewide and urban CTs, and in the warm season only. Effect modification results suggest that among SEP measures, poverty is most consistently associated with increased risk for CVDM. For example, across Missouri, the highest poverty CTs are at an elevated risk for CVDM (OR=1.010 (95% CI 1.007 to 1.014)) compared with the lowest poverty CTs (OR=1.004 (95% CI 1.000 to 1.008)). Other SEP modifiers generally display an inconsistent or null effect.

CONCLUSION

Overall, we find some evidence that area-level SEP modifies the relationship between ambient PM2.5 exposure and CVDM, and suggest that the relationship between air-pollution, area-level SEP and CVDM may be sensitive to spatial scale.

Identifying critical windows of prenatal phenol, paraben, and pesticide exposure and child neurodevelopment: Findings from a prospective cohort study

BACKGROUND

This study aimed to investigate how exposure to a mixture of endocrine disrupting chemicals (EDCs) during two points in pregnancy affects early childhood neurodevelopment.

METHODS

We analyzed publicly-available data from a high-risk cohort of mothers and their children (2007-2014) that measured six EDCs including methyl-, ethyl- and propyl parabens (MEPB, ETPB, PRPB), Bisphenol-A (BPA), 3,5,6-trichloro-2-pyridinol (TCPy), 3-phenoxybenzoic acid (3-PBA) in prenatal urine samples during the second and third trimesters. Neurodevelopmental scores were assessed using Mullen Scales of Early Learning (MSEL) at age 3. We used mean field variational Bayes for lagged kernel machine regression (MFVB-LKMR) to investigate the association between trimester-specific co-exposure to the six EDCs and MSEL scores at age 3, stratified by sex.

RESULTS

The analysis included 130 children. For females, the relationship between BPA and 3PBA with MSEL score varied between the two trimesters. In the second trimester, effect estimates for BPA were null but inversely correlated with MSEL score in the third trimester. 3PBA had a negative relationship with MSEL in the second trimester and positive correlation in the third trimester. For males, effect estimates for all EDCs were in opposing directions across trimesters. MFVB-LKMR analysis identified significant two-way interaction between EDCs for MSEL scores in both trimesters. For example, in females, the MSEL scores associated with increased exposure to TCPy were 1.75 units (95%credible interval -0.04, -3.47) lower in the 2nd trimester and 4.61 (95%CI -3.39, -5.84) lower in the third trimester when PRPB was fixed at the 75th percentile compared to when PRPB was fixed at the 25th percentile.

CONCLUSION

Our study provides evidence that timing of EDC exposure within the prenatal period may impact neurodevelopmental outcomes in children. More of these varying effects were identified among females. Future research is needed to explore EDC mixtures and the timing of exposure during pregnancy to enhance our understanding of how these chemicals impact child health.

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.

Interferon lambda restricts herpes simplex virus skin disease by suppressing neutrophil-mediated pathology

Type III interferons (IFN-λ) are antiviral and immunomodulatory cytokines that have been best characterized in respiratory and gastrointestinal infections, but the effects of IFN-λ against skin infections have not been extensively investigated. We sought to define the skin-specific effects of IFN-λ against the highly prevalent human pathogen, herpes simplex virus (HSV). We infected mice lacking the IFN-λ receptor (Ifnlr1-/-), both the IFN-λ and the IFN-α/β receptors (Ifnar1-/-Ifnlr1-/-), or IFN-λ cytokines (Ifnl2/3-/-) and found that IFN-λ restricts the severity of HSV-1 and HSV-2 skin lesions without affecting viral loads. We used RNAseq to define IFN-λ- and IFN-β-induced transcriptional responses in primary mouse keratinocytes. Using conditional knockout mice, we found that IFN-λ signaling in both keratinocytes and neutrophils was necessary to control HSV-1 skin lesion severity and that IFN-λ signaling in keratinocytes suppressed CXCL9-mediated neutrophil recruitment to the skin. Furthermore, depleting neutrophils or blocking CXCL9 protected against severe HSV-1 skin lesions in Ifnlr1-/- mice. Altogether, our results suggest that IFN-λ plays an immunomodulatory role in the skin that restricts neutrophil-mediated pathology during HSV infection and suggests potential applications for IFN-λ in treating viral skin infections.IMPORTANCEType III interferons (IFN-λ) have been shown to have antiviral and immunomodulatory effects at epithelial barriers such as the respiratory and gastrointestinal tracts, but their effects on the skin have not been extensively investigated. We used mice lacking IFN-λ signaling to investigate the skin-specific effects of IFN-λ against the herpes simplex virus (HSV), which targets epithelial tissues to cause cold sores and genital herpes. We found that IFN-λ limited the severity of HSV skin lesions without affecting viral load and that this protective effect required IFN-λ signaling in both keratinocytes and neutrophils. We found that IFN-λ signaling in keratinocytes suppressed neutrophil recruitment to the skin and that depleting neutrophils protected against severe HSV skin lesions in the absence of IFN-λ. Altogether, our results suggest that IFN-λ plays an immunomodulatory role in the skin that restricts neutrophil-mediated pathology during HSV infection and suggests potential applications for IFN-λ in treating viral skin infections.

Comparative efficacy of seven nonpharmacological interventions on global cognition in older adults with and without mild cognitive impairment: a network meta-analysis of randomized controlled trials

To maintain current cognitive function and access greater cognitive reserves, nonpharmacological interventions may be a viable alternative for older adults with or without cognitive impairment. This study aimed to compare different nonpharmacological interventions for enhancing global cognition, including mind-body exercise, physical exercise, non-invasive brain stimulation, cognitive training intervention (CTI), acutherapy (ACU), meditation, and music therapy, by applying a network meta-analysis (NMA). Sixty-one randomized controlled trials evaluating the efficacy of interventions on global cognition in older adults with or without mild cognitive decline were selected. An NMA was conducted to compare the efficacy of different nonpharmacological interventions. The NMA revealed that mind-body exercise (standardized mean difference, 1.384; 95% confidence interval, 0.777-1.992); ACU (1.283; 0.478-2.088); meditation (0.910; 0.097-1.724); non-invasive brain stimulation (1.242; 0.254-2.230); CTI (1.269; 0.736-1.802); and physical exercise (0.977; 0.212-1.742), showed positive effects compared to passive controls. There were no significant differences between the efficacies of other interventions. Nonpharmacological interventions may potentially enhance and maintain global cognition through various pathways, such as memorizing movements and enhancing brain plasticity by reducing stress in the older adult population. Additional studies are needed to clarify the impact of other variables, including intervention methods or psychological variables.

Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements

We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, ≤2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.

Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections

Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance.

IMPORTANCE

Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

20-year depressive symptoms, dementia, and structural neuropathology in older women

INTRODUCTION

The course of depressive symptoms and dementia risk is unclear, as are potential structural neuropathological common causes.

METHODS

Utilizing joint latent class mixture models, we identified longitudinal trajectories of annually assessed depressive symptoms and dementia risk over 21 years in 957 older women (baseline age 72.7 years old) from the Women's Health Initiative Memory Study. In a subsample of 569 women who underwent structural magnetic resonance imaging, we examined whether estimates of cerebrovascular disease and Alzheimer's disease (AD)-related neurodegeneration were associated with identified trajectories.

RESULTS

Five trajectories of depressive symptoms and dementia risk were identified. Compared to women with minimal symptoms, women who reported mild and stable and emerging depressive symptoms were at the highest risk of developing dementia and had more cerebrovascular disease and AD-related neurodegeneration.

DISCUSSION

There are heterogeneous profiles of depressive symptoms and dementia risk. Common neuropathological factors may contribute to both depression and dementia. Highlights The progression of depressive symptoms and concurrent dementia risk is heterogeneous. Emerging depressive symptoms may be a prodromal symptom of dementia. Cerebrovascular disease and AD are potentially shared neuropathological factors.

Development and Application of a Multidimensional Database for the Detection of Quaternary Ammonium Compounds and Their Phase I Hepatic Metabolites in Humans

The COVID-19 pandemic has led to significantly increased human exposure to the widely used disinfectants quaternary ammonium compounds (QACs). Xenobiotic metabolism serves a critical role in the clearance of environmental molecules, yet limited data are available on the routes of QAC metabolism or metabolite levels in humans. To address this gap and to advance QAC biomonitoring capabilities, we analyzed 19 commonly used QACs and their phase I metabolites by liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS). In vitro generation of QAC metabolites by human liver microsomes produced a series of oxidized metabolites, with metabolism generally occurring on the alkyl chain group, as supported by MS/MS fragmentation. Discernible trends were observed in the gas-phase IM behavior of QAC metabolites, which, despite their increased mass, displayed smaller collision cross-section (CCS) values than those of their respective parent compounds. We then constructed a multidimensional reference SQLite database consisting of m/z, CCS, retention time (rt), and MS/MS spectra for 19 parent QACs and 81 QAC metabolites. Using this database, we confidently identified 13 parent QACs and 35 metabolites in de-identified human fecal samples. This is the first study to integrate in vitro metabolite biosynthesis with LC-IM-MS/MS for the simultaneous monitoring of parent QACs and their metabolites in humans.

Distribution of 2,2',5,5'-Tetrachlorobiphenyl (PCB52) Metabolites in Adolescent Rats after Acute Nose-Only Inhalation Exposure

Inhalation of PCB-contaminated air is increasingly recognized as a route for PCB exposure. Because limited information about the disposition of PCBs following inhalation exposure is available, this study investigated the disposition of 2,2',5,5'-tetrachlorobiphenyl (PCB52) and its metabolites in rats following acute, nose-only inhalation of PCB52. Male and female Sprague-Dawley rats (50-58 days of age, 210 ± 27 g; n = 6) were exposed for 4 h by inhalation to approximately 14 or 23 μg/kg body weight of PCB52 using a nose-only exposure system. Sham animals (n = 6) were exposed to filtered lab air. Based on gas chromatography-tandem mass spectrometry (GC-MS/MS), PCB52 was present in adipose, brain, intestinal content, lung, liver, and serum. 2,2',5,5'-Tetrachlorobiphenyl-4-ol (4-OH-PCB52) and one unknown monohydroxylated metabolite were detected in these compartments except for the brain. Liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis identified several metabolites, including sulfated, methoxylated, and dechlorinated PCB52 metabolites. These metabolites were primarily found in the liver (7 metabolites), lung (9 metabolites), and serum (9 metabolites) due to the short exposure time. These results demonstrate for the first time that complex mixtures of sulfated, methoxylated, and dechlorinated PCB52 metabolites are formed in adolescent rats following PCB52 inhalation, laying the groundwork for future animal studies of the adverse effects of inhaled PCB52.

Heterogeneity in elevated glucose and A1C as predictors of the prediabetes to diabetes transition: Framingham Heart Study, Multi-Ethnic Study on Atherosclerosis, Jackson Heart Study, and Atherosclerosis Risk In Communities

Introduction

There are a number of glycemic definitions for prediabetes; however, the heterogeneity in diabetes transition rates from prediabetes across different glycemic definitions in major US cohorts has been unexplored. We estimate the variability in risk and relative risk of adiposity based on diagnostic criteria like fasting glucose and hemoglobin A1C% (HA1C%).

Research Design and Methods

We estimated transition rate from prediabetes, as defined by fasting glucose between 100-125 and/or 110-125 mg/dL, and HA1C% between 5.7-6.5% in participant data from the Framingham Heart Study, Multi-Ethnic Study on Atherosclerosis, Atherosclerosis Risk in Communities, and the Jackson Heart Study. We estimated the heterogeneity and prediction interval across cohorts, stratifying by age, sex, and body mass index. For individuals who were prediabetic, we estimated the relative risk for obesity, blood pressure, education, age, and sex for diabetes.

Results

There is substantial heterogeneity in diabetes transition rates across cohorts and prediabetes definitions with large prediction intervals. We observed the highest range of rates in individuals with fasting glucose of 110-125 mg/dL ranging from 2-18 per 100 person-years. Across different cohorts, the association obesity or hypertension in the progression to diabetes was consistent, yet it varied in magnitude. We provide a database of transition rates across subgroups and cohorts for comparison in future studies.

Conclusion

The absolute transition rate from prediabetes to diabetes significantly depends on cohort and prediabetes definitions.

Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia

BACKGROUND

Expansion of genome-wide association studies across population groups is needed to improve our understanding of shared and unique genetic contributions to breast cancer. We performed association and replication studies guided by a priori linkage findings from African ancestry (AA) relative pairs.

METHODS

We performed fixed-effect inverse-variance weighted meta-analysis under three significant AA breast cancer linkage peaks (3q26-27, 12q22-23, and 16q21-22) in 9241 AA cases and 10 193 AA controls. We examined associations with overall breast cancer as well as estrogen receptor (ER)-positive and negative subtypes (193,132 SNPs). We replicated associations in the African-ancestry Breast Cancer Genetic Consortium (AABCG).

RESULTS

In AA women, we identified two associations on chr12q for overall breast cancer (rs1420647, OR = 1.15, p = 2.50×10-6; rs12322371, OR = 1.14, p = 3.15×10-6), and one for ER-negative breast cancer (rs77006600, OR = 1.67, p = 3.51×10-6). On chr3, we identified two associations with ER-negative disease (rs184090918, OR = 3.70, p = 1.23×10-5; rs76959804, OR = 3.57, p = 1.77×10-5) and on chr16q we identified an association with ER-negative disease (rs34147411, OR = 1.62, p = 8.82×10-6). In the replication study, the chr3 associations were significant and effect sizes were larger (rs184090918, OR: 6.66, 95% CI: 1.43, 31.01; rs76959804, OR: 5.24, 95% CI: 1.70, 16.16).

CONCLUSION

The two chr3 SNPs are upstream to open chromatin ENSR00000710716, a regulatory feature that is actively regulated in mammary tissues, providing evidence that variants in this chr3 region may have a regulatory role in our target organ. Our study provides support for breast cancer variant discovery using prioritization based on linkage evidence.

Longitudinal Transitions Between Use of Combustible, Noncombustible, and Multiple Cannabis Products From Adolescence to Young Adulthood and Intersections With Nicotine Use

Understanding transitions across use of different types of cannabis products and multiple cannabis products and how they intersect with nicotine use in young people can inform etiology and prevention. In this study, we examined transitions across use of combustible and noncombustible forms of cannabis and multiple types of cannabis from adolescence to young adulthood and the role of nicotine use in transitions. In a Southern California longitudinal cohort study (n = 3,298; baseline mean age = 16.1 (standard deviation, 0.4) years) with 9 semiannual survey waves (2015-2021), we used Markov multistate transition modeling to estimate short-term (2-wave) and long-term (9-wave) probabilities of transition across 5 cannabis use states: never use of any product, prior use with no past-6-month (P6M) use of any product, and P6M use of exclusively noncombustible products, exclusively combustible products, and multiple (noncombustible + combustible) products. Sizable transition probabilities from prior and exclusive P6M noncombustible or combustible cannabis use to P6M poly-cannabis-product use were observed in short-term (10.7%-38.9%) and long-term (43.4%-43.8%) analyses. P6M nicotine use increased risk of transitioning from never and prior use to exclusive P6M noncombustible and combustible cannabis use. Cannabis use in any form, even temporary use, during midadolescence may often be followed by poly-cannabis-product use. Nicotine use may amplify the probability of future cannabis use onset or recurrence.

Integrating Data Across Multiple Sites in the Northeastern United States to Examine Associations Between a Prenatal Metal Mixture and Child Cognition

We applied a novel hierarchical Bayesian weighted quantile sum (HBWQS) regression to combine data across 3 study sites to examine associations between prenatal exposure to metals and cognitive functioning in childhood. Data from 326 mother-child dyads enrolled in an ongoing cohort study, the Programming of Intergenerational Stress Mechanisms (PRISM) Study, based in New York, New York (recruitment in 2013-2020) and Boston, Massachusetts (recruitment 2011-2013), and the First Thousand Days of Life (FTDL) cohort study (recruitment 2012-2019), based in northern Virginia, were used. Arsenic, cadmium, manganese, lead, and antimony were measured in urine collected during pregnancy. Cognitive functioning was assessed in children aged 3-11 years using the National Institutes of Health Toolbox Cognition Battery. The HBWQS regression showed a negative association between the urinary metal mixture and the Cognition Early Childhood Composite Score in the PRISM New York City (β = -3.67, 95% credible interval (CrI): -7.61, -0.01) and FTDL (β = -3.76, 95% CrI: -7.66, -0.24) samples, with a similar trend in the PRISM Boston sample (β = -3.24, 95% CrI: -6.77, 0.144). We did not detect these associations in traditionally pooled models. HBWQS regression allowed us to account for site heterogeneity and detect associations between prenatal metal-mixture exposure and cognitive outcomes in childhood. Given the ubiquity of metals exposure, interventions aimed at reducing prenatal exposure may improve cognitive outcomes in children. This article is part of a Special Collection on Environmental Epidemiology.

Ferroptosis and HMGB2 induced calreticulin translocation required for immunogenic cell death are controlled by the nuclear exporter XPO1

Cisplatin and oxaliplatin cause the secretion of high mobility group box 1 (HMGB1) from cancer cells, which is necessary for initiation of immunogenic cell death (ICD). Calreticulin (CRT) translocation from the endoplasmic reticulum to the plasma membrane is also required; oxaliplatin induces this translocation but cisplatin does not. We have discovered that oxaliplatin causes the secretion of both HMGB1 and HMGB2 from the nucleus into the extracellular milieu. We previously showed that cisplatin mediated secretion of HMGB1 is controlled by the nuclear exporter XPO1 (chromosomal maintenance 1; CRM1). We now find that XPO1 regulates oxaliplatin mediated secretion of both HMGB1 and HMGB2. XPO1 inhibition causes nuclear accumulation of both proteins, inhibition of oxaliplatin-mediated ferroptosis of colon cancer cells, and inhibition of CRT translocation to the plasma membrane of lung and colon cancer cells. Incubation of cancer cells with cell targeted (CT)-HMGB2 confirmed that HMGB2 is responsible for translocation of CRT to the plasma membrane. CT-HMGB2 is three orders of magnitude more potent than oxaliplatin at inducing CRT translocation. Inhibition of HMGB1 and HMGB2 secretion and/or their activation of nuclear factor-kappa B (NF-kB) has potential utility for treating cardiovascular, and neurodegenerative diseases; whereas CT-HMGB2 could augment therapeutic approaches to cancer treatment.