@article{chung_house_akhtari_makris_langston_islam_holmes_chadeau-hyam_smirnov_du_et al._2024, title={Decoding the exposome: data science methodologies and implications in exposome-wide association studies (ExWASs)}, url={https://doi.org/10.1093/exposome/osae001}, DOI={10.1093/exposome/osae001}, abstractNote={Abstract This paper explores the exposome concept and its role in elucidating the interplay between environmental exposures and human health. We introduce two key concepts critical for exposomics research. Firstly, we discuss the joint impact of genetics and environment on phenotypes, emphasizing the variance attributable to shared and nonshared environmental factors, underscoring the complexity of quantifying the exposome’s influence on health outcomes. Secondly, we introduce the importance of advanced data-driven methods in large cohort studies for exposomic measurements. Here, we introduce the exposome-wide association study (ExWAS), an approach designed for systematic discovery of relationships between phenotypes and various exposures, identifying significant associations while controlling for multiple comparisons. We advocate for the standardized use of the term “exposome-wide association study, ExWAS,” to facilitate clear communication and literature retrieval in this field. The paper aims to guide future health researchers in understanding and evaluating exposomic studies. Our discussion extends to emerging topics, such as FAIR Data Principles, biobanked healthcare datasets, and the functional exposome, outlining the future directions in exposomic research. This abstract provides a succinct overview of our comprehensive approach to understanding the complex dynamics of the exposome and its significant implications for human health.}, journal={Exposome}, author={Chung, Ming Kei and House, John S and Akhtari, Farida S and Makris, Konstantinos C and Langston, Michael A and Islam, Khandaker Talat and Holmes, Philip and Chadeau-Hyam, Marc and Smirnov, Alex I and Du, Xiuxia and et al.}, year={2024}, month={Feb} }
 @article{fleming_house_chappel_motsinger-reif_reif_2024, title={Guided optimization of ToxPi model weights using a Semi-Automated approach}, volume={29}, ISSN={["2468-1113"]}, DOI={10.1016/j.comtox.2023.100294}, abstractNote={The Toxicological Prioritization Index (ToxPi) is a visual analysis and decision support tool for dimension reduction and visualization of high throughput, multi-dimensional feature data. ToxPi was originally developed for assessing the relative toxicity of multiple chemicals or stressors by synthesizing complex toxicological data to provide a single comprehensive view of the potential health effects. It continues to be used for profiling chemicals and has since been applied to other types of “sample” entities, including geospatial (e.g. county-level Covid-19 risk and sites of historical PFAS exposure) and other profiling applications. For any set of features (data collected on a set of sample entities), ToxPi integrates the data into a set of weighted slices that provide a visual profile and a score metric for comparison. This scoring system is highly dependent on user-provided feature weights, yet users often lack knowledge of how to define these feature weights. Common methods for predicting feature weights are generally unusable due to inappropriate statistical assumptions and lack of global distributional expectation. However, users often have an inherent understanding of expected results for a small subset of samples. For example, in chemical toxicity, prior knowledge can often place subsets of chemicals into categories of low, moderate or high toxicity (reference chemicals). Ordinal regression can be used to predict weights based on these response levels that are applicable to the entire feature set, analogous to using positive and negative controls to contextualize an empirical distribution. We propose a semi-supervised method utilizing ordinal regression to predict a set of feature weights that produces the best fit for the known response (“reference”) data and subsequently fine-tunes the weights via a customized genetic algorithm. We conduct a simulation study to show when this method can improve the results of ordinal regression, allowing for accurate feature weight prediction and sample ranking in scenarios with minimal response data. To ground-truth the guided weight optimization, we test this method on published data to build a ToxPi model for comparison against expert-knowledge-driven weight assignments.}, journal={COMPUTATIONAL TOXICOLOGY}, author={Fleming, Jonathon F. and House, John S. and Chappel, Jessie R. and Motsinger-Reif, Alison A. and Reif, David M.}, year={2024}, month={Mar} }
 @article{lloyd_house_akhtari_schmitt_fargo_scholl_phillips_choksi_shah_hall_et al._2024, title={Interactive data sharing for multiple questionnaire-based exposome-wide association studies and exposome correlations in the Personalized Environment and Genes Study}, url={https://doi.org/10.1093/exposome/osae003}, DOI={10.1093/exposome/osae003}, abstractNote={The correlations among individual exposures in the exposome, which refers to all exposures an individual encounters throughout life, are important for understanding the landscape of how exposures co-occur, and how this impacts health and disease. Exposome-wide association studies (ExWAS), which are analogous to genome-wide association studies (GWAS), are increasingly being used to elucidate links between the exposome and disease. Despite increased interest in the exposome, tools and publications that characterize exposure correlations and their relationships with human disease are limited, and there is a lack of data and results sharing in resources like the GWAS catalog. To address these gaps, we developed the PEGS Explorer web application to explore exposure correlations in data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS) that were rigorously calculated to account for differing data types and previously published results from ExWAS. Through globe visualizations, PEGS Explorer allows users to explore correlations between exposures found to be associated with complex diseases. The exposome data used for analysis includes not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The web application addresses the lack of accessible data and results sharing, a major challenge in the field, and enables users to put results in context, generate hypotheses, and, importantly, replicate findings in other cohorts. PEGS Explorer will be updated with additional results as they become available, ensuring it is an up-to-date resource in exposome science.}, journal={Exposome}, author={Lloyd, Dillon and House, John S and Akhtari, Farida S and Schmitt, Charles P and Fargo, David C and Scholl, Elizabeth H and Phillips, Jason and Choksi, Shail and Shah, Ruchir and Hall, Janet E and et al.}, year={2024}, month={Feb} }
 @article{lloyd_house_akhtari_schmitt_fargo_scholl_phillips_choksi_shah_hall_et al._2024, title={Questionnaire-based exposome-wide association studies for common diseases in the Personalized Environment and Genes Study}, url={https://doi.org/10.1093/exposome/osae002}, DOI={10.1093/exposome/osae002}, abstractNote={The exposome collectively refers to all exposures, beginning in utero and continuing throughout life, and comprises not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The exposome interacts with individual genetic and epigenetic characteristics to affect human health and disease, but large-scale studies that characterize the exposome and its relationships with human disease are limited. To address this gap, we used extensive questionnaire data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS, n = 9, 429) to evaluate exposure associations in relation to common diseases. We performed an exposome-wide association study (ExWAS) to examine single exposure models and their associations with 11 common complex diseases, namely allergic rhinitis, asthma, bone loss, fibroids, high cholesterol, hypertension, iron-deficient anemia, ovarian cysts, lower GI polyps, migraines, and type 2 diabetes. Across diseases, we found associations with lifestyle factors and socioeconomic status as well as asbestos, various dust types, biohazardous material, and textile-related exposures. We also found disease-specific associations such as fishing with lead weights and migraines. To differentiate between a replicated result and a novel finding, we used an AI-based literature search and database tool that allowed us to examine the current literature. We found both replicated findings, especially for lifestyle factors such as sleep and smoking across diseases, and novel findings, especially for occupational exposures and multiple diseases.}, journal={Exposome}, author={Lloyd, Dillon and House, John S and Akhtari, Farida S and Schmitt, Charles P and Fargo, David C and Scholl, Elizabeth H and Phillips, Jason and Choksi, Shail and Shah, Ruchir and Hall, Janet E and et al.}, year={2024}, month={Feb} }
 @article{tsai_house_wright_chiu_rusyn_2023, title={A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo}, ISSN={["1096-0929"]}, url={https://doi.org/10.1093/toxsci/kfad041}, DOI={10.1093/toxsci/kfad041}, abstractNote={Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data has been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in six human cell types (induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that two cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, while the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.}, journal={TOXICOLOGICAL SCIENCES}, author={Tsai, Han-Hsuan Doris and House, John S. and Wright, Fred A. and Chiu, Weihsueh A. and Rusyn, Ivan}, year={2023}, month={Apr} }
 @article{house_gray_owen_jima_smart_hall_2023, title={C/EBP beta deficiency enhances the keratinocyte innate immune response to direct activators of cytosolic pattern recognition receptors}, volume={29}, ISSN={["1753-4267"]}, DOI={10.1177/17534259231162192}, abstractNote={The skin is the first line of defense to cutaneous microbes and viruses, and epidermal keratinocytes play a critical role in preventing infection by viruses and pathogens through activation of the type I interferon (IFN) response. Using RNAseq analysis, here we report that the conditional deletion of C/EBPβ transcription factor in mouse epidermis (CKOβ mice) resulted in the upregulation of IFNβ and numerous keratinocyte interferon-stimulated genes (ISGs). The expression of cytosolic pattern recognition receptors (cPRRs), that recognize viral RNA and DNA, were significantly increased, and enriched in the RNAseq data set. cPRRs stimulate a type I IFN response that can trigger cell death to eliminate infected cells. To determine if the observed increases in cPRRs had functional consequences, we transfected CKOβ primary keratinocytes with the pathogen and viral mimics poly(I:C) (dsRNA) or poly(dA:dT) (synthetic B-DNA) that directly activate PRRs. Transfected CKOβ primary keratinocytes displayed an amplified type I IFN response which was accompanied by increased activation of IRF3, enhanced ISG expression, enhanced activation of caspase-8, caspase-3 and increased apoptosis. Our results identify C/EBPβ as a critical repressor of the keratinocyte type I IFN response, and demonstrates that the loss of C/EBPβ primes keratinocytes to the activation of cytosolic PRRs by pathogen RNA and DNA to induce cell death mediated by caspase-8 and caspase-3.}, number={1-2}, journal={INNATE IMMUNITY}, author={House, John S. and Gray, Sophia and Owen, Jennifer R. and Jima, Dereje D. and Smart, Robert C. and Hall, Jonathan R.}, year={2023}, month={Jan}, pages={14–24} }
 @article{choudhary_monasso_karhunen_ronkainen_mancano_howe_niu_zeng_guan_dou_et al._2023, title={Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence}, volume={12}, ISSN={["1476-5578"]}, DOI={10.1038/s41380-023-02331-5}, abstractNote={Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.}, journal={MOLECULAR PSYCHIATRY}, author={Choudhary, Priyanka and Monasso, Giulietta S. and Karhunen, Ville and Ronkainen, Justiina and Mancano, Giulia and Howe, Caitlin G. and Niu, Zhongzheng and Zeng, Xuehuo and Guan, Weihua and Dou, John and et al.}, year={2023}, month={Dec} }
 @article{jackson_house_henriquez_schladweiler_jackson_fisher_snow_alewel_motsinger-reif_kodavanti_2023, title={Multi-tissue transcriptomic and serum metabolomic assessment reveals systemic implications of acute ozone-induced stress response in male Wistar Kyoto rats}, url={https://doi.org/10.1007/s11306-023-02043-5}, DOI={10.1007/s11306-023-02043-5}, journal={Metabolomics}, author={Jackson, Thomas W. and House, John S. and Henriquez, Andres R. and Schladweiler, Mette C. and Jackson, Kimberly MP and Fisher, Anna A. and Snow, Sam J. and Alewel, Devin I. and Motsinger-Reif, Allison A. and Kodavanti, Urmila P.}, year={2023}, month={Sep} }
 @article{wheeler_lim_house_shockley_john bailer_fostel_yang_talley_raghuraman_gift_et al._2023, title={ToxicR: A computational platform in R for computational toxicology and dose–response analyses}, volume={25}, ISSN={2468-1113}, url={http://dx.doi.org/10.1016/j.comtox.2022.100259}, DOI={10.1016/j.comtox.2022.100259}, abstractNote={The need to analyze the complex relationships observed in high-throughput toxicogenomic and other omic platforms has resulted in an explosion of methodological advances in computational toxicology. However, advancements in the literature often outpace the development of software researchers can implement in their pipelines, and existing software is frequently based on pre-specified workflows built from well-vetted assumptions that may not be optimal for novel research questions. Accordingly, there is a need for a stable platform and open-source codebase attached to a programming language that allows users to program new algorithms. To fill this gap, the Biostatistics and Computational Biology Branch of the National Institute of Environmental Health Sciences, in cooperation with the National Toxicology Program (NTP) and US Environmental Protection Agency (EPA), developed ToxicR, an open-source R programming package. The ToxicR platform implements many of the standard analyses used by the NTP and EPA, including dose-response analyses for continuous and dichotomous data that employ Bayesian, maximum likelihood, and model averaging methods, as well as many standard tests the NTP uses in rodent toxicology and carcinogenicity studies, such as the poly-K and Jonckheere trend tests. ToxicR is built on the same codebase as current versions of the EPA's Benchmark Dose software and NTP's BMDExpress software but has increased flexibility because it directly accesses this software. To demonstrate ToxicR, we developed a custom workflow to illustrate its capabilities for analyzing toxicogenomic data. The unique features of ToxicR will allow researchers in other fields to add modules, increasing its functionality in the future.}, journal={Computational Toxicology}, publisher={Elsevier BV}, author={Wheeler, Matthew W. and Lim, Sooyeong and House, John S. and Shockley, Keith R. and John Bailer, A. and Fostel, Jennifer and Yang, Longlong and Talley, Dawan and Raghuraman, Ashwin and Gift, Jeffery S. and et al.}, year={2023}, month={Feb}, pages={100259} }
 @article{house_rotroff_fonseca_hempe_mychaleckyj_doria_buse_motsinger reif_2022, title={143-OR: Mapping Genetic Determinants of Blood Glucose Control in the Action to Control Cardiovascular Risk in Diabetes Study Group (ACCORD)}, volume={71}, ISSN={0012-1797}, url={http://dx.doi.org/10.2337/db22-143-OR}, DOI={10.2337/db22-143-OR}, abstractNote={The hemoglobin glycation index (HGI) is the difference between observed HbA1c and predicted HbA1c from FPG using linear regression. HGI is an important biomarker of clinical management/drug treatment outcomes and can identify individuals at high risk for multiple adverse events and outcomes before the appearance of clinical symptoms. Here, we sought to test if variation in HGI has genetic determinants in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial using a genome-wide association approach (N = 7913) . We subsequently replicated the top hits (P < 1e-5) in the Atherosclerosis Risk in Communities Study (ARIC; N = 3741) . An intergenic SNP rs73407935 (7q11.22) was associated with HGI (P = 5.8e-10) with the locus replicating in ARIC. Further, multiple variants at suggestive genome-wide significance in discovery (P < 5e-6) replicated in ARIC including variants near or in ASAH1 (P = 2.4e-6) , a region previously associated with risk of CAD in T2D, LRRC4C (P = 2.4e-6) , SHLD1 (P = 3.7e-6) and FAM22B (P = 2.5e-6) . The top 2 replicated SNPs in FAM22B are characterized eQTLs for expression of multiple genes in cells from pancreas, brain, and the immune system, including TRAF4, PROCA1, and RPL23A. Many SNPs associated with HGI were distinct from those associated with FPG or HbA1c. In ACCORD, sex-specific HGI associations with SNPs in or near GALNT11 in females (P = 5e-9) and HECW2 (P = 1.5e-8) in males were observed. Further, analysis of 544 Hispanics revealed associations of a strong eQTL variant near USF1 (rs2516837; P = 1.5e-09) and SNPs near NXNL2/SPIN1 (rs141006133; P = 6.9e-9) with HGI. This work represents the first evaluation of the genetic etiology of HGI. We identified and replicated variants that merit further study in the development of precision medicine for treatment of T2D. The results of the stratified analyses highlight the potential importance of heterogeneity in these efforts.
 
 
 J.S.House: None. D.M.Rotroff: Research Support; Novo Nordisk, Stock/Shareholder; Clarified Precision Medicine. V.Fonseca: Consultant; Abbott, Asahi Kasei Corporation, Bayer AG, Novo Nordisk, Sanofi, Research Support; Fractyl Health, Inc., Jaguar Gene Therapy, Stock/Shareholder; Abbott, Amgen Inc., BRAVO4Health, Mellitus Health. J.M.Hempe: None. J.Mychaleckyj: None. A.Doria: Research Support; Novo Nordisk Foundation. J.B.Buse: Consultant; Alkahest, Anji, AstraZeneca, Boehringer Ingelheim International GmbH, Cirius Therapeutics, Inc., Eli Lilly and Company, Fortress biotech, GentiBio, Glycadia, Glyscend, Janssen Pharmaceuticals, Inc., Mellitus Health, Moderna, Inc., Pendulum Therapeutics, Praetego, LLC, Stability Health, Valo, Zealand Pharma A/S, Other Relationship; Adocia, AstraZeneca, Eli Lilly and Company, Intarcia Therapeutics, Inc., MannKind Corporation, Novo Nordisk, Sanofi, Senseonics, vTv Therapeutics, Research Support; AstraZeneca, Dexcom, Inc., Eli Lilly and Company, Novo Nordisk, vTv Therapeutics, Stock/Shareholder; Glyscend, Mellitus Health, Pendulum Therapeutics, PhaseBio Pharmaceuticals, Inc., Praetego, LLC, Stability Health. A.Motsinger-reif: None.
 
 
 
 NHLBI RO1HL110380NIDDK P30DK124723NCATS UL1TR002489
}, number={Supplement_1}, journal={Diabetes}, publisher={American Diabetes Association}, author={House, John S. and Rotroff, Daniel M. and Fonseca, Vivian and Hempe, James M. and Mychaleckyj, Josyf and Doria, Alessandro and Buse, John B. and Motsinger Reif, Alison}, year={2022}, month={Jun} }
 @article{shive_house_ferguson_jima_selmek_lloyd_2022, title={Abstract PR011: Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model}, volume={28}, ISSN={1557-3265}, url={http://dx.doi.org/10.1158/1557-3265.SARCOMAS22-PR011}, DOI={10.1158/1557-3265.SARCOMAS22-PR011}, abstractNote={
 Contributions of the microenvironment to soft tissue sarcoma progression are relatively undefined, representing a major impediment to identifying essential regulatory networks in sarcomagenesis. Furthermore, genetic and molecular characteristics that distinguish precancerous versus cancerous microenvironments are not well known across human cancer types. While animal models have the potential to reveal these complex processes, significant impediments to such inquiries include (1) the difficulty in distinguishing microenvironmental cells from precancerous or cancer cells in tissue specimens; and (2) the challenge in defining a discrete tissue with known cancer predilection that represents a precancerous microenvironment. We developed a unique zebrafish model that allows segregation of microenvironmental, precancerous, and cancerous cell populations by fluorescence-activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor (MPNST), a type of soft tissue sarcoma with a particularly poor prognosis due to aggressive growth, limited response to conventional treatment, and ineffective targeted therapy options. Using RNA-seq, we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model and determined that the precancerous and cancerous microenvironments exhibit broad activation of inflammatory and immune-associated signaling networks. Markers for both M1 and M2 macrophage polarization were upregulated in precancerous and cancerous microenvironments, suggesting the presence of a mixed macrophage population during sarcomagenesis. Patterns of ligand and receptor expression based on a previously defined human ligand-receptor network identified significant upregulation of multiple tumor-promoting ligands in both precancerous and cancerous microenvironments. We also identified specific ligand-receptor pairs that may mediate key signaling events during sarcoma initiation and progression. Together this work provide new insight into distinguishing characteristics of the cancer-prone cellular microenvironment that may promote MPNST initiation and progression in vertebrates.
 Citation Format: Heather R. Shive, John S. House, Jordan L. Ferguson, Dereje D. Jima, Aubrie A. Selmek, Dillon T. Lloyd. Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR011.}, number={18_Supplement}, journal={Clinical Cancer Research}, publisher={American Association for Cancer Research (AACR)}, author={Shive, Heather R. and House, John S. and Ferguson, Jordan L. and Jima, Dereje D. and Selmek, Aubrie A. and Lloyd, Dillon T.}, year={2022}, month={Sep}, pages={PR011–PR011} }
 @article{jackson_henriquez_snow_schladweiler_fisher_alewel_house_kodavanti_2022, title={Adrenal Stress Hormone Regulation of Hepatic Homeostatic Function After an Acute Ozone Exposure in Wistar-Kyoto Male Rats}, volume={189}, ISSN={1096-6080 1096-0929}, url={http://dx.doi.org/10.1093/toxsci/kfac065}, DOI={10.1093/toxsci/kfac065}, abstractNote={Ozone-induced lung injury and inflammation and pulmonary/hypothalamus gene expression changes are diminished in adrenalectomized (AD) rats. Acute ozone exposure induces metabolic alterations concomitant with increases in epinephrine and corticosterone. We hypothesized that adrenal hormones are responsible for observed hepatic ozone effects, and in AD rats, these changes would be diminished. 5-7 days after sham (SH) or AD surgeries, male Wistar-Kyoto rats were exposed to air or 0.8-ppm ozone for 4-hrs. Serum samples were analyzed for metabolites and liver for transcriptional changes immediately post-exposure. Ozone increased circulating triglycerides, cholesterol, free fatty-acids, and leptin in SH but not AD rats. Ozone-induced inhibition of glucose-mediated insulin release was absent in AD rats. Unlike diminution of ozone-induced hypothalamus and lung mRNA expression changes, AD in air-exposed rats (AD-air/SH-air) caused differential hepatic expression of ∼1000 genes. Likewise, ozone in AD rats caused differential expression of ∼1000 genes (AD-ozone/AD-air). Ozone-induced hepatic changes in SH rats reflected enrichment for pathways involving metabolic processes, including acetyl-CoA biosynthesis, TCA cycle, and sirtuins. Upstream predictor analysis identified similarity to responses produced by glucocorticoids and pathways involving forskolin. These changes were absent in AD rats exposed to ozone. However, ozone caused unique changes in AD liver mRNA reflecting activation of synaptogenesis, neurovascular coupling, neuroinflammation, and insulin signaling with inhibition of senescence pathways. In these rats, upstream predictor analysis identified numerous microRNAs involved in glucocorticoid insufficiency. These data demonstrate the critical role of adrenal stress hormones in ozone-induced hepatic homeostasis and necessitate further research elucidating their role in propagating environmentally driven diseases.}, number={1}, journal={Toxicological Sciences}, publisher={Oxford University Press (OUP)}, author={Jackson, Thomas W and Henriquez, Andres R and Snow, Samantha J and Schladweiler, Mette C and Fisher, Anna A and Alewel, Devin I and House, John S and Kodavanti, Urmila P}, year={2022}, month={Jun}, pages={73–90} }
 @article{lloyd_skinner_maguire_murphy_motsinger-reif_hoyo_house_2022, title={Clomifene and Assisted Reproductive Technology in Humans Are Associated with Sex-Specific Offspring Epigenetic Alterations in Imprinted Control Regions}, volume={23}, ISSN={["1422-0067"]}, url={https://doi.org/10.3390/ijms231810450}, DOI={10.3390/ijms231810450}, abstractNote={Children conceived with assisted reproductive technology (ART) have an increased risk of adverse outcomes, including congenital malformations and imprinted gene disorders. In a retrospective North Carolina-based-birth-cohort, we examined the effect of ovulation drugs and ART on CpG methylation in differentially methylated CpGs in known imprint control regions (ICRs). Nine ICRs containing 48 CpGs were assessed for methylation status by pyrosequencing in mixed leukocytes from cord blood. After restricting to non-smoking, college-educated participants who agreed to follow-up, ART-exposed (n = 27), clomifene-only-exposed (n = 22), and non-exposed (n = 516) groups were defined. Associations of clomifene and ART with ICR CpG methylation were assessed with linear regression and stratifying by offspring sex. In males, ART was associated with hypomethylation of the PEG3 ICR [β(95% CI) = −1.46 (−2.81, −0.12)] and hypermethylation of the MEG3 ICR [3.71 (0.01, 7.40)]; clomifene-only was associated with hypomethylation of the NNAT ICR [−5.25 (−10.12, −0.38)]. In female offspring, ART was associated with hypomethylation of the IGF2 ICR [−3.67 (−6.79, −0.55)]. Aberrant methylation of these ICRs has been associated with cardiovascular disease and metabolic and behavioral outcomes in children. The results suggest that the increased risk of adverse outcomes in offspring conceived through ART may be due in part to altered methylation of ICRs. Larger studies utilizing epigenome-wide interrogation are warranted.}, number={18}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Lloyd, Dillon T. and Skinner, Harlyn G. and Maguire, Rachel and Murphy, Susan K. and Motsinger-Reif, Alison A. and Hoyo, Cathrine and House, John S.}, year={2022}, month={Sep} }
 @article{wolkin_collier_house_reif_motsinger-reif_duca_sharpe_2022, title={Comparison of National Vulnerability Indices Used by the Centers for Disease Control and Prevention for the COVID-19 Response}, volume={137}, ISSN={0033-3549 1468-2877}, url={http://dx.doi.org/10.1177/00333549221090262}, DOI={10.1177/00333549221090262}, abstractNote={Objective: Vulnerability indices use quantitative indicators and geospatial data to examine the level of vulnerability to morbidity in a community. The Centers for Disease Control and Prevention (CDC) uses 3 indices for the COVID-19 response: the CDC Social Vulnerability Index (CDC-SVI), the US COVID-19 Community Vulnerability Index (CCVI), and the Pandemic Vulnerability Index (PVI). The objective of this review was to describe these tools and explain the similarities and differences between them. Methods: We described the 3 indices, outlined the underlying data sources and metrics for each, and discussed their use by CDC for the COVID-19 response. We compared the percentile score for each county for each index by calculating Spearman correlation coefficients (Spearman ρ). Results: These indices have some, but not all, component metrics in common. The CDC-SVI is a validated metric that estimates social vulnerability, which comprises the underlying population-level characteristics that influence differences in health risk among communities. To address risk specific to the COVID-19 pandemic, the CCVI and PVI build on the CDC-SVI and include additional variables. The 3 indices were highly correlated. Spearman ρ for comparisons between the CDC-SVI score and the CCVI and between the CCVI and the PVI score was 0.83. Spearman ρ for the comparison between the CDC-SVI score and PVI score was 0.73. Conclusion: The indices can empower local and state public health officials with additional information to focus resources and interventions on disproportionately affected populations to combat the ongoing pandemic and plan for future pandemics.}, number={4}, journal={Public Health Reports}, publisher={SAGE Publications}, author={Wolkin, Amy and Collier, Sarah and House, John S. and Reif, David and Motsinger-Reif, Alison and Duca, Lindsey and Sharpe, J. Danielle}, year={2022}, month={May}, pages={803–812} }
 @article{jima_skaar_planchart_motsinger-reif_cevik_park_cowley_wright_house_liu_et al._2022, title={Genomic map of candidate human imprint control regions: the imprintome}, volume={6}, ISSN={["1559-2308"]}, url={https://doi.org/10.1080/15592294.2022.2091815}, DOI={10.1080/15592294.2022.2091815}, abstractNote={ABSTRACT Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.}, journal={EPIGENETICS}, author={Jima, Dereje D. and Skaar, David A. and Planchart, Antonio and Motsinger-Reif, Alison and Cevik, Sebnem E. and Park, Sarah S. and Cowley, Michael and Wright, Fred and House, John and Liu, Andy and et al.}, year={2022}, month={Jun} }
 @article{house_grimm_klaren_dalzell_kuchi_zhang_lenz_boogaard_ketelslegers_gant_et al._2022, title={Grouping of UVCB Substances with Dose-Response Transcriptomics Data from Human Cell-Based Assays}, volume={39}, ISSN={["1868-8551"]}, DOI={10.14573/altex.2107051}, abstractNote={The application of in vitro biological assays as new approach methodologies (NAMs) to support grouping of UVCB (unknown or variable composition, complex reaction products, and biological materials) substances has recently been demonstrated. In addition to cell-based phenotyping as NAMs, in vitro transcriptomic profiling is used to gain deeper mechanistic understanding of biological responses to chemicals and to support grouping and read-across. However, the value of gene expression profiling for characterizing complex substances like UVCBs has not been explored. Using 141 petroleum substance extracts, we performed dose-response transcriptomic profiling in human induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as cell lines MCF7 and A375. The goal was to determine whether transcriptomic data can be used to group these UVCBs and to further characterize the molecular basis for in vitro biological responses. We found distinct transcriptional responses for petroleum substances by manufacturing class. Pathway enrichment informed interpretation of effects of substances and UVCB petroleum-class. Transcriptional activity was strongly correlated with concentration of polycyclic aromatic compounds (PAC), especially in iPSC-derived hepatocytes. Supervised analysis using transcriptomics, alone or in combination with bioactivity data collected on these same substances/cells, suggest that transcriptomics data provide useful mechanistic information, but only modest additional value for grouping. Overall, these results further demonstrate the value of NAMs for grouping of UVCBs, identify informative cell lines, and provide data that could be used for justifying selection of substances for further testing that may be required for registration.}, number={3}, journal={ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION}, author={House, John S. and Grimm, Fabian A. and Klaren, William D. and Dalzell, Abigail and Kuchi, Srikeerthana and Zhang, Shu-Dong and Lenz, Klaus and Boogaard, Peter J. and Ketelslegers, Hans B. and Gant, Timothy W. and et al.}, year={2022}, pages={388–404} }
 @article{brown_shekhar_delaney_burkholder_plummer_mericq_merino_quinton_lewis_shaw_et al._2022, title={LBMON114 Enrichment Of Rare Sequence Variants In Genes That Communicate Metabolic Signals To The GnRH System In Hypothalamic Amenorrhea}, volume={6}, ISSN={2472-1972}, url={http://dx.doi.org/10.1210/jendso/bvac150.970}, DOI={10.1210/jendso/bvac150.970}, abstractNote={Abstract Introduction Functional hypothalamic amenorrhea (HA) is commonly associated with increased exercise or decreased caloric intake and often with stress. We have previously demonstrated an increased burden of rare sequence variants (RSVs) in genes involved in GnRH ontogeny and upstream regulation in women with HA, but the role of metabolic and stress signaling to the GnRH neuronal system is poorly defined in this population. Methods The study included 100 women with a confirmed diagnosis of HA. The control cohort consisted of 468 women (aged 45-65 years) drawn from the NIH ClinSeq® Project. Exome sequencing was performed on peripheral blood genomic DNA. A subset of 72 genes was analyzed that have been shown to: 1) link metabolic or stress with reproductive phenotypes or 2) integrate metabolic and stress pathways with control of GnRH secretion. Joint genotyping of case and control samples was performed using the GATK GenotypeGVCFs function, locus-filtering using the VariantRecalibrator function, and genotype refinement using CalculateGenotypePosteriors with computation of median depths. Median depth positions <10, positions failing GATK VQSR or GATK genotype quality scores <20 were excluded. RSVs were identified by < 1% frequency in any subpopulation in gnomeAD for all-subjects (AS) and < 1% frequency in non-Finnish Europeans for Caucasians (CS). Data were analyzed for AS and for CS using a one-sided Fisher exact test for metabolism genes and stress genes. An additional regression analysis was conducted on the number of RSVs in a given gene as a predictor of HA vs. control. Comparisons with a p-value of < 0.1 are reported. Results HA patients exhibited an increased burden of RSVs in metabolism genes vs. controls (AS p=0. 043; CS p=0.105). The total number of RSVs per gene highlighted differences between HA and controls for the following genes: ADAMTSL1, GRINA, GRIN1, HCRTR1, TENM3, and NOS1 (AS p<0. 001, p=0. 032, p=0. 057, p=0. 082, p=0. 091, p=0. 095; CS p=0. 024, p=0. 044, p=0. 044, p NS, p=0. 086, p NS). Interestingly, RSVs in NOS1 and TENM3 appeared to be protective for HA (odds ratio <1 for both). In contrast, candidate stress genes were not significant in either the AS or CS (p=0.788, p=0.910). Conclusions These data suggest that RSVs in genes involved in phenotypes or signaling pathways that link metabolism to GnRH secretion may predispose to development of HA in the setting of decreased energy balance, but not for stress-related genes. GRINA and GRIN1 are important components of glutamate signaling that facilitate both appetite and GnRH secretion either directly or through kisspeptin. HCRTR1 plays a similar role in linking appetite and GnRH secretion while NOS1, which facilitates kisspeptin signaling, may be protective. This work highlights the need for further studies to understand the potential roles of ADAMTSL1 and TENM3 as risk factors for HA. Presentation: Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.}, number={Supplement_1}, journal={Journal of the Endocrine Society}, publisher={The Endocrine Society}, author={Brown, Ethan and Shekhar, Skand and Delaney, Angela and Burkholder, Adam B and Plummer, Lacey and Mericq, Veronica and Merino, Paulina M and Quinton, Richard and Lewis, Katie L and Shaw, Natalie D and et al.}, year={2022}, month={Nov}, pages={A466–A467} }
 @article{mcgee_shi_house_drude_gonzalez_martin_chen_rogers_njunge_hodge_et al._2022, title={Longitudinal Serological Surveillance for COVID-19 Antibodies after Infection and Vaccination}, volume={10}, ISSN={2165-0497}, url={http://dx.doi.org/10.1128/spectrum.02026-22}, DOI={10.1128/spectrum.02026-22}, abstractNote={The COVID-19 pandemic continues to impact societies and health care systems worldwide and is continuously evolving. Immunity via vaccination or prior infection is the first and most important line of defense against COVID-19. ABSTRACT The impact of COVID-19 is still felt around the world, and more information is needed regarding infection risk, vaccination responses, and the timing of booster vaccinations. We aimed to evaluate the association of vaccination with closely followed, longitudinal antibody titers and COVID-19 infection events. We conducted a natural history study in a convenience cohort in an ambulatory research unit. We measured anti-nucleocapsid and anti-spike antibody levels every 3 months for 1 year and captured weekly reports of medically confirmed COVID-19 infections. We analyzed the association of antibody titers with infection events as well as the association of the decision to receive vaccination with social, medical, and behavioral characteristics. 629 subjects were followed for 1 year, and 82.8% of them were vaccinated. 90 cases of medically confirmed COVID-19 infection were reported. Notable findings from our study include: an association of vaccination choice with social distancing, a qualitatively different anti-spike response in participants receiving the Ad26.COV2.S vaccine compared to those receiving mRNA vaccines, a muted anti-nucleocapsid response in breakthrough infections compared to unvaccinated infections, and the identification of a low antibody titer threshold associated with the risk of breakthrough infections. We conclude that, in a real-life setting, vaccination and social distancing behavior are positively correlated. The observed effect of vaccination in preventing COVID-19 may include both vaccine-mediated protection and the associated more cautious behavior exhibited by vaccinated individuals. In addition, we identified an antibody threshold associated with breakthrough infections in mRNA vaccinees, and this threshold may be used in medical decision-making regarding the timing of booster vaccinations. Therefore, our data may aid in the refinement of vaccination strategies during the COVID-19 pandemic. IMPORTANCE The COVID-19 pandemic continues to impact societies and health care systems worldwide and is continuously evolving. Immunity via vaccination or prior infection is the first and most important line of defense against COVID-19. We still do not have complete information on how vaccination-induced or infection-induced antibody titers change with time or on how this information can be used to guide decisions regarding booster vaccination. In a longitudinal observational study of a cohort of 629 subjects, 82% of breakthrough infections in vaccinees occurred when their anti-spike antibody titers were below 3,000 AU/mL. Our findings suggest that there may be an antibody threshold associated with breakthrough infections and that this threshold could possibly be used to aid decision-making regarding booster vaccinations. In addition, the use of anti-nucleocapsid antibody tiers may significantly underestimate the prevalence of breakthrough infections in vaccinated individuals.}, number={5}, journal={Microbiology Spectrum}, publisher={American Society for Microbiology}, author={McGee, Christopher and Shi, Min and House, John and Drude, Anna and Gonzalez, Gladys and Martin, Negin and Chen, Shih-Heng and Rogers, Heidi and Njunge, Alex and Hodge, Xiomara and et al.}, editor={Laeyendecker, OliverEditor}, year={2022}, month={Oct} }
 @article{gonzalez-nahm_marchesoni_maity_maguire_house_tucker_atkinson_murphy_hoyo_2022, title={Maternal Mediterranean Diet Adherence and Its Associations with Maternal Prenatal Stressors and Child Growth}, volume={6}, ISSN={["2475-2991"]}, DOI={10.1093/cdn/nzac146}, abstractNote={ABSTRACT Background Psychosocial and physiologic stressors, such as depression and obesity, during pregnancy can have negative consequences, such as increased systemic inflammation, contributing to chronic disease for both mothers and their unborn children. These conditions disproportionately affect racial/ethnic minorities. The effects of recommended dietary patterns in mitigating the effects of these stressors remain understudied. Objectives We aimed to evaluate the relations between maternal Mediterranean diet adherence (MDA) and maternal and offspring outcomes during the first decade of life in African Americans, Hispanics, and Whites. Methods This study included 929 mother–child dyads from the NEST (Newborn Epigenetics STudy), a prospective cohort study. FFQs were used to estimate MDA in pregnant women. Weight and height were measured in children between birth and age 8 y. Multivariable linear regression models were used to examine associations between maternal MDA, inflammatory cytokines, and pregnancy and postnatal outcomes. Results More than 55% of White women reported high MDA during the periconceptional period compared with 22% of Hispanic and 18% of African American women (P < 0.05). Higher MDA was associated with lower likelihood of depressive mood (β = −0.45; 95% CI: −0.90, −0.18; P = 0.02) and prepregnancy obesity (β = −0.29; 95% CI: −0.57, −0.0002; P = 0.05). Higher MDA was also associated with lower body size at birth, which was maintained to ages 3–5 and 6–8 y—this association was most apparent in White children (3–5 y: β = −2.9, P = 0.02; 6–8 y: β = −3.99, P = 0.01). Conclusions If replicated in larger studies, our data suggest that MDA provides a potent avenue by which effects of prenatal stressors on maternal and fetal outcomes can be mitigated to reduce ethnic disparities in childhood obesity.}, number={11}, journal={CURRENT DEVELOPMENTS IN NUTRITION}, author={Gonzalez-Nahm, Sarah and Marchesoni, Joddy and Maity, Arnab and Maguire, Rachel L. and House, John S. and Tucker, Rachel and Atkinson, Tamara and Murphy, Susan K. and Hoyo, Cathrine}, year={2022}, month={Nov} }
 @article{gonzalez-nahm_marchesoni_maity_maguire_house_tucker_atkinson_murphy_hoyo_2022, title={Maternal Periconceptional Stressors, Mediterranean Diet Adherence, and Child Outcomes}, volume={6}, ISSN={2475-2991}, url={http://dx.doi.org/10.1093/cdn/nzac061.034}, DOI={10.1093/cdn/nzac061.034}, abstractNote={Abstract Objectives To evaluate the relationships between maternal periconceptional Mediterranean diet adherence and 1) maternal periconceptional BMI, 2) subsequent maternal depression during pregnancy, 3) prenatal inflammatory cytokine IL-17A, 4) child birthweight, and 5) child weight-for-height at ages 0–8 years in African American, Hispanic and White mother-child dyads from the Newborn Epigenetics STudy (NEST). Methods Food frequency questionnaires were used to estimate periconceptional Mediterranean diet adherence in mothers. Maternal depression during pregnancy was assessed using the Centers for Epidemiological Studies Depression scale. Weight and height were measured in children between birth and age 8 years. Linear and logistic regression models were used to examine associations between maternal adherence to a Mediterranean diet, inflammatory cytokines and pregnancy and postnatal outcomes, adjusted for education, maternal age at delivery, maternal smoking, gestational age, age and sex of child, breastfeeding, parity, maternal BMI. Results Adherence to a Mediterranean diet varied widely by ethnicity with > 55% of White mothers reporting high adherence during the periconceptional period, compared to 22% of Hispanic mothers, and 18% of African American mothers (P < 0.05). Higher adherence to this diet was associated with lower risk of depressive mood (β = −0.45, p = 0.02) and pre-pregnancy obesity (β = −0.29, p = 0.05). Higher maternal adherence to this diet pattern was also associated with lower body weight at birth, that was maintained to ages 3–5 and 6–8 years—these associations were most apparent in White children (3–5 years: β = −2.9, p = 0.02; 6–8 years: β = −3.99, p = 0.01). Higher diet adherence was associated with lower levels of prenatal IL-17A levels in African American mother-child dyads (β = 0.21, p = 0.03). Conclusions Our data suggest that maternal Mediterranean diet adherence provides a potent avenue by which effects of prenatal stressors on maternal and fetal outcomes can be mitigated to reduce ethnic disparities in childhood obesity. Funding Sources This research was funded by grants from the National Institute of Minority Health and Health Disparities and the National Institute of Environmental Health Sciences, and supported in part by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences.}, journal={Current Developments in Nutrition}, publisher={Elsevier BV}, author={Gonzalez-Nahm, Sarah and Marchesoni, Joddy and Maity, Arnab and Maguire, Rachel and House, John and Tucker, Rachel and Atkinson, Tamara and Murphy, Susan and Hoyo, Cathrine}, year={2022}, month={Jun}, pages={650} }
 @article{akhtari_lloyd_burkholder_tong_house_lee_buse_schurman_fargo_schmitt_et al._2022, title={Questionnaire-Based Polyexposure Assessment Outperforms Polygenic Scores for Classification of Type 2 Diabetes in a Multiancestry Cohort}, volume={11}, ISSN={0149-5992 1935-5548}, url={http://dx.doi.org/10.2337/dc22-0295}, DOI={10.2337/dc22-0295}, abstractNote={OBJECTIVE Environmental exposures may have greater predictive power for type 2 diabetes than polygenic scores (PGS). Studies examining environmental risk factors, however, have included only individuals with European ancestry, limiting the applicability of results. We conducted an exposome-wide association study in the multiancestry Personalized Environment and Genes Study to assess the effects of environmental factors on type 2 diabetes. RESEARCH DESIGN AND METHODS Using logistic regression for single-exposure analysis, we identified exposures associated with type 2 diabetes, adjusting for age, BMI, household income, and self-reported sex and race. To compare cumulative genetic and environmental effects, we computed an overall clinical score (OCS) as a weighted sum of BMI and prediabetes, hypertension, and high cholesterol status and a polyexposure score (PXS) as a weighted sum of 13 environmental variables. Using UK Biobank data, we developed a multiancestry PGS and calculated it for participants. RESULTS We found 76 significant associations with type 2 diabetes, including novel associations of asbestos and coal dust exposure. OCS, PXS, and PGS were significantly associated with type 2 diabetes. PXS had moderate power to determine associations, with larger effect size and greater power and reclassification improvement than PGS. For all scores, the results differed by race. CONCLUSIONS Our findings in a multiancestry cohort elucidate how type 2 diabetes odds can be attributed to clinical, genetic, and environmental factors and emphasize the need for exposome data in disease-risk association studies. Race-based differences in predictive scores highlight the need for genetic and exposome-wide studies in diverse populations.}, journal={Diabetes Care}, publisher={American Diabetes Association}, author={Akhtari, Farida S. and Lloyd, Dillon and Burkholder, Adam and Tong, Xiaoran and House, John S. and Lee, Eunice Y. and Buse, John and Schurman, Shepherd H. and Fargo, David C. and Schmitt, Charles P. and et al.}, year={2022}, month={Nov}, pages={dc220295} }
 @article{lee_akhtari_house_simpson_schmitt_fargo_schurman_hall_motsinger-reif_2022, title={Questionnaire-based exposome-wide association studies (ExWAS) reveal expected and novel risk factors associated with cardiovascular outcomes in the Personalized Environment and Genes Study}, volume={212}, ISSN={0013-9351}, url={http://dx.doi.org/10.1016/j.envres.2022.113463}, DOI={10.1016/j.envres.2022.113463}, abstractNote={While multiple factors are associated with cardiovascular disease (CVD), many environmental exposures that may contribute to CVD have not been examined. To understand environmental effects on cardiovascular health, we performed an exposome-wide association study (ExWAS), a hypothesis-free approach, using survey data on endogenous and exogenous exposures at home and work and data from health and medical histories from the North Carolina-based Personalized Environment and Genes Study (PEGS) (n = 5015). We performed ExWAS analyses separately on six cardiovascular outcomes (cardiac arrhythmia, congestive heart failure, coronary artery disease, heart attack, stroke, and a combined atherogenic-related outcome comprising angina, angioplasty, atherosclerosis, coronary artery disease, heart attack, and stroke) using logistic regression and a false discovery rate of 5%. For each CVD outcome, we tested 502 single exposures and built multi-exposure models using the deletion-substitution-addition (DSA) algorithm. To evaluate complex nonlinear relationships, we employed the knockoff boosted tree (KOBT) algorithm. We adjusted all analyses for age, sex, race, BMI, and annual household income. ExWAS analyses revealed novel associations that include blood type A (Rh-) with heart attack (OR[95%CI] = 8.2[2.2:29.7]); paint exposures with stroke (paint related chemicals: 6.1[2.2:16.0], acrylic paint: 8.1[2.6:22.9], primer: 6.7[2.2:18.6]); biohazardous materials exposure with arrhythmia (1.8[1.5:2.3]); and higher paternal education level with reduced risk of multiple CVD outcomes (stroke, heart attack, coronary artery disease, and combined atherogenic outcome). In multi-exposure models, trouble sleeping and smoking remained important risk factors. KOBT identified significant nonlinear effects of sleep disorder, regular intake of grapefruit, and a family history of blood clotting problems for multiple CVD outcomes (combined atherogenic outcome, congestive heart failure, and coronary artery disease). In conclusion, using statistics and machine learning, these findings identify novel potential risk factors for CVD, enable hypothesis generation, provide insights into the complex relationships between risk factors and CVD, and highlight the importance of considering multiple exposures when examining CVD outcomes.}, journal={Environmental Research}, publisher={Elsevier BV}, author={Lee, Eunice Y. and Akhtari, Farida and House, John S. and Simpson, Ross J., Jr. and Schmitt, Charles P. and Fargo, David C. and Schurman, Shepherd H. and Hall, Janet E. and Motsinger-Reif, Alison A.}, year={2022}, month={Sep}, pages={113463} }
 @article{henriquez_snow_jackson_house_alewel_schladweiler_valdez_freeborn_miller_grindstaff_et al._2022, title={Social isolation exacerbates acute ozone inhalation induced pulmonary and systemic health outcomes}, volume={457}, ISSN={0041-008X}, url={http://dx.doi.org/10.1016/j.taap.2022.116295}, DOI={10.1016/j.taap.2022.116295}, abstractNote={Psychosocially-stressed individuals might have exacerbated responses to air pollution exposure. Acute ozone exposure activates the neuroendocrine stress response leading to systemic metabolic and lung inflammatory changes. We hypothesized chronic mild stress (CS) and/or social isolation (SI) would cause neuroendocrine, inflammatory, and metabolic phenotypes that would be exacerbated by an acute ozone exposure. Male 5-week-old Wistar-Kyoto rats were randomly assigned into 3 groups: no stress (NS) (pair-housed, regular-handling); SI (single-housed, minimal-handling); CS (single-housed, subjected to mild unpredicted-randomized stressors [restraint-1 h, tilted cage-1 h, shaking-1 h, intermittent noise-6 h, and predator odor-1 h], 1-stressor/day*5-days/week*8-weeks. All animals then 13-week-old were subsequently exposed to filtered-air or ozone (0.8-ppm) for 4 h and immediately necropsied. CS, but not SI animals had increased adrenal weights. However, relative to NS, both CS and SI had lower circulating luteinizing hormone, prolactin, and follicle-stimulating hormone regardless of exposure (SI > CS), and only CS demonstrated lower thyroid-stimulating hormone levels. SI caused more severe systemic inflammation than CS, as evidenced by higher circulating cytokines and cholesterol. Ozone exposure increased urine corticosterone and catecholamine metabolites with no significant stressor effect. Ozone-induced lung injury, and increases in lavage-fluid neutrophils and IL-6, were exacerbated by SI. Ozone severely lowered circulating thyroid-stimulating hormone, prolactin, and luteinizing hormone in all groups and exacerbated systemic inflammation in SI. Ozone-induced increases in serum glucose, leptin, and triglycerides were consistent across stressors; however, increases in cholesterol were exacerbated by SI. Collectively, psychosocial stressors, especially SI, affected the neuroendocrine system and induced adverse metabolic and inflammatory effects that were exacerbated by ozone exposure.}, journal={Toxicology and Applied Pharmacology}, publisher={Elsevier BV}, author={Henriquez, Andres R. and Snow, Samantha J. and Jackson, Thomas W. and House, John S. and Alewel, Devin I. and Schladweiler, Mette C. and Valdez, Matthew C. and Freeborn, Danielle L. and Miller, Colette N. and Grindstaff, Rachel and et al.}, year={2022}, month={Dec}, pages={116295} }
 @article{henriquez_snow_jackson_house_motsinger-reif_ward-caviness_schladweiler_alewel_miller_farraj_et al._2022, title={Stress Drivers of Glucose Dynamics during Ozone Exposure Measured Using Radiotelemetry in Rats}, volume={130}, ISSN={0091-6765 1552-9924}, url={http://dx.doi.org/10.1289/EHP11088}, DOI={10.1289/EHP11088}, abstractNote={Background: Inhaled irritant air pollutants may trigger stress-related metabolic dysfunction associated with altered circulating adrenal-derived hormones. Objectives: We used implantable telemetry in rats to assess real-time changes in circulating glucose during and after exposure to ozone and mechanistically linked responses to neuroendocrine stress hormones. Methods: First, using a cross-over design, we monitored glucose during ozone exposures (0.0, 0.2, 0.4, and 0.8 ppm) and nonexposure periods in male Wistar Kyoto rats implanted with glucose telemeters. A second cohort of unimplanted rats was exposed to ozone (0.0, 0.4 or 0.8 ppm) for 30 min, 1 h, 2 h, or 4 h with hormones measured immediately post exposure. We assessed glucose metabolism in sham and adrenalectomized rats, with or without supplementation of adrenergic/glucocorticoid receptor agonists, and in a separate cohort, antagonists. Results: Ozone (0.8 ppm) was associated with significantly higher blood glucose and lower core body temperature beginning 90 min into exposure, with reversal of effects 4–6 h post exposure. Glucose monitoring during four daily 4-h ozone exposures revealed duration of glucose increases, adaptation, and diurnal variations. Ozone-induced glucose changes were preceded by higher levels of adrenocorticotropic hormone, corticosterone, and epinephrine but lower levels of thyroid-stimulating hormone, prolactin, and luteinizing hormones. Higher glucose and glucose intolerance were inhibited in rats that were adrenalectomized or treated with adrenergic plus glucocorticoid receptor antagonists but exacerbated by agonists. Discussion: We demonstrated the temporality of neuroendocrine-stress–mediated biological sequalae responsible for ozone-induced glucose metabolic dysfunction and mechanism in a rodent model. Stress hormones assessment with real-time glucose monitoring may be useful in identifying interactions among irritant pollutants and stress-related illnesses. https://doi.org/10.1289/EHP11088}, number={12}, journal={Environmental Health Perspectives}, publisher={Environmental Health Perspectives}, author={Henriquez, Andres R. and Snow, Samantha J. and Jackson, Thomas W. and House, John S. and Motsinger-Reif, Alison A. and Ward-Caviness, Cavin K. and Schladweiler, Mette C. and Alewel, Devin I. and Miller, Colette N. and Farraj, Aimen K. and et al.}, year={2022}, month={Dec} }
 @article{mcdonough_warren_jack_motsinger‐reif_armstrong_bis_house_singh_el rouby_gong_et al._2021, title={Adverse Cardiovascular Outcomes and Antihypertensive Treatment: A Genome‐Wide Interaction Meta‐Analysis in the International Consortium for Antihypertensive Pharmacogenomics Studies}, volume={110}, ISSN={0009-9236 1532-6535}, url={http://dx.doi.org/10.1002/cpt.2355}, DOI={10.1002/cpt.2355}, abstractNote={We sought to identify genome‐wide variants influencing antihypertensive drug response and adverse cardiovascular outcomes, utilizing data from four randomized controlled trials in the International Consortium for Antihypertensive Pharmacogenomics Studies (ICAPS). Genome‐wide antihypertensive drug‐single nucleotide polymorphism (SNP) interaction tests for four drug classes (β‐blockers, n = 9,195; calcium channel blockers (CCBs), n = 10,511; thiazide/thiazide‐like diuretics, n = 3,516; ACE‐inhibitors/ARBs, n = 2,559) and cardiovascular outcomes (incident myocardial infarction, stroke, or death) were analyzed among patients with hypertension of European ancestry. Top SNPs from the meta‐analyses were tested for replication of cardiovascular outcomes in an independent Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) study (n = 21,267), blood pressure (BP) response in independent ICAPS studies (n = 1,552), and ethnic validation in African Americans from the Genetics of Hypertension Associated Treatment study (GenHAT; n = 5,115). One signal reached genome‐wide significance in the β‐blocker‐SNP interaction analysis (rs139945292, Interaction P = 1.56 × 10−8). rs139945292 was validated through BP response to β‐blockers, with the T‐allele associated with less BP reduction (systolic BP response P = 6 × 10−4, Beta = 3.09, diastolic BP response P = 5 × 10−3, Beta = 1.53). The T‐allele was also associated with increased adverse cardiovascular risk within the β‐blocker treated patients’ subgroup (P = 2.35 × 10−4, odds ratio = 1.57, 95% confidence interval = 1.23–1.99). The locus showed nominal replication in CHARGE, and consistent directional trends in β‐blocker treated African Americans. rs139945292 is an expression quantitative trait locus for the 50 kb upstream gene NTM (neurotrimin). No SNPs attained genome‐wide significance for any other drugs classes. Top SNPs were located near CALB1 (CCB), FLJ367777 (ACE‐inhibitor), and CES5AP1 (thiazide). The NTM region is associated with increased risk for adverse cardiovascular outcomes and less BP reduction in β‐blocker treated patients. Further investigation into this region is warranted.}, number={3}, journal={Clinical Pharmacology & Therapeutics}, publisher={Wiley}, author={McDonough, Caitrin W. and Warren, Helen R. and Jack, John R. and Motsinger‐Reif, Alison A. and Armstrong, Nicole D. and Bis, Joshua C. and House, John S. and Singh, Sonal and El Rouby, Nihal M. and Gong, Yan and et al.}, year={2021}, month={Aug}, pages={723–732} }
 @article{maguire_house_lloyd_skinner_allen_raffi_skaar_park_mccullough_kollins_et al._2021, title={Associations between maternal obesity, gestational cytokine levels and child obesity in the NEST cohort}, volume={16}, ISSN={["2047-6302"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098446153&partnerID=MN8TOARS}, DOI={10.1111/ijpo.12763}, abstractNote={Although maternal systemic inflammation is hypothesized to link maternal pre‐pregnancy obesity to offspring metabolic dysfunction, patient empirical data are limited.}, number={7}, journal={PEDIATRIC OBESITY}, author={Maguire, Rachel L. and House, John S. and Lloyd, Dillon T. and Skinner, Harlyn G. and Allen, Terrence K. and Raffi, Asifa Mohamed and Skaar, David A. and Park, Sarah S. and McCullough, Lauren E. and Kollins, Scott H. and et al.}, year={2021}, month={Jul} }
 @article{henriquez_snow_jackson_house_motsinger-reif_ward-caviness_schladweiler_alewel_miller_farraj_et al._2021, title={Glucose dynamics during ozone exposure measured using radiotelemetry: Stress drivers}, volume={12}, url={https://doi.org/10.1101/2021.12.09.471963}, DOI={10.1101/2021.12.09.471963}, abstractNote={Background Stress-related neurobehavioral and metabolic disorders are associated with altered circulating adrenal-derived hormones and hyperglycemia. Temporal assessment of glucose and these hormones is critical for insights on an individual’s health. Objectives Here we used implantable-telemetry in rats to assess real-time changes in circulating glucose during and after exposure to the air pollutant ozone, and link responses to circulating neuroendocrine stress and metabolic hormones. We also compared rodent glucose and corticosterone (cortisol in humans) responses to humans exposed to ozone. Methods First, using a cross-over design, we monitored glucose levels during single or repeated ozone exposures (0.0, 0.2, 0.4 and 0.8-ppm) and non-exposure periods in male Wistar-Kyoto-rats implanted with glucose-telemeters. A second cohort of un-implanted rats was exposed to ozone (0.0, 0.4 or 0.8-ppm) for 30-min, 1-hour, 2-hour, or 4-hour with hormones measured immediately after exposure. Then we assessed glucose metabolism in sham and adrenalectomized rats with or without pharmacological interventions of adrenergic and glucocorticoid receptors. Finally, we assessed glucose and cortisol in serum samples from a clinical study involving exposure of human volunteers to air or 0.3 ppm ozone. Results Ozone (0.8-ppm) caused hyperglycemia and hypothermia beginning 90-min into exposure, with reversal of effects 4-6 hours post-exposure. Glucose monitoring during four daily 4-hour ozone exposures revealed duration of hyperglycemia, adaptation, and diurnal variations. Ozone-induced hyperglycemia was preceded by increased adrenocorticotropic hormone, corticosterone, and epinephrine, but depletion of thyroid-stimulating, prolactin, and luteinizing hormones. Hyperglycemia was inhibited in rats that were adrenalectomized and/or treated with glucocorticoid inhibitor. The depletion of cortisol was dampened in humans exposed to ozone during intermittent exercise. Discussion We demonstrate for the first time the temporality of neuroendocrine-stress-mediated biological sequalae responsible for ozone-induced metabolic dysfunction as exposure occurs. Real-time glucose monitoring with stress hormones assessment may be useful in identifying interactions among pollutants and stress-related illnesses.}, publisher={Cold Spring Harbor Laboratory}, author={Henriquez, Andres R. and Snow, Samantha J. and Jackson, Thomas W. and House, John S. and Motsinger-Reif, Alison A. and Ward-Caviness, Cavin K. and Schladweiler, Mette C. and Alewel, Devin I. and Miller, Colette N. and Farraj, Aimen K. and et al.}, year={2021}, month={Dec} }
 @article{house_grimm_klaren_dalzell_kuchi_zhang_lenz_boogaard_ketelslegers_gant_et al._2021, title={Grouping of UVCB Substances with New Approach Methodologies (NAMs) Data}, volume={38}, ISSN={["1868-8551"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85100279673&partnerID=MN8TOARS}, DOI={10.14573/altex.2006262}, abstractNote={One of the most challenging areas in regulatory science is assessment of the substances known as UVCB (unknown or variable composition, complex reaction products and biological materials). Because the inherent complexity and variability of UVCBs present considerable challenges for establishing sufficient substance similarity based on chemical characteristics or other data, we hypothesized that new approach methodologies (NAMs), including in vitro test-derived biological activity signatures to characterize substance similarity, could be used to support grouping of UVCBs. We tested 141 petroleum substances as representative UVCBs in a compendium of 15 human cell types representing a variety of tissues. Petroleum substances were assayed in dilution series to derive point of departure estimates for each cell type and phenotype. Extensive quality control measures were taken to ensure that only high-confidence in vitro data were used to determine whether current groupings of these petroleum substances, based largely on the manufacturing process and physico-chemical properties, are justifiable. We found that bioactivity data-based groupings of petroleum substances were generally consistent with the manufacturing class-based categories. We also showed that these data, especially bioactivity from human induced pluripotent stem cell (iPSC)-derived and primary cells, can be used to rank substances in a manner highly concordant with their expected in vivo hazard potential based on their chemical compositional profile. Overall, this study demonstrates that NAMs can be used to inform groupings of UVCBs, to assist in identification of representative substances in each group for testing when needed, and to fill data gaps by read-across.}, number={1}, journal={ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION}, author={House, John S. and Grimm, Fabian A. and Klaren, William D. and Dalzell, Abigail and Kuchi, Srikeerthana and Zhang, Shu-Dong and Lenz, Klaus and Boogaard, Peter J. and Ketelslegers, Hans B. and Gant, Timothy W. and et al.}, year={2021}, pages={123–137} }
 @article{akhtari_green_small_havener_house_roell_reif_mcleod_wiltshire_motsinger-reif_2021, title={High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs}, volume={17}, ISSN={["1553-7404"]}, url={https://doi.org/10.1371/journal.pgen.1009732}, DOI={10.1371/journal.pgen.1009732}, abstractNote={Cancer patients exhibit a broad range of inter-individual variability in response and toxicity to widely used anticancer drugs, and genetic variation is a major contributor to this variability. To identify new genes that influence the response of 44 FDA-approved anticancer drug treatments widely used to treat various types of cancer, we conducted high-throughput screening and genome-wide association mapping using 680 lymphoblastoid cell lines from the 1000 Genomes Project. The drug treatments considered in this study represent nine drug classes widely used in the treatment of cancer in addition to the paclitaxel + epirubicin combination therapy commonly used for breast cancer patients. Our genome-wide association study (GWAS) found several significant and suggestive associations. We prioritized consistent associations for functional follow-up using gene-expression analyses. The NAD(P)H quinone dehydrogenase 1 (NQO1) gene was found to be associated with the dose-response of arsenic trioxide, erlotinib, trametinib, and a combination treatment of paclitaxel + epirubicin. NQO1 has previously been shown as a biomarker of epirubicin response, but our results reveal novel associations with these additional treatments. Baseline gene expression of NQO1 was positively correlated with response for 43 of the 44 treatments surveyed. By interrogating the functional mechanisms of this association, the results demonstrate differences in both baseline and drug-exposed induction.}, number={8}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Akhtari, Farida S. and Green, Adrian J. and Small, George W. and Havener, Tammy M. and House, John S. and Roell, Kyle R. and Reif, David M. and McLeod, Howard L. and Wiltshire, Timothy and Motsinger-Reif, Alison A.}, editor={Vazquez, FranciscaEditor}, year={2021}, month={Aug} }
 @article{nichols_house_li_ward_wyss_williams_deterding_bradbury_miller_zeldin_et al._2021, title={Lrp1 regulation of pulmonary function follow-up of human GWAS in mice}, volume={64}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85101877952&partnerID=MN8TOARS}, DOI={10.1165/rcmb.2019-0444OC}, abstractNote={Human genome-wide association studies (GWAS) have identified over 270 loci associated with pulmonary function; however, follow-up studies to determine causal genes at these loci are few. Single nucleotide polymorphisms (SNPs) in low-density lipoprotein receptor-related protein 1 (LRP1) are associated with human pulmonary function in GWAS. Using murine models, we investigated the effect of genetic disruption of the Lrp1 gene in smooth muscle cells on pulmonary function in naïve animals and after exposure to bacterial lipopolysaccharide (LPS) or house dust mite extract (HDME). Disruption of Lrp1 in smooth muscle cells leads to an increase in tissue resistance, elastance, and tissue elastance at baseline. Further, disruption of Lrp1 in smooth muscle increases airway responsiveness as measured by increased total lung resistance and airway resistance after methacholine. Immune cell counts in bronchoalveolar lavage fluid were increased in animals with Lrp1 disruption. The difference in airway responsiveness by genotype observed in naïve animals was not observed following LPS or HDME exposure. To further explore the mechanisms contributing to changes in pulmonary function, we identified several ligands dysregulated with Lrp1 disruption in smooth muscle cells. These data suggest that dysregulation of LRP1 in smooth muscle cells affects baseline pulmonary function and airway responsiveness and helps establish LRP1 as the causal gene at this GWAS locus.}, number={3}, journal={American Journal of Respiratory Cell and Molecular Biology}, author={Nichols, C.E. and House, J.S. and Li, H. and Ward, J.M. and Wyss, A. and Williams, J.G. and Deterding, L.J. and Bradbury, J.A. and Miller, L. and Zeldin, D.C. and et al.}, year={2021}, pages={368–378} }
 @article{alick_maguire_murphy_fuemmeler_hoyo_house_2021, title={Periconceptional Maternal Diet Characterized by High Glycemic Loading Is Associated with Offspring Behavior in NEST}, volume={13}, url={https://doi.org/10.3390/nu13093180}, DOI={10.3390/nu13093180}, abstractNote={Maternal periconceptional diets have known associations with proper offspring neurodevelopment. Mechanisms for such associations include improper energy/nutrient balances between mother and fetus, as well as altered offspring epigenetics during development due to maternal nutrient and inflammatory status. Using a comprehensive food frequency questionnaire and assessing offspring temperament with the Infant-Toddler Social and Emotional Assessment (n = 325, mean age = 13.9 months), we sought to test whether a maternal periconceptional diet characterized by high glycemic loading (MGL) would affect offspring temperament using adjusted ordinal regression. After limiting false discovery to 10%, offspring born to mothers in tertile 3 of glycemic loading (referent = tertile 1) were more likely to be in the next tertile of anxiety [OR (95% CI) = 4.51 (1.88–11.07)] and inhibition-related behaviors [OR (95% CI) = 3.42 (1.49–7.96)]. Male offspring were more likely to exhibit impulsive [OR (95% CI) = 5.55 (1.76–18.33)], anxiety [OR (95% CI) = 4.41 (1.33–15.30)], sleep dysregulation [OR (95% CI) = 4.14 (1.34–13.16)], empathy [6.68 (1.95–24.40)], and maladaptive behaviors [OR (95% CI) = 9.86 (2.81–37.18)], while females were more likely to exhibit increased anxiety-related behaviors [OR (95% CI) = 15.02 (3.14–84.27)]. These associations persisted when concurrently modeled with the maternal–Mediterranean dietary pattern. In a subset (n = 142), we also found MGL associated with increased mean methylation of the imprint control region of SGCE/PEG10. In conclusion, these findings highlight the importance of maternal dietary patterns on offspring neurodevelopment, offering avenues for prevention options for mothers.}, number={9}, journal={Nutrients}, publisher={MDPI AG}, author={Alick, Candice L. and Maguire, Rachel L. and Murphy, Susan K. and Fuemmeler, Bernard F. and Hoyo, Cathrine and House, John S.}, year={2021}, month={Sep}, pages={3180} }
 @article{snow_henriquez_fisher_vallanat_house_schladweiler_wood_kodavanti_2021, title={Peripheral metabolic effects of ozone exposure in healthy and diabetic rats on normal or high-cholesterol diet}, volume={415}, ISSN={0041-008X}, url={http://dx.doi.org/10.1016/j.taap.2021.115427}, DOI={10.1016/j.taap.2021.115427}, abstractNote={Epidemiological studies show that individuals with underlying diabetes and diet-associated ailments are more susceptible than healthy individuals to adverse health effects of air pollution. Exposure to air pollutants can induce metabolic stress and increase cardiometabolic disease risk. Using male Wistar and Wistar-derived Goto-Kakizaki (GK) rats, which exhibit a non-obese type-2 diabetes phenotype, we investigated whether two key metabolic stressors, type-2 diabetes and a high-cholesterol atherogenic diet, exacerbate ozone-induced metabolic effects. Rats were fed a normal control diet (ND) or high-cholesterol diet (HCD) for 12 weeks and then exposed to filtered air or 1.0-ppm ozone (6 h/day) for 1 or 2 days. Metabolic responses were analyzed at the end of each day and after an 18-h recovery period following the 2-day exposure. In GK rats, baseline hyperglycemia and glucose intolerance were exacerbated by HCD vs. ND and by ozone vs. air. HCD also resulted in higher insulin in ozone-exposed GK rats and circulating lipase, aspartate transaminase, and alanine transaminase in all groups (Wistar>GK). Histopathological effects induced by HCD in the liver, which included macrovesicular vacuolation and hepatocellular necrosis, were more severe in Wistar vs. GK rats. Liver gene expression in Wistar and GK rats fed ND showed numerous strain differences, including evidence of increased lipid metabolizing activity and ozone-induced alterations in glucose and lipid transporters, specifically in GK rats. Collectively, these findings indicate that peripheral metabolic alterations induced by diabetes and high-cholesterol diet can enhance susceptibility to the metabolic effects of inhaled pollutants.}, journal={Toxicology and Applied Pharmacology}, publisher={Elsevier BV}, author={Snow, Samantha J. and Henriquez, Andres R. and Fisher, Anna and Vallanat, Beena and House, John S. and Schladweiler, Mette C. and Wood, Charles E. and Kodavanti, Urmila P.}, year={2021}, month={Mar}, pages={115427} }
 @misc{marvel_house_wheeler_song_zhou_wright_chiu_rusyn_motsinger-reif_reif_2021, title={The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning}, volume={129}, ISSN={["1552-9924"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85099420902&partnerID=MN8TOARS}, DOI={10.1289/EHP8690}, abstractNote={Vol. 129, No. 1 Research LetterOpen AccessThe COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning Skylar W. Marvel, John S. House, Matthew Wheeler, Kuncheng Song, Yi-Hui Zhou, Fred A. Wright, Weihsueh A. Chiu, Ivan Rusyn, Alison Motsinger-Reif, and David M. Reif Skylar W. Marvel Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA Search for more papers by this author , John S. House Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA Search for more papers by this author , Matthew Wheeler Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA Search for more papers by this author , Kuncheng Song Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA Search for more papers by this author , Yi-Hui Zhou Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA Search for more papers by this author , Fred A. Wright Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA Department of Statistics, NCSU, Raleigh, North Carolina, USA Search for more papers by this author , Weihsueh A. Chiu Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA Search for more papers by this author , Ivan Rusyn Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA Search for more papers by this author , Alison Motsinger-Reif Address correspondence to Alison Motsinger-Reif, 111 T.W. Alexander Dr., Rall Building, Research Triangle Park, NC 27709 USA. Email: E-mail Address: [email protected], or David M. Reif, Box 7566, 1 Lampe Dr., Raleigh NC 27695 USA. Email: E-mail Address: [email protected] Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA Search for more papers by this author , and David M. Reif Address correspondence to Alison Motsinger-Reif, 111 T.W. Alexander Dr., Rall Building, Research Triangle Park, NC 27709 USA. Email: E-mail Address: [email protected], or David M. Reif, Box 7566, 1 Lampe Dr., Raleigh NC 27695 USA. Email: E-mail Address: [email protected] Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA Search for more papers by this author Published:5 January 2021CID: 017701https://doi.org/10.1289/EHP8690AboutSectionsPDF ToolsDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InReddit IntroductionExpert groups have coalesced around a roadmap to address the current COVID-19 pandemic centered on social distancing, monitoring case counts and health care capacity, and, eventually, moving to pharmaceutical interventions. However, responsibility for navigating the pandemic response falls largely on state and local officials. To make equitable decisions on allocating resources, caring for vulnerable subpopulations, and implementing local- and state-level interventions, access to current pandemic data and key vulnerabilities at the community level are essential (National Academies of Sciences, Engineering, and Medicine 2020). Although numerous predictive models and interactive monitoring applications have been developed using pandemic-related data sets (Wynants et al. 2020), their capacity to aid in dynamic, community-level decision-making is limited. We developed the interactive COVID-19 Pandemic Vulnerability Index (PVI) Dashboard ( https://covid19pvi.niehs.nih.gov/) to address this need by presenting a visual synthesis of dynamic information at the county level to monitor disease trajectories, communicate local vulnerabilities, forecast key outcomes, and guide informed responses (Figure 1).Figure 1. COVID-19 PVI Dashboard. Dashboard screenshot displaying PVI profiles atop a choropleth map layer indicating overall COVID-19 PVI rank. The PVI Scorecard and associated data for Clarendon County, South Carolina, has been selected. The scorecard summarizes the overall PVI score and rank compared with all 3,142 U.S. counties on each indicator slice. The scrollable score distributions at left compare the selected county PVI to the distributions of overall and slice-wise scores across the United States. The panels below the map are populated with county-specific information on observed trends in cases and deaths, cumulative numbers for the county, historical timelines (for cumulative cases, cumulative deaths, PVI, and PVI rank), daily case and death counts for the most recent 14-d period, and a 14-d forecast of predicted cases and deaths. The information displayed for both observed COVID-19 data and PVI layers is scrollable back through March 2020. Documentation of additional features and usage, including advanced options (accessible via the collapsed menu at the upper left), is provided in a Quick Start Guide (linked at the upper right corner). Note: Pop, population; PVI, Pandemic Vulnerability Index.MethodsThe current PVI model integrates multiple data streams into an overall score derived from 12 key indicators—including well-established, general vulnerability factors for public health, plus emerging factors relevant to the pandemic—distributed across four domains: current infection rates, baseline population concentration, current interventions, and health and environmental vulnerabilities. The PVI profiles translate numerical results into visual representations, with each vulnerability factor represented as a component slice of a radar chart (Figure 2). The PVI profile for each county is calculated using the Toxicological Prioritization Index (ToxPi) framework for data integration within a geospatial context (Marvel et al. 2018; Bhandari et al. 2020). Data sources in the current model (version 11.2.1) include the Social Vulnerability Index (SVI) of the Centers for Disease Control and Prevention (CDC) for emergency response and hazard mitigation planning (Horney et al. 2017), testing rates from the COVID Tracking Project (Atlantic Monthly Group 2020), social distancing metrics from mobile device data ( https://www.unacast.com/covid19/social-distancing-scoreboard), and dynamic measures of disease spread and case numbers ( https://usafacts.org/issues/coronavirus/). Methodological details concerning the integration of data streams—plus the complete, daily time series of all source data since February 2020 and resultant PVI scores—are maintained on the public Github project page (COVID19PVI 2020). Over this period, the PVI has been strongly associated with key vulnerability-related outcome metrics (by rank-correlation), with updates of its performance assessment posted with model updates alongside data at the Github project page (COVID19PVI 2020).Figure 2. Translation of data into COVID-19 PVI profiles. Information from all 3,142 U.S. counties is translated into PVI slices. The illustration shows how air pollution data (average density of fine particulate matterPM2.5 per county) are compared for two example counties. The county with the higher relative measurement (County Y) has a longer air pollution slice than the county with a lower measurement (County X). This procedure is repeated for all slices, resulting in an integrated, overall PVI profile. Note: pop, population; PVI, Pandemic Vulnerability Index.In addition to the PVI itself—which is a summary, human-centric visualization of relative vulnerability drivers—the dashboard is supported by rigorous statistical modeling of the underlying data to enable quantitative analysis and provide short-term, local predictions of cases and deaths [complete methodological details are maintained at the Github project page (COVID19PVI 2020)]. Generalized linear models of cumulative outcome data indicated that, after population size, the most significant predictors were the proportion of Black residents, mean fine particulate matter [particulate matter less than or equal to 2.5 micrometers≤2.5μm in diameter (fine particulate matterPM2.5)], percentage of population with insurance coverage (which was positively associated), and proportion of Hispanic residents. The local predictions of cases and deaths (see the “Predictions” panel in Figure 1) are updated daily using a Bayesian spatiotemporal random-effects model to build forecasts up to 2 weeks out.DiscussionThe PVI Dashboard supports decision-making and dynamic monitoring in several ways. The display can be tailored to add or remove layers of information, filtered by region (e.g., all counties within a state) or clustered by profile shape similarity. The timelines for both PVI models and observed COVID-19 outcomes facilitate tracking the impact of interventions and directing local resource allocations. The “Predictions” panel (Figure 1) connects these historical numbers to local forecasts of cases and deaths. By communicating an integrated concept of vulnerability that considers both dynamic (infection rate and interventions) and static (community population and health care characteristics) drivers, the interactive dashboard can promote buy-in from diverse audiences, which is necessary for effective public health interventions. This messaging can assist in addressing known racial disparities in COVID-19 case and death rates (Tan et al. 2020) or populations, and the PVI Dashboard is part of the “Unique Populations” tab of the CDC’s COVID-19 Data Tracker ( https://covid.cdc.gov/covid-data-tracker). By filtering the display to highlight vulnerability drivers within an overall score context, the dashboard can inform targeted interventions for specific localities.Unfortunately, the pandemic endures across the United States, with broad disparities based on the local environment (Tan et al. 2020). We present the PVI Dashboard as a dynamic container for contextualizing these disparities. It is a modular tool that will evolve to incorporate new data sources and analytics as they emerge (e.g., concurrent flu infections, school and business reopening statistics, heterogeneous public health practices). This flexibility positions it well as a resource for integrated prioritization of eventual vaccine distribution and monitoring its local impact. The PVI Dashboard can empower local and state officials to take informed action to combat the pandemic by communicating interactive, visual profiles of vulnerability atop an underlying statistical framework that enables the comparison of counties and the evaluation of the PVI’s component data.AcknowledgmentsWe thank the information technology and web services staff at the National Institute of Environmental Health Sciences (NIEHS)/National Institutes of Health (NIH) for their help and support, as well as J.K. Cetina and D.J. Reif for their useful technical input and advice. This work was supported by NIEHS/NIH grants (P42 ES027704, P30 ES029067, P42 ES031009, and P30 ES025128) and NIEHS/NIH intramural funds (Z ES103352-01).ReferencesAtlantic Monthly Group.2020. The COVID Tracking Project. https://covidtracking.com/ [accessed 15 November 2020]. Google ScholarBhandari S, Lewis PGT, Craft E, Marvel SW, Reif DM, Chiu WA. 2020. HGBEnviroScreen: enabling community action through data integration in the Houston–Galveston–Brazoria region. Int J Environ Res Public Health 17(4):1130, PMID: 32053902, 10.3390/ijerph17041130. Crossref, Medline, Google ScholarCOVID19PVI.2020. COVID19PVI/data. https://github.com/COVID19PVI/data [accessed 15 November 2020]. Google ScholarHorney J, Nguyen M, Salvesen D, Dwyer C, Cooper J, Berke P. 2017. Assessing the quality of rural hazard mitigation plans in the southeastern United States. J Plan Educ Res 37(1):56–65, 10.1177/0739456X16628605. Crossref, Google ScholarMarvel SW, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. 2018. ToxPi Graphical User Interface 2.0: dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics 19(1):80, PMID: 29506467, 10.1186/s12859-018-2089-2. Crossref, Medline, Google ScholarNational Academies of Sciences, Engineering, and Medicine.2020. Framework for Equitable Allocation of COVID-19 Vaccine. Gayle H, Foege W, Brown L, Kahn B, eds. Washington, DC: National Academies Press. Google ScholarTan TQ, Kullar R, Swartz TH, Mathew TA, Piggott DA, Berthaud V. 2020. Location matters: geographic disparities and impact of coronavirus disease 2019. J Infect Dis 222(12):1951–1954, PMID: 32942299, 10.1093/infdis/jiaa583. Crossref, Medline, Google ScholarWynants L, Van Calster B, Collins GS, Riley RD, Heinze G, Schuit E, et al.2020. Prediction models for diagnosis and prognosis of covid-19: systematic review and critical appraisal. BMJ 369:m1328, PMID: 32265220, 10.1136/bmj.m1328. Crossref, Medline, Google ScholarThe authors declare they have no actual or potential competing financial interests.FiguresReferencesRelatedDetails Vol. 129, No. 1 January 2021Metrics About Article Metrics Publication History Manuscript received20 November 2020Manuscript revised14 December 2020Manuscript accepted21 December 2020Originally published5 January 2021 Financial disclosuresPDF download License information EHP is an open-access journal published with support from the National Institute of Environmental Health Sciences, National Institutes of Health. All content is public domain unless otherwise noted. Note to readers with disabilities EHP strives to ensure that all journal content is accessible to all readers. However, some figures and Supplemental Material published in EHP articles may not conform to 508 standards due to the complexity of the information being presented. If you need assistance accessing journal content, please contact [email protected]. Our staff will work with you to assess and meet your accessibility needs within 3 working days.}, number={1}, journal={ENVIRONMENTAL HEALTH PERSPECTIVES}, author={Marvel, Skylar W. and House, John S. and Wheeler, Matthew and Song, Kuncheng and Zhou, Yi-Hui and Wright, Fred A. and Chiu, Weihsueh A. and Rusyn, Ivan and Motsinger-Reif, Alison and Reif, David M.}, year={2021}, month={Jan} }
 @article{colonna_henriquez_house_motsinger-reif_alewel_fisher_ren_snow_schladweiler_miller_et al._2021, title={The Role of Hepatic Vagal Tone in Ozone-Induced Metabolic Dysfunction in the Liver}, volume={181}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85107319660&partnerID=MN8TOARS}, DOI={10.1093/toxsci/kfab025}, abstractNote={Air pollution has been associated with metabolic diseases and hepatic steatosis-like changes. We have shown that ozone alters liver gene expression for metabolic processes through neuroendocrine activation. This study aimed to further characterize ozone-induced changes and to determine the impact of hepatic vagotomy (HV) which reduces parasympathetic influence. Twelve-week-old male Wistar-Kyoto rats underwent HV or sham surgery five-six days prior to air or ozone exposure (0 or 1 ppm; 4 h/d for one or two days). Ozone-induced lung injury, hyperglycemia, glucose intolerance, and increases in circulating cholesterol, triglycerides, and leptin were similar in rats with HV and sham surgery. However, decreases in circulating insulin and increased HDL and LDL were observed only in ozone-exposed HV rats. Ozone exposure resulted in changed liver gene expression in both sham and HV rats (sham>HV), however, HV did not change expression in air-exposed rats. Upstream target analysis revealed that ozone-induced transcriptomic changes were similar to responses induced by glucocorticoid-mediated processes in both sham and HV rats. The directionality of ozone-induced changes reflecting cellular response to stress, metabolic pathways, and immune surveillance was similar in sham and HV rats. However, pathways regulating cell-cycle, regeneration, proliferation, cell growth, and survival were enriched by ozone in a directionally-opposing manner between sham and HV rats. In conclusion, parasympathetic innervation modulated ozone-induced liver transcriptional responses for cell growth and regeneration without affecting stress-mediated metabolic changes. Thus, impaired neuroendocrine axes and parasympathetic innervation could collectively contribute to adverse effects of air pollutants on the liver.}, number={2}, journal={Toxicological Sciences}, publisher={Oxford University Press (OUP)}, author={Colonna, Catherine H and Henriquez, Andres R and House, John S and Motsinger-Reif, Alison A and Alewel, Devin I and Fisher, Anna and Ren, Hongzu and Snow, Samantha J and Schladweiler, Mette C and Miller, Desinia B and et al.}, year={2021}, pages={229–245} }
 @article{gonzalez-nahm_nihlani_s. house_l. maguire_g. skinner_hoyo_2020, title={Associations between Maternal Cadmium Exposure with Risk of Preterm Birth and Low after Birth Weight Effect of Mediterranean Diet Adherence on Affected Prenatal Outcomes}, volume={8}, ISSN={["2305-6304"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85094109102&partnerID=MN8TOARS}, DOI={10.3390/toxics8040090}, abstractNote={Prenatal cadmium exposure at non-occupational levels has been associated with poor birth outcomes. The intake of essential metals, such as iron and selenium, may mitigate cadmium exposure effects. However, at high levels, these metals can be toxic. The role of dietary patterns rich in these metals is less studied. We used a linear and logistic regression in a cohort of 185 mother–infant pairs to assess if a Mediterranean diet pattern during pregnancy modified the associations between prenatal cadmium exposure and (1) birth weight and (2) preterm birth. We found that increased cadmium exposure during pregnancy was associated with lower birth weight (β = −210.4; 95% CI: −332.0, −88.8; p = 0.008) and preterm birth (OR = 0.11; 95% CI: 0.01, 0.72; p = 0.04); however, these associations were comparable in offspring born to women reporting high adherence to a Mediterranean diet (β = −274.95; 95% CI: −701.17, 151.26; p = 0.20) and those with low adherence (β = −64.76; 95% CI: −359.90, 230.37; p = 0.66). While the small sample size limits inference, our findings suggest that adherence to a Mediterranean dietary pattern may not mitigate cadmium exposure effects. Given the multiple organs targeted by cadmium and its slow excretion rate, larger studies are required to clarify these findings.}, number={4}, journal={TOXICS}, publisher={MDPI AG}, author={Gonzalez-Nahm, Sarah and Nihlani, Kiran and S. House, John and L. Maguire, Rachel and G. Skinner, Harlyn and Hoyo, Cathrine}, year={2020}, month={Dec} }
 @article{house_motsinger-reif_2020, title={Fibrate pharmacogenomics: Expanding past the genome}, volume={21}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85082767117&partnerID=MN8TOARS}, DOI={10.2217/pgs-2019-0140}, abstractNote={Fibrates are a medication class prescribed for decades as 'broad-spectrum' lipid-modifying agents used to lower blood triglyceride levels and raise high-density lipoprotein cholesterol levels. Such lipid changes are associated with a decrease in cardiovascular disease, and fibrates are commonly used to reduce risk of dangerous cardiovascular outcomes. As with most drugs, it is well established that response to fibrate treatment is variable, and this variation is heritable. This has motivated the investigation of pharmacogenomic determinants of response, and multiple studies have discovered a number of genes associated with fibrate response. Similar to other complex traits, the interrogation of single nucleotide polymorphisms using candidate gene or genome-wide approaches has not revealed a substantial portion of response variation. However, recent innovations in technological platforms and advances in statistical methodologies are revolutionizing the use and integration of other 'omes' in pharmacogenomics studies. Here, we detail successes, challenges, and recent advances in fibrate pharmacogenomics.}, number={4}, journal={Pharmacogenomics}, author={House, J.S. and Motsinger-Reif, A.A.}, year={2020}, pages={293–306} }
 @article{house_bouzos_fahy_francisco_lloyd_wright_motsinger-reif_asuri_wheeler_2020, title={Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells}, volume={16}, ISSN={["1613-6829"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85082473420&partnerID=MN8TOARS}, DOI={10.1002/smll.202000299}, abstractNote={Silver nanoparticles (AgNPs) are widely incorporated into consumer and biomedical products for their antimicrobial and plasmonic properties with limited risk assessment of low-dose cumulative exposure in humans. To evaluate cellular responses to low-dose AgNP exposures across time, human liver cells (HepG2) are exposed to AgNPs with three different surface charges (1.2 µg mL-1 ) and complete gene expression is monitored across a 24 h period. Time and AgNP surface chemistry mediate gene expression. In addition, since cells are fed, time has marked effects on gene expression that should be considered. Surface chemistry of AgNPs alters gene transcription in a time-dependent manner, with the most dramatic effects in cationic AgNPs. Universal to all surface coatings, AgNP-treated cells responded by inactivating proliferation and enabling cell cycle checkpoints. Further analysis of these universal features of AgNP cellular response, as well as more detailed analysis of specific AgNP treatments, time points, or specific genes, is facilitated with an accompanying application. Taken together, these results provide a foundation for understanding hepatic response to low-dose AgNPs for future risk assessment.}, number={21}, journal={SMALL}, author={House, John S. and Bouzos, Evangelia and Fahy, Kira M. and Francisco, Victorino Miguel and Lloyd, Dillon T. and Wright, Fred A. and Motsinger-Reif, Alison A. and Asuri, Prashanth and Wheeler, Korin E.}, year={2020}, month={May} }
 @article{marvel_house_wheeler_song_zhou_wright_chiu_rusyn_motsinger-reif_reif_2020, title={The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098201055&partnerID=MN8TOARS}, DOI={10.1101/2020.08.10.20169649}, abstractNote={While the COVID-19 pandemic presents a global challenge, the U.S. response places substantial responsibility for both decision-making and communication on local health authorities. To better support counties and municipalities, we integrated baseline data on relevant community vulnerabilities with dynamic data on local infection rates and interventions into a Pandemic Vulnerability Index (PVI). The PVI presents a visual synthesis of county-level vulnerability indicators that can be compared in a regional, state, or nationwide context. We describe use of the PVI, supporting epidemiological modeling and machine-learning forecasts, and deployment of an interactive, web Dashboard. The Dashboard facilitates decision-making and communication among government officials, scientists, community leaders, and the public to enable more effective and coordinated action to combat the pandemic.}, journal={medRxiv}, publisher={Cold Spring Harbor Laboratory}, author={Marvel, Skylar W. and House, John S. and Wheeler, Matthew and Song, Kuncheng and Zhou, Yihui and Wright, Fred A. and Chiu, Weihsueh A. and Rusyn, Ivan and Motsinger-Reif, Alison and Reif, David M.}, year={2020} }
 @article{sakolish_house_chramiec_liu_chen_halligan_vunjak-novakovic_rusyn_2020, title={Tissue-Engineered Bone Tumor as a Reproducible Human in Vitro Model for Studies of Anticancer Drugs}, volume={173}, ISSN={["1096-0929"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077489572&partnerID=MN8TOARS}, DOI={10.1093/toxsci/kfz220}, abstractNote={Abstract}, number={1}, journal={TOXICOLOGICAL SCIENCES}, author={Sakolish, Courtney and House, John S. and Chramiec, Alan and Liu, Yizhong and Chen, Zunwei and Halligan, Susan P. and Vunjak-Novakovic, Gordana and Rusyn, Ivan}, year={2020}, month={Jan}, pages={65–76} }
 @article{tam_hall_messenger_jima_house_linder_smart_2019, title={C/EBP beta suppresses keratinocyte autonomous type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer}, volume={40}, ISSN={["1460-2180"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85083447649&partnerID=MN8TOARS}, DOI={10.1093/carcin/bgz012}, abstractNote={Abstract}, number={9}, journal={CARCINOGENESIS}, author={Tam, Hann W. and Hall, Jonathan R. and Messenger, Zachary J. and Jima, Dereje D. and House, John S. and Linder, Keith and Smart, Robert C.}, year={2019}, month={Sep}, pages={1099–1109} }
 @article{house_hall_park_planchart_money_maguire_huang_mattingly_skaar_tzeng_et al._2019, title={Cadmium exposure and MEG3 methylation differences between Whites and African Americans in the NEST Cohort}, volume={5}, ISSN={2058-5888}, url={http://dx.doi.org/10.1093/eep/dvz014}, DOI={10.1093/eep/dvz014}, abstractNote={Abstract}, number={3}, journal={Environmental Epigenetics}, publisher={Oxford University Press (OUP)}, author={House, John S and Hall, Jonathan and Park, Sarah S and Planchart, Antonio and Money, Eric and Maguire, Rachel L and Huang, Zhiqing and Mattingly, Carolyn J and Skaar, David and Tzeng, Jung Ying and et al.}, editor={Skinner, MikeEditor}, year={2019}, month={Jul} }
 @article{onel_beykal_ferguson_chiu_mcdonald_zhou_house_wright_sheen_rusyn_et al._2019, title={Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization}, volume={14}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85073118823&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0223517}, abstractNote={A detailed characterization of the chemical composition of complex substances, such as products of petroleum refining and environmental mixtures, is greatly needed in exposure assessment and manufacturing. The inherent complexity and variability in the composition of complex substances obfuscate the choices for their detailed analytical characterization. Yet, in lieu of exact chemical composition of complex substances, evaluation of the degree of similarity is a sensible path toward decision-making in environmental health regulations. Grouping of similar complex substances is a challenge that can be addressed via advanced analytical methods and streamlined data analysis and visualization techniques. Here, we propose a framework with unsupervised and supervised analyses to optimally group complex substances based on their analytical features. We test two data sets of complex oil-derived substances. The first data set is from gas chromatography-mass spectrometry (GC-MS) analysis of 20 Standard Reference Materials representing crude oils and oil refining products. The second data set consists of 15 samples of various gas oils analyzed using three analytical techniques: GC-MS, GC×GC-flame ionization detection (FID), and ion mobility spectrometry-mass spectrometry (IM-MS). We use hierarchical clustering using Pearson correlation as a similarity metric for the unsupervised analysis and build classification models using the Random Forest algorithm for the supervised analysis. We present a quantitative comparative assessment of clustering results via Fowlkes–Mallows index, and classification results via model accuracies in predicting the group of an unknown complex substance. We demonstrate the effect of (i) different grouping methodologies, (ii) data set size, and (iii) dimensionality reduction on the grouping quality, and (iv) different analytical techniques on the characterization of the complex substances. While the complexity and variability in chemical composition are an inherent feature of complex substances, we demonstrate how the choices of the data analysis and visualization methods can impact the communication of their characteristics to delineate sufficient similarity.}, number={10}, journal={PLOS ONE}, author={Onel, Melis and Beykal, Burcu and Ferguson, Kyle and Chiu, Weihsueh A. and McDonald, Thomas J. and Zhou, Lan and House, John S. and Wright, Fred A. and Sheen, David A. and Rusyn, Ivan and et al.}, year={2019}, month={Oct} }
 @article{grimm_house_wilson_sirenko_iwata_wright_ball_rusyn_2019, title={Multi-dimensional in vitro bioactivity profiling for grouping of glycol ethers}, volume={101}, ISSN={["1096-0295"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85057214979&partnerID=MN8TOARS}, DOI={10.1016/j.yrtph.2018.11.011}, abstractNote={High-content screening data derived from physiologically-relevant in vitro models promise to improve confidence in data-integrative groupings for read-across in human health safety assessments. The biological data-based read-across concept is especially applicable to bioactive chemicals with defined mechanisms of toxicity; however, the challenge of data-derived groupings for chemicals that are associated with little or no bioactivity has not been explored. In this study, we apply a suite of organotypic and population-based in vitro models for comprehensive bioactivity profiling of twenty E-Series and P-Series glycol ethers, solvents with a broad variation in toxicity ranging from relatively non-toxic to reproductive and hematopoetic system toxicants. Both E-Series and P-Series glycol ethers elicited cytotoxicity only at high concentrations (mM range) in induced pluripotent stem cell-derived hepatocytes and cardiomyocytes. Population-variability assessment comprised a study of cytotoxicity in 94 human lymphoblast cell lines from 9 populations and revealed differences in inter-individual variability across glycol ethers, but did not indicate population-specific effects. Data derived from various phenotypic and transcriptomic assays revealed consistent bioactivity trends between both cardiomyocytes and hepatocytes, indicating a more universal, rather than cell-type specific mode-of-action for the tested glycol ethers in vitro. In vitro bioactivity-based similarity assessment using Toxicological Priority Index (ToxPi) showed that glycol ethers group according to their alcohol chain length, longer chains were associated with increased bioactivity. While overall in vitro bioactivity profiles did not correlate with in vivo toxicity data on glycol ethers, in vitro bioactivity of E-series glycol ethers were indicative of and correlated with in vivo irritation scores.}, journal={REGULATORY TOXICOLOGY AND PHARMACOLOGY}, publisher={Elsevier BV}, author={Grimm, Fabian A. and House, John S. and Wilson, Melinda R. and Sirenko, Oksana and Iwata, Yasuhiro and Wright, Fred A. and Ball, Nicholas and Rusyn, Ivan}, year={2019}, month={Feb}, pages={91–102} }
 @article{sai_parsons_house_kathariou_ninomiya-tsuji_2019, title={Necroptosis mediators RIPK3 and MLKL suppress intracellular Listeria replication independently of host cell killing}, volume={218}, ISSN={["1540-8140"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85067213651&partnerID=MN8TOARS}, DOI={10.1083/jcb.201810014}, abstractNote={RIPK3, a key mediator of necroptosis, has been implicated in the host defense against viral infection primary in immune cells. However, gene expression analysis revealed that RIPK3 is abundantly expressed not only in immune organs but also in the gastrointestinal tract, particularly in the small intestine. We found that orally inoculated Listeria monocytogenes, a bacterial foodborne pathogen, efficiently spread and caused systemic infection in Ripk3-deficient mice while almost no dissemination was observed in wild-type mice. Listeria infection activated the RIPK3-MLKL pathway in cultured cells, which resulted in suppression of intracellular replication of Listeria. Surprisingly, Listeria infection–induced phosphorylation of MLKL did not result in host cell killing. We found that MLKL directly binds to Listeria and inhibits their replication in the cytosol. Our findings have revealed a novel functional role of the RIPK3-MLKL pathway in nonimmune cell-derived host defense against Listeria invasion, which is mediated through cell death–independent mechanisms.}, number={6}, journal={JOURNAL OF CELL BIOLOGY}, publisher={Rockefeller University Press}, author={Sai, Kazuhito and Parsons, Cameron and House, John S. and Kathariou, Sophia and Ninomiya-Tsuji, Jun}, year={2019}, month={Jun}, pages={1994–2005} }
 @article{henriquez_house_snow_miller_schladweiler_fisher_ren_valdez_kodavanti_kodavanti_2019, title={Ozone-Induced Dysregulation of Neuroendocrine Axes Requires Adrenal-Derived Stress Hormones}, volume={172}, ISSN={["1096-0929"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077224518&partnerID=MN8TOARS}, DOI={10.1093/toxsci/kfz182}, abstractNote={Abstract}, number={1}, journal={TOXICOLOGICAL SCIENCES}, author={Henriquez, Andres R. and House, John S. and Snow, Samantha J. and Miller, Colette N. and Schladweiler, Mette C. and Fisher, Anna and Ren, Hongzu and Valdez, Matthew and Kodavanti, Prasada R. and Kodavanti, Urmila P.}, year={2019}, month={Nov}, pages={38–50} }
 @article{burnett_blanchette_grimm_house_reif_wright_chiu_rusyn_2019, title={Population-based toxicity screening in human induced pluripotent stem cell-derived cardiomyocytes}, volume={381}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85070968757&partnerID=MN8TOARS}, DOI={10.1016/j.taap.2019.114711}, abstractNote={The potential for cardiotoxicity is carefully evaluated for pharmaceuticals, as it is a major safety liability. However, environmental chemicals are seldom tested for their cardiotoxic potential. Moreover, there is a large variability in both baseline and drug-induced cardiovascular risk in humans, but data are lacking on the degree to which susceptibility to chemically-induced cardiotoxicity may also vary. Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes have become an important in vitro model for drug screening. Thus, we hypothesized that a population-based model of iPSC-derived cardiomyocytes from a diverse set of individuals can be used to assess potential hazard and inter-individual variability in chemical effects on these cells. We conducted concentration-response screening of 134 chemicals (pharmaceuticals, industrial and environmental chemicals and food constituents) in iPSC-derived cardiomyocytes from 43 individuals, comprising both sexes and diverse ancestry. We measured kinetic calcium flux and conducted high-content imaging following chemical exposure, and utilized a panel of functional and cytotoxicity parameters in concentration-response for each chemical and donor. We show reproducible inter-individual variability in both baseline and chemical-induced effects on iPSC-derived cardiomyocytes. Further, chemical-specific variability in potency and degree of population variability were quantified. This study shows the feasibility of using an organotypic population-based human in vitro model to quantitatively assess chemicals for which little cardiotoxicity information is available. Ultimately, these results advance in vitro toxicity testing methodologies by providing an innovative tool for population-based cardiotoxicity screening, contributing to the paradigm shift from traditional animal models of toxicity to in vitro toxicity testing methods.}, journal={Toxicology and Applied Pharmacology}, author={Burnett, S.D. and Blanchette, A.D. and Grimm, F.A. and House, J.S. and Reif, D.M. and Wright, F.A. and Chiu, W.A. and Rusyn, I.}, year={2019} }
 @article{grimm_blanchette_house_ferguson_hsieh_dalaijamts_wright_anson_wright_chiu_et al._2018, title={A Human Population-Based Organotypic In Vitro Model for Cardiotoxicity Screening}, volume={35}, ISSN={["1868-8551"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85054462389&partnerID=MN8TOARS}, DOI={10.14573/altex.1805301}, abstractNote={Assessing inter-individual variability in responses to xenobiotics remains a substantial challenge, both in drug development with respect to pharmaceuticals and in public health with respect to environmental chemicals. Although approaches exist to characterize pharmacokinetic variability, there are no methods to routinely address pharmacodynamic variability. In this study, we aimed to demonstrate the feasibility of characterizing inter-individual variability in a human in vitro model. Specifically, we hypothesized that genetic variability across a population of iPSC-derived cardiomyocytes translates into reproducible variability in both baseline phenotypes and drug responses. We measured baseline and drug-related effects in iPSC-derived cardiomyocytes from 27 healthy donors on kinetic Ca2+ flux and high-content live cell imaging. Cells were treated in concentration-response with cardiotoxic drugs: isoproterenol (β-adrenergic receptor agonist/positive inotrope), propranolol (β-adrenergic receptor antagonist/negative inotrope), and cisapride (hERG channel inhibitor/QT prolongation). Cells from four of the 27 donors were further evaluated in terms of baseline and treatment-related gene expression. Reproducibility of phenotypic responses was evaluated across batches and time. iPSC-derived cardiomyocytes exhibited reproducible donor-specific differences in baseline function and drug-induced effects. We demonstrate the feasibility of using a panel of population-based organotypic cells from healthy donors as an animal replacement experimental model. This model can be used to rapidly screen drugs and chemicals for inter-individual variability in cardiotoxicity. This approach demonstrates the feasibility of quantifying inter-individual variability in xenobiotic responses and can be expanded to other cell types for which in vitro populations can be derived from iPSCs.}, number={4}, journal={ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION}, author={Grimm, Fabian A. and Blanchette, Alexander and House, John S. and Ferguson, Kyle and Hsieh, Nan-Hung and Dalaijamts, Chimeddulam and Wright, Alec A. and Anson, Blake and Wright, Fred A. and Chiu, Weihsueh A. and et al.}, year={2018}, pages={441–452} }
 @article{messenger_hall_jima_house_tam_tokarz_smart_2018, title={C/EBPβ deletion in oncogenic Ras skin tumors is a synthetic lethal event}, volume={9}, ISSN={2041-4889}, url={http://dx.doi.org/10.1038/S41419-018-1103-Y}, DOI={10.1038/s41419-018-1103-y}, abstractNote={Abstract}, number={11}, journal={Cell Death & Disease}, publisher={Springer Science and Business Media LLC}, author={Messenger, Zachary J. and Hall, Jonathan R. and Jima, Dereje D. and House, John S. and Tam, Hann W. and Tokarz, Debra A. and Smart, Robert C.}, year={2018}, month={Oct} }
 @article{house_mendez_maguire_gonzalez-nahm_huang_daniels_murphy_fuemmeler_wright_hoyo_2018, title={Periconceptional maternal mediterranean diet is associated with favorable offspring behaviors and altered CpG methylation of imprinted genes}, volume={6}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85053720031&partnerID=MN8TOARS}, DOI={10.3389/fcell.2018.00107}, abstractNote={Background: Maternal diet during pregnancy has been shown to influence the child neuro-developmental outcomes. Studies examining effects of dietary patterns on offspring behavior are sparse. Objective: Determine if maternal adherence to a Mediterranean diet is associated with child behavioral outcomes assessed early in life, and to evaluate the role of differentially methylated regions (DMRs) regulating genomically imprinted genes in these associations. Methods: Among 325 mother/infant pairs, we used regression models to evaluate the association between tertiles of maternal periconceptional Mediterranean diet adherence (MDA) scores derived from a Food Frequency Questionnaire, and social and emotional scores derived from the Infant Toddler Social and Emotional Assessment (ITSEA) questionnaire in the second year of life. Methylation of nine genomically imprinted genes was measured to determine if MDA was associated with CpG methylation. Results: Child depression was inversely associated with maternal MDA (Bonferroni-corrected p = 0.041). While controlling for false-discovery, compared to offspring of women with the lowest MDA tertile, those with MDA scores in middle and high MDA tertiles had decreased odds for atypical behaviors [OR (95% CI) = 0.40 (0.20, 0.78) for middle and 0.40 (0.17, 0.92) for highest tertile], for maladaptive behaviors [0.37 (0.18, 0.72) for middle tertile and 0.42 (0.18, 0.95) for highest tertile] and for an index of autism spectrum disorder behaviors [0.46 (0.23, 0.90) for middle and 0.35 (0.15, 0.80) for highest tertile]. Offspring of women with the highest MDA tertile were less likely to exhibit depressive [OR = 0.28 (0.12, 0.64)] and anxiety [0.42 (0.18, 0.97)] behaviors and increased odds of social relatedness [2.31 (1.04, 5.19)] behaviors when compared to low MDA mothers. Some associations varied by sex. Perinatal MDA score was associated with methylation differences for imprinted control regions of PEG10/SGCE [females: Beta (95% CI) = 1.66 (0.52, 2.80) – Bonferroni-corrected p = 0.048; males: -0.56 (-1.13, -0.00)], as well as both MEG3 and IGF2 in males [0.97 (0.00, 1.94)] and -0.92 (-1.65, -0.19) respectively. Conclusion: In this ethnically diverse cohort, maternal adherence to a Mediterranean diet in early pregnancy was associated with favorable neurobehavioral outcomes in early childhood and with sex-dependent methylation differences of MEG3, IGF2, and SGCE/PEG10 DMRs.}, number={SEP}, journal={Frontiers in Cell and Developmental Biology}, author={House, John S. and Mendez, M. and Maguire, R.L. and Gonzalez-Nahm, S. and Huang, Z. and Daniels, J. and Murphy, S.K. and Fuemmeler, B.F. and Wright, F.A. and Hoyo, C.}, year={2018}, pages={107} }
 @article{venkatratnam_house_konganti_mckenney_threadgill_chiu_aylor_wright_rusyn_2018, title={Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse}, volume={29}, ISSN={["1432-1777"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85040693289&partnerID=MN8TOARS}, DOI={10.1007/s00335-018-9734-y}, abstractNote={Studies of gene expression are common in toxicology and provide important clues to mechanistic understanding of adverse effects of chemicals. Most prior studies have been performed in a single strain or cell line; however, gene expression is heavily influenced by the genetic background, and these genotype-expression differences may be key drivers of inter-individual variation in response to chemical toxicity. In this study, we hypothesized that the genetically diverse Collaborative Cross mouse population can be used to gain insight and suggest mechanistic hypotheses for the dose- and genetic background-dependent effects of chemical exposure. This hypothesis was tested using a model liver toxicant trichloroethylene (TCE). Liver transcriptional responses to TCE exposure were evaluated 24 h after dosing. Transcriptomic dose–responses were examined for both TCE and its major oxidative metabolite trichloroacetic acid (TCA). As expected, peroxisome- and fatty acid metabolism-related pathways were among the most dose–responsive enriched pathways in all strains. However, nearly half of the TCE-induced liver transcriptional perturbation was strain-dependent, with abundant evidence of strain/dose interaction, including in the peroxisomal signaling-associated pathways. These effects were highly concordant between the administered TCE dose and liver levels of TCA. Dose–response analysis of gene expression at the pathway level yielded points of departure similar to those derived from the traditional toxicology studies for both non-cancer and cancer effects. Mapping of expression–genotype–dose relationships revealed some significant associations; however, the effects of TCE on gene expression in liver appear to be highly polygenic traits that are challenging to positionally map. This study highlights the usefulness of mouse population-based studies in assessing inter-individual variation in toxicological responses, but cautions that genetic mapping may be challenging because of the complexity in gene exposure–dose relationships.}, number={1-2}, journal={MAMMALIAN GENOME}, author={Venkatratnam, Abhishek and House, John S. and Konganti, Kranti and McKenney, Connor and Threadgill, David W. and Chiu, Weihsueh A. and Aylor, David L. and Wright, Fred A. and Rusyn, Ivan}, year={2018}, month={Feb}, pages={168–181} }
 @article{sakolish_weber_kelly_himmelfarb_mouneimne_grimm_house_wade_han_chiu_et al._2018, title={Technology Transfer of the Microphysiological Systems: A Case Study of the Human Proximal Tubule Tissue Chip}, volume={8}, ISSN={["2045-2322"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85054437254&partnerID=MN8TOARS}, DOI={10.1038/s41598-018-33099-2}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Sakolish, Courtney and Weber, Elijah J. and Kelly, Edward J. and Himmelfarb, Jonathan and Mouneimne, Roula and Grimm, Fabian A. and House, John S. and Wade, Terry and Han, Arum and Chiu, Weihsueh A. and et al.}, year={2018}, month={Oct} }
 @article{house_grimm_jima_zhou_rusyn_wright_2017, title={A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85034032104&partnerID=MN8TOARS}, DOI={10.3389/fgene.2017.00168}, abstractNote={Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation. Analyses of high-throughput toxicogenomics data require renewed attention to read-calling algorithms and simplified dose–response modeling for datasets with relatively few samples. Using data from induced pluripotent stem cell-derived cardiomyocytes treated with chemicals at varying concentrations, we describe here and make available a pipeline for handling expression data generated by TempO-Seq to align reads, clean and normalize raw count data, identify differentially expressed genes, and calculate transcriptomic concentration–response points of departure. The methods are extensible to other forms of concentration–response gene-expression data, and we discuss the utility of the methods for assessing variation in susceptibility and the diseased cellular state.}, number={NOV}, journal={Frontiers in Genetics}, author={House, JS and Grimm, FA and Jima, DD and Zhou, YH and Rusyn, I and Wright, FA}, year={2017} }
 @article{henriquez_house_miller_snow_fisher_ren_schladweiler_ledbetter_wright_kodavanti_2017, title={Adrenal-derived stress hormones modulate ozone-induced lung injury and inflammation}, volume={329}, ISSN={["1096-0333"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85020944922&partnerID=MN8TOARS}, DOI={10.1016/j.taap.2017.06.009}, abstractNote={Ozone-induced systemic effects are modulated through activation of the neuro-hormonal stress response pathway. Adrenal demedullation (DEMED) or bilateral total adrenalectomy (ADREX) inhibits systemic and pulmonary effects of acute ozone exposure. To understand the influence of adrenal-derived stress hormones in mediating ozone-induced lung injury/inflammation, we assessed global gene expression (mRNA sequencing) and selected proteins in lung tissues from male Wistar-Kyoto rats that underwent DEMED, ADREX, or sham surgery (SHAM) prior to their exposure to air or ozone (1 ppm), 4 h/day for 1 or 2 days. Ozone exposure significantly changed the expression of over 2300 genes in lungs of SHAM rats, and these changes were markedly reduced in DEMED and ADREX rats. SHAM surgery but not DEMED or ADREX resulted in activation of multiple ozone-responsive pathways, including glucocorticoid, acute phase response, NRF2, and PI3K-AKT. Predicted targets from sequencing data showed a similarity between transcriptional changes induced by ozone and adrenergic and steroidal modulation of effects in SHAM but not ADREX rats. Ozone-induced increases in lung Il6 in SHAM rats coincided with neutrophilic inflammation, but were diminished in DEMED and ADREX rats. Although ozone exposure in SHAM rats did not significantly alter mRNA expression of Ifnγ and Il-4, the IL-4 protein and ratio of IL-4 to IFNγ (IL-4/IFNγ) proteins increased suggesting a tendency for a Th2 response. This did not occur in ADREX and DEMED rats. We demonstrate that ozone-induced lung injury and neutrophilic inflammation require the presence of circulating epinephrine and corticosterone, which transcriptionally regulates signaling mechanisms involved in this response.}, journal={TOXICOLOGY AND APPLIED PHARMACOLOGY}, author={Henriquez, Andres and House, John and Miller, Desinia B. and Snow, Samantha J. and Fisher, Anna and Ren, Hongzu and Schladweiler, Mette C. and Ledbetter, Allen D. and Wright, Fred and Kodavanti, Urmila P.}, year={2017}, month={Aug}, pages={249–258} }
 @article{house_wyss_hoppin_richards_long_umbach_henneberger_freeman_le_dp_et al._2017, title={Early-life farm exposures and adult asthma and atopy in the Agricultural Lung Health Study}, volume={140}, ISSN={0091-6749}, url={http://dx.doi.org/10.1016/j.jaci.2016.09.036}, DOI={10.1016/j.jaci.2016.09.036}, abstractNote={BackgroundPrevious studies, mostly from Europe, suggest that early-life farming exposures protect against childhood asthma and allergy; few data exist on asthma and allergy in adults.ObjectiveWe sought to examine associations between early-life farming exposures and current asthma and atopy in an older adult US farming population.MethodsWe analyzed data from 1746 farmers and 1555 spouses (mean age, 63) from a case-control study nested within the Agricultural Health Study. Current asthma and early-life farming exposures were assessed via questionnaires. We defined atopy based on specific IgE > 0.70 IU/mL to at least 1 of 10 allergens measured in blood. We used logistic regression, adjusted for age, sex, race, state (Iowa or North Carolina), and smoking (pack years), to estimate associations between early-life exposures and asthma (1198 cases and 2031 noncases) or atopy (578 cases and 2526 noncases).ResultsExposure to the farming environment in utero and in early childhood had little or no association with asthma but was associated with reduced odds of atopy. The strongest association was seen for having a mother who performed farm activities while pregnant (odds ratio, 0.60; 95% CI, 0.48-0.74) and remained significant in models with correlated early-life exposures including early childhood farm animal contact and raw milk consumption.ConclusionsIn a large US farming population, early-life farm exposures, particularly maternal farming activities while pregnant, were strongly associated with reduced risk of atopy in adults. These results extend previous work done primarily on childhood outcomes and suggest that protective associations of early-life farming exposures on atopy endure across the life course. Previous studies, mostly from Europe, suggest that early-life farming exposures protect against childhood asthma and allergy; few data exist on asthma and allergy in adults. We sought to examine associations between early-life farming exposures and current asthma and atopy in an older adult US farming population. We analyzed data from 1746 farmers and 1555 spouses (mean age, 63) from a case-control study nested within the Agricultural Health Study. Current asthma and early-life farming exposures were assessed via questionnaires. We defined atopy based on specific IgE > 0.70 IU/mL to at least 1 of 10 allergens measured in blood. We used logistic regression, adjusted for age, sex, race, state (Iowa or North Carolina), and smoking (pack years), to estimate associations between early-life exposures and asthma (1198 cases and 2031 noncases) or atopy (578 cases and 2526 noncases). Exposure to the farming environment in utero and in early childhood had little or no association with asthma but was associated with reduced odds of atopy. The strongest association was seen for having a mother who performed farm activities while pregnant (odds ratio, 0.60; 95% CI, 0.48-0.74) and remained significant in models with correlated early-life exposures including early childhood farm animal contact and raw milk consumption. In a large US farming population, early-life farm exposures, particularly maternal farming activities while pregnant, were strongly associated with reduced risk of atopy in adults. These results extend previous work done primarily on childhood outcomes and suggest that protective associations of early-life farming exposures on atopy endure across the life course.}, number={1}, journal={Journal of Allergy and Clinical Immunology}, publisher={Elsevier BV}, author={House, J.S. and Wyss, A.B. and Hoppin, J.A. and Richards, M. and Long, S. and Umbach, D.M. and Henneberger, P.K. and Freeman, Beane and Le, Sandler and Dp, Long O.'Connell and et al.}, year={2017}, month={Jul}, pages={249–256.e14} }
 @article{wyss_house_hoppin_richards_hankinson_long_henneberger_beane freeman_sandler_o’connell_et al._2017, title={Raw milk consumption and other early-life farm exposures and adult pulmonary function in the Agricultural Lung Health Study}, volume={73}, ISSN={0040-6376 1468-3296}, url={http://dx.doi.org/10.1136/thoraxjnl-2017-210031}, DOI={10.1136/thoraxjnl-2017-210031}, abstractNote={Literature suggests that early exposure to the farming environment protects against atopy and asthma; few studies have examined pulmonary function. We evaluated associations between early-life farming exposures and pulmonary function in 3061 adults (mean age=63) from a US farming population using linear regression. Childhood raw milk consumption was associated with higher FEV1 (β=49.5 mL, 95% CI 2.8 to 96.1 mL, p=0.04) and FVC (β=66.2 mL, 95% CI 13.2 to 119.1 mL, p=0.01). We did not find appreciable associations with other early-life farming exposures. We report a novel association between raw milk consumption and higher pulmonary function that lasts into older adulthood.}, number={3}, journal={Thorax}, publisher={BMJ}, author={Wyss, Annah B and House, John S and Hoppin, Jane A and Richards, Marie and Hankinson, John L and Long, Stuart and Henneberger, Paul K and Beane Freeman, Laura E and Sandler, Dale P and O’Connell, Elizabeth Long and et al.}, year={2017}, month={Jul}, pages={279–282} }
 @article{house_nichols_li_brandenberger_virgincar_degraff_driehuys_zeldin_london_2017, title={Vagal innervation is required for pulmonary function phenotype in htr4 <sup>–/–</sup> mice}, volume={312}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85017032088&partnerID=MN8TOARS}, DOI={10.1152/ajplung.00495.2016}, abstractNote={Human genome-wide association studies have identified over 50 loci associated with pulmonary function and related phenotypes, yet follow-up studies to determine causal genes or variants are rare. Single nucleotide polymorphisms in serotonin receptor 4 (HTR4) are associated with human pulmonary function in genome-wide association studies and follow-up animal work has demonstrated that Htr4 is causally associated with pulmonary function in mice, although the precise mechanisms were not identified. We sought to elucidate the role of neural innervation and pulmonary architecture in the lung phenotype of Htr4-/- animals. We report here that the Htr4-/- phenotype in mouse is dependent on vagal innervation to the lung. Both ex vivo tracheal ring reactivity and in vivo flexiVent pulmonary functional analyses demonstrate that vagotomy abrogates the Htr4-/- airway hyperresponsiveness phenotype. Hyperpolarized 3He gas magnetic resonance imaging and stereological assessment of wild-type and Htr4-/- mice reveal no observable differences in lung volume, inflation characteristics, or pulmonary microarchitecture. Finally, control of breathing experiments reveal substantive differences in baseline breathing characteristics between mice with/without functional HTR4 in breathing frequency, relaxation time, flow rate, minute volume, time of inspiration and expiration and breathing pauses. These results suggest that HTR4's role in pulmonary function likely relates to neural innervation and control of breathing.}, number={4}, journal={American Journal of Physiology - Lung Cellular and Molecular Physiology}, publisher={American Physiological Society}, author={House, John S. and Nichols, Cody E. and Li, Huiling and Brandenberger, Christina and Virgincar, Rohan S. and DeGraff, Laura M. and Driehuys, Bastiaan and Zeldin, Darryl C. and London, Stephanie J.}, year={2017}, pages={L520–L530} }
 @article{house_li_degraff_flake_zeldin_london_2015, title={Genetic variation in HTR4 and lung function: GWAS follow-up in mouse.}, volume={29}, url={http://europepmc.org/abstract/med/25342126}, DOI={10.1096/fj.14-253898}, abstractNote={Human genome‐wide association studies (GWASs) have identified numerous associations between single nucleotide polymorphisms (SNPs) and pulmonary function. Proving that there is a causal relationship between GWAS SNPs, many of which are noncoding and without known functional impact, and these traits has been elusive. Furthermore, noncoding GWAS‐identified SNPs may exert trans‐regulatory effects rather than impact the proximal gene. Noncoding variants in 5‐hydroxytryptamine (serotonin) receptor 4 (HTR4) are associated with pulmonary function in human GWASs. To gain insight into whether this association is causal, we tested whether Htr4‐null mice have altered pulmonary function. We found that HTR4‐deficient mice have 12% higher baseline lung resistance and also increased methacholine‐induced airway hyperresponsiveness (AHR) as measured by lung resistance (27%), tissue resistance (48%), and tissue elastance (30%). Furthermore, Htr4‐null mice were more sensitive to serotonin‐induced AHR. In models of exposure to bacterial lipopolysaccharide, bleomycin, and allergic airway inflammation induced by house dust mites, pulmonary function and cytokine profiles in Htr4‐null mice differed little from their wild‐type controls. The findings of altered baseline lung function and increased AHR in Htr4‐null mice support a causal relationship between genetic variation in HTR4 and pulmonary function identified in human GWAS.‐House J. S., Li, H., DeGraff, L. M., Flake, G., Zeldin, D. C., London, S. J. Genetic variation in HTR4 and lung function: GWAS follow‐up in mouse. FASEB J. 29, 323–335 (2015). www.fasebj.org}, number={1}, journal={FASEB Journal}, author={House, JS and Li, H and DeGraff, LM and Flake, G and Zeldin, DC and London, SJ}, year={2015}, month={Jan}, pages={323–335} }
 @article{graves_gruzdev_bradbury_degraff_li_house_hoopes_edin_zeldin_2015, title={Quantitative Polymerase Chain Reaction Analysis of the Mouse Cyp2j Subfamily: Tissue Distribution and Regulation.}, volume={43}, url={http://europepmc.org/abstract/med/25994032}, DOI={10.1124/dmd.115.064139}, abstractNote={Members of the cytochrome P450 CYP2J subfamily are expressed in multiple tissues in mice and humans. These enzymes are active in the metabolism of fatty acids to generate bioactive compounds. Herein we report new methods and results for quantitative polymerase chain reaction (qPCR) analysis for the seven genes (Cyp2j5, Cyp2j6, Cyp2j8, Cyp2j9, Cyp2j11, Cyp2j12, and Cyp2j13) of the mouse Cyp2j subfamily. SYBR Green primer sets were developed and compared with commercially available TaqMan primer/probe assays for specificity toward mouse Cyp2j cDNA, and analysis of tissue distribution and regulation of Cyp2j genes. Each TaqMan primer/probe set and SYBR Green primer set were shown to be specific for their intended mouse Cyp2j cDNA. Tissue distribution of the mouse Cyp2j isoforms confirmed similar patterns of expression between the two qPCR methods. Cyp2j5 and Cyp2j13 were highly expressed in male kidneys, and Cyp2j11 was highly expressed in both male and female kidneys. Cyp2j6 was expressed in multiple tissues, with the highest expression in the small intestine and duodenum. Cyp2j8 was detected in various tissues, with highest expression found in the skin. Cyp2j9 was highly expressed in the brain, liver, and lung. Cyp2j12 was predominately expressed in the brain. We also determined the Cyp2j isoform expression in Cyp2j5 knockout mice to determine whether there was compensatory regulation of other Cyp2j isoforms, and we assessed Cyp2j isoform regulation during various inflammatory models, including influenza A, bacterial lipopolysaccharide, house dust mite allergen, and corn pollen. Both qPCR methods detected similar suppression of Cyp2j6 and Cyp2j9 during inflammation in the lung.}, number={8}, journal={Drug Metabolism and Disposition}, author={Graves, JP and Gruzdev, A and Bradbury, JA and DeGraff, LM and Li, H and House, JS and Hoopes, SL and Edin, ML and Zeldin, DC}, year={2015}, month={Aug}, pages={1169–1180} }
 @article{london_gao_gharib_hancock_wilk_house_gibbs_muzny_lumley_franceschini_et al._2014, title={ADAM19 and HTR4 variants and pulmonary function: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study.}, volume={7}, url={http://europepmc.org/abstract/med/24951661}, DOI={10.1161/circgenetics.113.000066}, abstractNote={Background—The pulmonary function measures of forced expiratory volume in 1 second (FEV1) and its ratio to forced vital capacity (FVC) are used in the diagnosis and monitoring of lung diseases and predict cardiovascular mortality in the general population. Genome-wide association studies (GWASs) have identified numerous loci associated with FEV1 and FEV1/FVC, but the causal variants remain uncertain. We hypothesized that novel or rare variants poorly tagged by GWASs may explain the significant associations between FEV1/FVC and 2 genes: ADAM19 and HTR4. Methods and Results—We sequenced ADAM19 and its promoter region along with the ≈21-kb portion of HTR4 harboring GWAS single-nucleotide polymorphisms for pulmonary function and analyzed associations with FEV1/FVC among 3983 participants of European ancestry from Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Meta-analysis of common variants in each region identified statistically significant associations (316 tests; P<1.58×10−4) with FEV1/FVC for 14 ADAM19 single-nucleotide polymorphisms and 24 HTR4 single-nucleotide polymorphisms. After conditioning on the sentinel GWASs hit in each gene (ADAM19 rs1422795, minor allele frequency=0.33 and HTR4 rs11168048, minor allele frequency=0.40], 1 single-nucleotide polymorphism remained statistically significant (ADAM19 rs13155908, minor allele frequency=0.12; P=1.56×10−4). Analysis of rare variants (minor allele frequency <1%) using sequence kernel association test did not identify associations with either region. Conclusions—Sequencing identified 1 common variant associated with FEV1/FVC independent of the sentinel ADAM19 GWAS hit and supports the original HTR4 GWAS findings. Rare variants do not seem to underlie GWAS associations with pulmonary function for common variants in ADAM19 and HTR4.}, number={3}, journal={Circulation: Cardiovascular Genetics}, author={London, S.J. and Gao, W. and Gharib, S.A. and Hancock, D.B. and Wilk, J.B. and House, J.S. and Gibbs, R.A. and Muzny, D.M. and Lumley, T. and Franceschini, N. and et al.}, year={2014}, month={Jun}, pages={350–358} }
 @article{thompson_zhu_hall_house_ranjan_burr_he_owens_smart_2011, title={C/EBP alpha Expression Is Downregulated in Human Nonmelanoma Skin Cancers and Inactivation of C/EBP alpha Confers Susceptibility to UVB-Induced Skin Squamous Cell Carcinomas}, volume={131}, ISSN={["0022-202X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79956039252&partnerID=MN8TOARS}, DOI={10.1038/jid.2011.31}, abstractNote={Human epidermis is routinely subjected to DNA damage induced by UVB solar radiation. Cell culture studies have revealed an unexpected role for C/EBPα (CCAAT/enhancer-binding protein-α) in the DNA damage response network, where C/EBPα is induced following UVB DNA damage, regulates the G1 checkpoint, and diminished or ablated expression of C/EBPα results in G1 checkpoint failure. In the current study we observed that C/EBPα is induced in normal human epidermal keratinocytes and in the epidermis of human subjects exposed to UVB radiation. The analysis of human skin precancerous and cancerous lesions (47 cases) for C/EBPα expression was conducted. Actinic keratoses, a precancerous benign skin growth and precursor to squamous cell carcinoma (SCC), expressed levels of C/EBPα similar to normal epidermis. Strikingly, all invasive SCCs no longer expressed detectable levels of C/EBPα. To determine the significance of C/EBPα in UVB-induced skin cancer, SKH-1 mice lacking epidermal C/EBPα (CKOα) were exposed to UVB. CKOα mice were highly susceptible to UVB-induced SCCs and exhibited accelerated tumor progression. CKOα mice displayed keratinocyte cell cycle checkpoint failure in vivo in response to UVB that was characterized by abnormal entry of keratinocytes into S phase. Our results demonstrate that C/EBPα is silenced in human SCC and loss of C/EBPα confers susceptibility to UVB-induced skin SCCs involving defective cell cycle arrest in response to UVB. Human epidermis is routinely subjected to DNA damage induced by UVB solar radiation. Cell culture studies have revealed an unexpected role for C/EBPα (CCAAT/enhancer-binding protein-α) in the DNA damage response network, where C/EBPα is induced following UVB DNA damage, regulates the G1 checkpoint, and diminished or ablated expression of C/EBPα results in G1 checkpoint failure. In the current study we observed that C/EBPα is induced in normal human epidermal keratinocytes and in the epidermis of human subjects exposed to UVB radiation. The analysis of human skin precancerous and cancerous lesions (47 cases) for C/EBPα expression was conducted. Actinic keratoses, a precancerous benign skin growth and precursor to squamous cell carcinoma (SCC), expressed levels of C/EBPα similar to normal epidermis. Strikingly, all invasive SCCs no longer expressed detectable levels of C/EBPα. To determine the significance of C/EBPα in UVB-induced skin cancer, SKH-1 mice lacking epidermal C/EBPα (CKOα) were exposed to UVB. CKOα mice were highly susceptible to UVB-induced SCCs and exhibited accelerated tumor progression. CKOα mice displayed keratinocyte cell cycle checkpoint failure in vivo in response to UVB that was characterized by abnormal entry of keratinocytes into S phase. Our results demonstrate that C/EBPα is silenced in human SCC and loss of C/EBPα confers susceptibility to UVB-induced skin SCCs involving defective cell cycle arrest in response to UVB. CCAAT/enhancer-binding protein-α DNA damage response immunohistochemical keratin 5 minimum erythemic dose phosphate-buffered saline squamous cell carcinoma 12-O-tetradecanoylphorbol-13-acetate The epidermis is routinely subject to DNA damage by UVB, which is considered to be the principal carcinogenic component of sunlight. Exposure to UVB results in DNA damage in the form of cyclobutane pyrimidine dimers, 6–4 photoproducts, DNA strand breaks, and DNA crosslinks (Brash, 1997Brash D.E. Sunlight and the onset of skin cancer.Trends Genet. 1997; 13: 410-414Abstract Full Text PDF PubMed Scopus (259) Google Scholar; de Gruijl et al., 2001de Gruijl F.R. van Kranen H.J. Mullenders L.H. UV-induced DNA damage, repair, mutations and oncogenic pathways in skin cancer.J Photochem Photobiol B. 2001; 63: 19-27Crossref PubMed Scopus (385) Google Scholar). If not repaired or if misrepaired, this DNA damage can result in mutations in the genome, and can ultimately contribute to the development of skin cancers (Brash et al., 1991Brash D.E. Rudolph J.A. Simon J.A. et al.A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma.Proc Natl Acad Sci USA. 1991; 88: 10124-10128Crossref PubMed Scopus (1643) Google Scholar). Solar radiation is responsible for >1,000,000 nonmelanoma skin cancer cases per year in the United States, and these cases account for 40% of all new cancer cases diagnosed each year in the United States (American Cancer Society, 2008American Cancer SocietyCancer Facts & Figures 2008.in: 2008http://www.cancer.org/Research/CancerFactsFigures/cancer-facts-figures-2008Google Scholar). To maintain genome integrity and to prevent heritable mutations that lead to cancer, cells respond to DNA damage produced by intrinsic or environmental factors by engaging the DNA damage response (DDR) network. This network entails signaling pathways involving cell cycle checkpoints, DNA repair, transcription programs, and apoptosis. Cell cycle checkpoints can occur in any phase of the cell cycle and are characterized as a pause in the cell cycle that allows time for the repair of damaged DNA. Defective checkpoints can contribute to genome instability and cancer pathogenesis (Kastan and Bartek, 2004Kastan M.B. Bartek J. Cell-cycle checkpoints and cancer.Nature. 2004; 432: 316-323Crossref PubMed Scopus (2028) Google Scholar). C/EBPα (CCAAT/enhancer-binding protein-α) is one of the six members of the C/EBP family of basic leucine zipper transcription factors (Ramji and Foka, 2002Ramji D.P. Foka P. CCAAT/enhancer-binding proteins: structure, function and regulation.Biochem J. 2002; 365: 561-575Crossref PubMed Google Scholar; Johnson, 2005Johnson P.F. Molecular stop signs: regulation of cell-cycle arrest by C/EBP transcription factors.J Cell Sci. 2005; 118: 2545-2555Crossref PubMed Scopus (221) Google Scholar). C/EBPα has been established as a tumor-suppressor gene in human acute myeloid leukemia (Pabst et al., 2001Pabst T. Mueller B.U. Zhang P. et al.Dominant-negative mutations of CEBPA, encoding CCAAT/enhancer binding protein-alpha (C/EBPalpha), in acute myeloid leukemia.Nat Genet. 2001; 27: 263-270Crossref PubMed Scopus (705) Google Scholar). Additionally, there is circumstantial evidence for its function as a tumor suppressor based on diminished C/EBPα expression in a multitude of human tumor types including liver (Xu et al., 2001Xu L. Hui L. Wang S. et al.Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma.Cancer Res. 2001; 61: 3176-3181PubMed Google Scholar), lung (Halmos et al., 2002Halmos B. Huettner C.S. Kocher O. et al.Down-regulation and antiproliferative.Cancer Res. 2002; 62: 528-534PubMed Google Scholar), breast (Gery et al., 2005Gery S. Tanosaki S. Bose S. et al.Down-regulation and growth inhibitory role of C/EBPalpha in breast cancer.Clin Cancer Res. 2005; 11: 3184-3190Crossref PubMed Scopus (76) Google Scholar), endometrial (Takai et al., 2005Takai N. Kawamata N. Walsh C.S. et al.Discovery of epigenetically masked tumor suppressor genes in endometrial cancer.Mol Cancer Res. 2005; 3: 261-269Crossref PubMed Scopus (63) Google Scholar), and head and neck squamous cell carcinomas (SCCs; Bennett et al., 2007Bennett K.L. Hackanson B. Smith L.T. et al.Tumor suppressor activity of CCAAT/e.Cancer Res. 2007; 67: 4657-4664Crossref PubMed Scopus (70) Google Scholar). The traditional view of C/EBPα in cell biology involves its role in cellular differentiation and metabolism (Roesler, 2001Roesler W.J. The role of C/EBP in nutrient and hormonal regulation of gene expression.Annu Rev Nutr. 2001; 21: 141-165Crossref PubMed Scopus (81) Google Scholar); in cancer, the traditional view holds that it has a tumor-suppressor role, where the loss of expression/function results in an impaired differentiation commitment accompanied by deregulated proliferation (Schuster and Porse, 2006Schuster M.B. Porse B.T. C/EBPalpha: a tumour suppressor in multiple tissues?.Biochim Biophys Acta. 2006; 1766: 88-103PubMed Google Scholar; Koschmieder et al., 2009Koschmieder S. Halmos B. Levantini E. et al.Dysregulation of the C/EBPalpha differentiation pathway in human cancer.J Clin Oncol. 2009; 27: 619-628Crossref PubMed Scopus (155) Google Scholar). However, recent studies indicate that the role of C/EBPα in cells/cancer is more complex and multifaceted than originally thought (Yoon and Smart, 2004Yoon K. Smart R.C. C/EBPalpha is a DNA damage-inducible p53-regulated mediator of the G1 checkpoint in keratinocytes.Mol Cell Biol. 2004; 24: 10650-10660Crossref PubMed Scopus (53) Google Scholar; Loomis et al., 2007Loomis K.D. Zhu S. Yoon K. et al.Genetic ablation of CCAAT/enhancer binding protein {alpha.Cancer Res. 2007; 67: 6768-6776Crossref PubMed Scopus (34) Google Scholar; Ranjan et al., 2009Ranjan R. Thompson E.A. Yoon K. et al.C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.Oncogene. 2009; 28: 3235-3245Crossref PubMed Scopus (8) Google Scholar). Cell culture studies have revealed an unexpected role for C/EBPα in the DDR in keratinocytes where C/EBPα is induced following UVB-induced DNA damage, and it regulates the G1 checkpoint. Diminished or ablated expression of C/EBPα results in G1 checkpoint failure following UVB-induced DNA damage (Yoon and Smart, 2004Yoon K. Smart R.C. C/EBPalpha is a DNA damage-inducible p53-regulated mediator of the G1 checkpoint in keratinocytes.Mol Cell Biol. 2004; 24: 10650-10660Crossref PubMed Scopus (53) Google Scholar; Ranjan et al., 2009Ranjan R. Thompson E.A. Yoon K. et al.C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.Oncogene. 2009; 28: 3235-3245Crossref PubMed Scopus (8) Google Scholar). In further support of a nonparadigmatic C/EBPα tumor-suppressor function, mice lacking C/EBPα in their epidermis do not display alterations in differentiation or proliferation and are susceptible to chemical carcinogen-induced skin tumorigenesis (Loomis et al., 2007Loomis K.D. Zhu S. Yoon K. et al.Genetic ablation of CCAAT/enhancer binding protein {alpha.Cancer Res. 2007; 67: 6768-6776Crossref PubMed Scopus (34) Google Scholar). Given the function of C/EBPα as a mediator of the G1 checkpoint in keratinocytes in response to UVB, it is possible that C/EBPα functions as a suppressor of UVB-induced tumorigenesis. Whereas C/EBPα expression is diminished in mouse skin SCCs (Oh and Smart, 1998Oh H.S. Smart R.C. Expression of CCAAT/enhancer binding proteins (C/EBP) is associated with squamous differentiation in epidermis and isolated primary keratinocytes and is altered in skin neoplasms.J Invest Dermatol. 1998; 110: 939-945Crossref PubMed Scopus (79) Google Scholar; Shim et al., 2005Shim M. Powers K.L. Ewing S.J. et al.Diminished expression of C/EBPalpha in skin carcinomas is linked to oncogenic Ras and reexpression of C/EBPalpha in carcinoma cells inhibits proliferation.Cancer Res. 2005; 65: 861-867PubMed Google Scholar), C/EBPα levels have not been examined in human skin precancerous and cancerous lesions. Therefore, the objectives of this study were: to examine the expression of C/EBPα in human skin precancerous and cancerous lesions, to characterize the response of C/EBPα to UVB in human keratinocytes and human skin; and to develop an in vivo SKH-1 mouse model to determine the in vivo physiological significance of C/EBPα in UVB-induced skin tumorigenesis. We examined the expression of C/EBPα in normal human epidermis, precancerous actinic keratoses, keratoacanthomas, SCCs in situ, and invasive SCCs as well as basal cell carcinomas. Immunohistochemical (IHC) staining for C/EBPα in human skin showed that C/EBPα was extensively expressed in the nuclei of nondividing keratinocytes of the suprabasal layers of the epidermis (Figure 1a). C/EBPα expression was also detected, although less frequently, in keratinocytes in the proliferative basal layer of epidermis. Actinic keratoses, a precancerous benign skin growth of which a small percentage progress to SCC, expressed levels of C/EBPα similar to normal epidermis (Figure 1a and b). Keratoacanthomas, once considered as terminally benign but now regarded and treated by many dermatologists as a malignant growth that can progress to SCC, expressed reduced levels of C/EBPα with 20% of keratoacanthomas no longer expressing detectable levels of C/EBPα (Figure 1a and b). Most striking, however, were the SCCs where the majority of both SCCs in situ (80%) and invasive SCCs (100%) no longer expressed detectable levels of C/EBPα (Figure 1a and b). Similarly, the IHC staining for C/EBPα was absent in 14/16 basal cell carcinoma cases (data not shown). Most human nonmelanoma skin cancers are caused by solar radiation, and UVB radiation is considered the most carcinogenic component of sunlight. To characterize the effects of UVB exposure on the expression of C/EBPα in human keratinocytes, we exposed subconfluent proliferating normal human epidermal keratinocytes to 5, 10, or 15mJcm2 UVB. Immunoblot analysis for C/EBPα revealed that the expression of C/EBPα protein was induced at all doses (Figure 2a). To characterize the effects of UVB exposure on the expression of C/EBPα in human skin in vivo, biopsies from UVB-treated human skin (1 minimum erythemic dose (MED) UVB) (N=5) were compared with biopsies from non-sun-exposed human skin (N=5) for C/EBPα expression. C/EBPα levels were increased throughout the epidermis of UVB-treated human skin as determined by the increased C/EBPα IHC nuclear staining intensity as well as by the overall statistically significant increase in the number of keratinocytes staining positively for C/EBPα (Figure 2b–d and Supplementary Figure S1 online). Although UVB treatment increased the percentage of C/EBPα-expressing keratinocytes in the spinous and granular nondividing suprabasal layers by 2.3-fold, we observed a 4.3-fold increase in the number of basal keratinocytes expressing C/EBPα (Figure 2b–d). Download .pdf (.66 MB) Help with pdf files Supplementary Figures S1 and S2 We treated SKH-1 hairless mice, a well-characterized mouse model frequently utilized to study the effects of UVB in skin in vivo (Benavides et al., 2009Benavides F. Oberyszyn T.M. VanBuskirk A.M. et al.The hairless mouse in skin research.J Dermatol Sci. 2009; 53: 10-18Abstract Full Text Full Text PDF PubMed Scopus (153) Google Scholar), with UVB (50mJcm2) and, similar to human skin, we observed a significant increase in C/EBPα-expressing keratinocytes in the suprabasal and basal proliferative compartments of epidermis (Figure 3a). There was an ∼2-fold increase in the number of C/EBPα positively stained suprabasal cells, and a 3-fold increase in the number of C/EBPα positively stained basal keratinocytes (Figure 3b). To begin to determine the physiological significance of UVB-induced epidermal C/EBPα in vivo, we generated an epidermal-specific C/EBPα knockout SKH-1 mouse, hereafter referred to as conditional knockout (CKOα). CKOα mice were generated from C/EBPαfl/fl SKH-1 mice and keratin 5 (K5) Cre (K5Cre) SKH-1 mice where the K5 promoter directs Cre recombinase expression to the epidermis and other stratified squamous epithelia. As shown in Figure 3c, C/EBPα protein was not detectable in epidermal protein extracts prepared from CKOα mice. CKOα mice did not display any abnormal gross or morphological skin phenotype (data not shown). The most susceptible human population to UVB-induced damage is classified as type 1 according to the Fitzpatrick Classification Scale. These individuals have very fair and often freckled skin, have blond or red hair, always sun burn, and are highly susceptible to solar radiation-induced nonmelanoma skin cancer. The MED of UVB for this susceptible population is ∼20–25mJcm2. Therefore, we exposed CKOα and K5Cre control mice to 20mJcm2 UVB three times weekly to test whether the loss of C/EBPα in skin keratinocytes confers susceptibility to UVB-induced tumorigenesis. As shown in Figure 4a and b, CKOα mice were highly susceptibility to UVB-induced skin tumorigenesis as evidenced by decreased latency (18 weeks), increased tumor incidence (85 vs. 25%), and a 6-fold increase in tumor multiplicity. Histological analysis of all skin tumors at the termination of experiment revealed that the majority of tumors (∼90%) in both genotypes were SCCs (in situ or invasive). Most importantly, we observed that 48% of SCCs in CKOα mice were invasive SCCs compared with 15% in the UVB-treated K5Cre control mice (Figure 4c). Invasive carcinomas were identified by severe dysplasia to anaplastic growth, marked atypia in all cell layers, and most importantly, invasion through the panniculus carnosus and/or basement membrane (Supplementary Figure S2 online). To demonstrate that these tumors were the result of UVB treatment and not advanced age, 8 CKOα mice were held for 52 weeks and no skin tumors of any kind were detected. Collectively, these results indicate that loss of C/EBPα confers susceptibility to UVB-induced skin cancer at a biologically relevant dose and loss of C/EBPα accelerates skin tumor progression. To determine whether the ablation of epidermal C/EBPα alters the ability of keratinocytes to undergo a cell cycle arrest in response to UVB treatment in vivo in mouse skin, we treated K5Cre control mice and CKOα mice with UVB, and then examined the number of actively replicating keratinocytes post-UVB by measuring the incorporation of the nucleotide analog BrdU (1hour BrdU pulse before skin collection). As shown in Figure 5a, UVB-treated control mice (K5Cre) displayed a significant cell cycle arrest; at 4hours post-UVB treatment, there was ∼60% decrease in the number of BrdU-positive S-phase basal keratinocytes in the epidermis and this decrease was sustained at 6 and 10hours post-UVB (Figure 5a). At 12hours post-UVB, the number of BrdU-positive S-phase basal keratinocytes returned to untreated control levels (data not shown). Although UVB-treated CKOα mice displayed a similar cell cycle arrest as UVB-treated control mice at 4hours post-UVB treatment, this inhibition was not sustained and cells resumed their progression in the cell cycle prematurely. At 6hours post-UVB, the number of BrdU-positive S-phase cells was significantly increased and by 10hours post-UVB treatment, there was a 3-fold increase in BrdU-positive S-phase basal keratinocytes in CKOα epidermis compared with UVB-treated control mice. Representative examples of BrdU-positive S-phase staining at 10hours post-UVB in K5Cre and CKOα mouse epidermis are shown in Figure 5a (right panel). These results indicate that the loss of C/EBPα in epidermis results in an impaired cell cycle arrest in response to UVB in vivo. To further investigate the role of C/EBPα in UVB-induced cell cycle checkpoints in epidermis in vivo, we utilized an in vivo model of cell cycle regulation involving the induction of synchronous cell proliferation induced by the potent mitogen, 12-O-tetradecanoylphorbol-13-acetate (TPA) (Foley et al., 1993Foley J. Ton T. Maronpot R. et al.Comparison of proliferating cell nuclear antigen to tritiated thymidine as a marker of proliferating hepatocytes in rats.Environ Health Perspect. 1993; 101: 199-205Crossref PubMed Scopus (96) Google Scholar; Kim et al., 1997Kim T.W. Porter K.L. Foley J.F. et al.Evidence that mirex promotes a unique population of epidermal cells that cannot be distinguished by their mutant Ha-ras genotype.Mol Carcinog. 1997; 20: 115-124Crossref PubMed Scopus (9) Google Scholar; Rodriguez-Puebla et al., 1998Rodriguez-Puebla M.L. Robles A.I. Johnson D.G. et al.Synchronized proliferation induced by 12-O-tetradecanoylphorbol-13-acetate treatment of mouse skin: an in vivo model for cell cycle regulation.Cell Growth Differ. 1998; 9: 31-39PubMed Google Scholar). A single topical treatment of TPA resulted in synchronous entry of G1 keratinocytes into S phase as determined by BrdU-positive basal cells at 12hours post-TPA treatment and S-phase cells further increased at 14 and 16hours in control mice (1hour BrdU pulse before skin collection; Figure 5b). TPA-treated CKOα mice responded similarly and the numbers of S-phase cells were not significantly different from TPA-treated control mice at all time points (P>0.3, data not shown). To determine the effect of UVB on this entry into S phase, K5Cre and CKOα mice were treated with TPA, and 4hours later, a time when keratinocytes are still in G1, were either treated with UVB (50mJcm2) or left untreated. The number of BrdU-positive S-phase cells were then determined at 14hours post-TPA treatment and 10hours post-UVB. As shown in Figure 5c, TPA-treated K5Cre and CKOα mice not exposed to UVB displayed a 3-fold increase in the number of BrdU-positive S-phase keratinocytes. UVB treatment of TPA-treated mice resulted in dramatic decreases in the number of BrdU-positive S-phase cells in the epidermis of both genotypes compared with TPA treatment alone (Figure 5c). However, CKOα mice displayed ∼3 times more BrdU-positive S-phase cells than similarly treated K5Cre mice. Collectively, our findings suggest that the loss of epidermal C/EBPα results in an impaired cell cycle arrest involving the G1- to S-phase transition in response to UVB in vivo in mouse epidermis. Because p53 is an important player in the DDR and a key mediator of checkpoints following DNA damage, we wanted to determine whether the impaired cell cycle arrest at the G1- to S-phase transition observed in the CKOα mice following UVB treatment could be related to deficiencies in p53. We performed immunoblot analysis for p53 on epidermal lysates from both UVB-treated (50mJcm2) and untreated K5Cre and CKOα mice, and observed an induction in p53 protein in both genotypes following UVB treatment (Figure 5d). To further determine whether p53 was induced to a similar extent in both genotypes, IHC staining and quantitation of p53-positive basal cells were performed, and no statistically significant differences were found (Figure 5d). C/EBPα is abundantly expressed in the mouse and human epidermis (Swart et al., 1997Swart G.W. van Groningen J.J. van Ruissen F. et al.Transcription factor C/EBPalpha: novel sites of expression and cloning of the human gene.Biol Chem. 1997; 378: 373-379Crossref PubMed Scopus (29) Google Scholar; Maytin and Habener, 1998Maytin E.V. Habener J.F. Transcription factors C/EBP alpha, C/EBP beta, and CHOP (Gadd153) expressed during the differentiation program of keratinocytes in vitro and in vivo.J Invest Dermatol. 1998; 110: 238-246Crossref PubMed Scopus (119) Google Scholar; Oh and Smart, 1998Oh H.S. Smart R.C. Expression of CCAAT/enhancer binding proteins (C/EBP) is associated with squamous differentiation in epidermis and isolated primary keratinocytes and is altered in skin neoplasms.J Invest Dermatol. 1998; 110: 939-945Crossref PubMed Scopus (79) Google Scholar) and in this study we report that C/EBPα is induced by UVB in human epidermal keratinocytes and human epidermis. Analysis of C/EBPα expression in human skin and human skin precancerous and cancerous lesions revealed that C/EBPα expression is downregulated in SCCs in situ and in invasive SCCs and that expression of C/EBPα is normal in actinic keratoses. These results indicate that loss of C/EBPα expression is not an early event in SCC development but occurs during progression from actinic keratoses to invasive SCCs. The mechanism through which C/EBPα is downregulated in human and mouse SCCs is unknown; however, promoter hypermethylation is a candidate as C/EBPα promoter hypermethylation has been shown to be important in the decreased expression of C/EBPα in breast cancer as well as head and neck cancers (Gery et al., 2005Gery S. Tanosaki S. Bose S. et al.Down-regulation and growth inhibitory role of C/EBPalpha in breast cancer.Clin Cancer Res. 2005; 11: 3184-3190Crossref PubMed Scopus (76) Google Scholar; Bennett et al., 2007Bennett K.L. Hackanson B. Smith L.T. et al.Tumor suppressor activity of CCAAT/e.Cancer Res. 2007; 67: 4657-4664Crossref PubMed Scopus (70) Google Scholar). p53 is frequently mutated in human skin cancer and this is an early essential event (Brash, 1997Brash D.E. Sunlight and the onset of skin cancer.Trends Genet. 1997; 13: 410-414Abstract Full Text PDF PubMed Scopus (259) Google Scholar). Although actinic keratoses are the precursor lesion to SCCs, only a small percentage of actinic keratoses (1–10%) actually progress to SCCs, even though both actinic keratoses and SCCs share a high frequency (70%) of mutant p53 and similar p53 mutation spectra (Callen et al., 1997Callen J.P. Bickers D.R. Moy R.L. Actinic keratoses.J Am Acad Dermatol. 1997; 36: 650-653Abstract Full Text Full Text PDF PubMed Scopus (147) Google Scholar; Ortonne, 2002Ortonne J.P. From actinic keratosis to squamous cell carcinoma.Br J Dermatol. 2002; 146: 20-23Crossref PubMed Scopus (101) Google Scholar; Giglia-Mari and Sarasin, 2003Giglia-Mari G. Sarasin A. TP53 mutations in human skin cancers.Hum Mutat. 2003; 21: 217-228Crossref PubMed Scopus (197) Google Scholar; Stockfleth and Kerl, 2006Stockfleth E. Kerl H. Guidelines for the management of actinic keratoses.Eur J Dermatol. 2006; 16: 599-606PubMed Google Scholar). These results indicate that mutant p53 is not sufficient for the progression of actinic keratoses to SCCs and that additional events are required for actinic keratosis progression. One such event may be the loss of C/EBPα, as C/EBPα expression is retained in actinic keratoses, but C/EBPα expression is silenced in SCCs. These results suggest that loss of C/EBPα expression may be a critical event in the progression of precancerous actinic keratoses to invasive SCCs. Our current results in CKOα mice demonstrate that the ablation of C/EBPα in mouse epidermis confers susceptibility to UVB-induced SCCs at a biologically relevant dose and results in the acceleration of skin cancer progression to invasive SCCs. Additionally, earlier studies showed that mice lacking C/EBPα in their epidermis are also more susceptible to chemical carcinogen-induced skin tumorigenesis, and tumors that develop in these mice exhibited an accelerated rate of malignant progression to invasive SCCs (Loomis et al., 2007Loomis K.D. Zhu S. Yoon K. et al.Genetic ablation of CCAAT/enhancer binding protein {alpha.Cancer Res. 2007; 67: 6768-6776Crossref PubMed Scopus (34) Google Scholar). Collectively, these results indicate an important role for the loss of C/EBPα in skin cancer progression induced by UVB radiation or chemical carcinogens. The recent comprehensive genomic characterization of human cancers has revealed that genomic instability is a common characteristic of cancer, that human cancer cells contain hundreds if not thousands of mutations, and that the mutation rate in cancer cells greatly exceeds that in normal cells (Lengauer et al., 1998Lengauer C. Kinzler K.W. Vogelstein B. Genetic instabilities in human cancers.Nature. 1998; 396: 643-649Crossref PubMed Scopus (3268) Google Scholar; Bielas et al., 2006Bielas J.H. Loeb K.R. Rubin B.P. et al.Human cancers express a mutator phenotype.Proc Natl Acad Sci USA. 2006; 103: 18238-18242Crossref PubMed Scopus (276) Google Scholar; The Cancer Genome Atlas Research Network, 2008The Cancer Genome Atlas Research NetworkComprehensive genomic characterization defines human glioblastoma genes and core pathways.Nature. 2008; 455: 1061-1068Crossref PubMed Scopus (5212) Google Scholar; Ding et al., 2008Ding L. Getz G. Wheeler D.A. et al.Somatic mutations affect key pathways in lung adenocarcinoma.Nature. 2008; 455: 1069-1075Crossref PubMed Scopus (2004) Google Scholar; Nancarrow et al., 2008Nancarrow D.J. Handoko H.Y. Smithers B.M. et al.Genome-wide copy number analysis in esophageal adenocarcinoma using high-density single-nucleotide polymorphism arrays.Cancer Res. 2008; 68: 4163-4172Crossref PubMed Scopus (73) Google Scholar). It is the accumulation of genome alterations in critical genes over time that drives the cancer process. There is substantial evidence for a mutator phenotype in cancer in which the mutation rate in cancer cells is much greater than in normal cells, resulting in increases in random and clonal somatic mutations (Bielas and Loeb, 2005Bielas J.H. Loeb L.A. Quantification of random genomic mutations.Nat Methods. 2005; 2: 285-290Crossref PubMed Scopus (75) Google Scholar; Bielas et al., 2006Bielas J.H. Loeb K.R. Rubin B.P. et al.Human cancers express a mutator phenotype.Proc Natl Acad Sci USA. 2006; 103: 18238-18242Crossref PubMed Scopus (276) Google Scholar; Loeb et al., 2008Loeb L.A. Bielas J.H. Beckman R.A. Cancers exhibit a mutator phenotype: clinical implications.Cancer Res. 2008; 68 (discussion 3557): 3551-3557Crossref PubMed Scopus (159) Google Scholar). Studies in genetically engineered mice and keratinocytes in culture have revealed a critical role for C/EBPα in the DDR network where following DNA damage, C/EBPα is highly induced and has a critical role in the G1-cell cycle checkpoint (Yoon and Smart, 2004Yoon K. Smart R.C. C/EBPalpha is a DNA damage-inducible p53-regulated mediator of the G1 checkpoint in keratinocytes.Mol Cell Biol. 2004; 24: 10650-10660Crossref PubMed Scopus (53) Google Scholar; Ranjan et al., 2009Ranjan R. Thompson E.A. Yoon K. et al.C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.Oncogene. 2009; 28: 3235-3245Crossref PubMed Scopus (8) Google Scholar). The genetic ablation or knockdown of C/EBPα in keratinocytes results in G1 checkpoint failure in which cells inappropriately enter S phase following U}, number={6}, journal={JOURNAL OF INVESTIGATIVE DERMATOLOGY}, author={Thompson, Elizabeth A. and Zhu, Songyun and Hall, Jonathan R. and House, John S. and Ranjan, Rakesh and Burr, Jeanne A. and He, Yu-Ying and Owens, David M. and Smart, Robert C.}, year={2011}, month={Jun}, pages={1339–1346} }
 @article{house_zhu_ranjan_linder_smart_2010, title={C/EBP alpha and C/EBP beta Are Required for Sebocyte Differentiation and Stratified Squamous Differentiation in Adult Mouse Skin}, volume={5}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79952118221&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0009837}, abstractNote={C/EBPα and C/EBPβ are bZIP transcription factors that are highly expressed in the interfollicular epidermis and sebaceous glands of skin and yet germ line deletion of either family member alone has only mild or no effect on keratinocyte biology and their role in sebocyte biology has never been examined. To address possible functional redundancies and reveal functional roles of C/EBPα and C/EBPβ in postnatal skin, mouse models were developed in which either family member could be acutely ablated alone or together in the epidermis and sebaceous glands of adult mice. Acute removal of either C/EBPα or C/EBPβ alone in adult mouse skin revealed modest to no discernable changes in epidermis or sebaceous glands. In contrast, co-ablation of C/EBPα and C/EBPβ in postnatal epidermis resulted in disruption of stratified squamous differentiation characterized by hyperproliferation of basal and suprabasal keratinocytes and a defective basal to spinous keratinocyte transition involving an expanded basal compartment and a diminished and delayed spinous compartment. Acute co-ablation of C/EBPα and C/EBPβ in sebaceous glands resulted in severe morphological defects, and sebocyte differentiation was blocked as determined by lack of sebum production and reduced expression of stearoyl-CoA desaturase (SCD3) and melanocortin 5 receptor (MC5R), two markers of terminal sebocyte differentiation. Specialized sebocytes of Meibomian glands and preputial glands were also affected. Our results indicate that in adult mouse skin, C/EBPα and C/EBPβ are critically involved in regulating sebocyte differentiation and epidermal homeostasis involving the basal to spinous keratinocyte transition and basal cell cycle withdrawal.}, number={3}, journal={PLOS ONE}, author={House, John S. and Zhu, Songyun and Ranjan, Rakesh and Linder, Keith and Smart, Robert C.}, year={2010}, month={Mar} }
 @article{ewing_zhu_zhu_house_smart_2008, title={C/EBP beta represses p53 to promote cell survival downstream of DNA damage independent of oncogenic Ras and p19(Arf)}, volume={15}, ISSN={["1476-5403"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54049144611&partnerID=MN8TOARS}, DOI={10.1038/cdd.2008.105}, abstractNote={CCAAT/enhancer-binding protein-β (C/EBPβ) is a mediator of cell survival and tumorigenesis. When C/EBPβ−/− mice are treated with carcinogens that produce oncogenic Ras mutations in keratinocytes, they respond with abnormally elevated keratinocyte apoptosis and a block in skin tumorigenesis. Although this aberrant carcinogen-induced apoptosis results from abnormal upregulation of p53, it is not known whether upregulated p53 results from oncogenic Ras and its ability to induce p19Arf and/or activate DNA-damage response pathways or from direct carcinogen-induced DNA damage. We report that p19Arf is dramatically elevated in C/EBPβ−/− epidermis and that C/EBPβ represses a p19Arf promoter reporter. To determine whether p19Arf is responsible for the proapoptotic phenotype in C/EBPβ−/− mice, C/EBPβ−/−;p19Arf−/− mice were generated. C/EBPβ−/−;p19Arf−/− mice responded to carcinogen treatment with increased p53 and apoptosis, indicating p19Arf is not essential. To ascertain whether oncogenic Ras activation induces aberrant p53 and apoptosis in C/EBPβ−/− epidermis, we generated K14-ER:Ras;C/EBPβ−/− mice. Oncogenic Ras activation induced by 4-hydroxytamoxifen did not produce increased p53 or apoptosis. Finally, when C/EBPβ−/− mice were treated with differing types of DNA-damaging agents, including alkylating chemotherapeutic agents, they displayed aberrant levels of p53 and apoptosis. These results indicate that C/EBPβ represses p53 to promote cell survival downstream of DNA damage and suggest that inhibition of C/EBPβ may be a target for cancer cotherapy to increase the efficacy of alkylating chemotherapeutic agents.}, number={11}, journal={CELL DEATH AND DIFFERENTIATION}, author={Ewing, S. J. and Zhu, S. and Zhu, F. and House, J. S. and Smart, R. C.}, year={2008}, month={Nov}, pages={1734–1744} }