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Boye C, Nirmalan S, Ranjbaran A, Luca F. Genotype × environment interactions in gene regulation and complex traits. Nat Genet 2024; 56:1057-1068. [PMID: 38858456 DOI: 10.1038/s41588-024-01776-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Genotype × environment interactions (GxE) have long been recognized as a key mechanism underlying human phenotypic variation. Technological developments over the past 15 years have dramatically expanded our appreciation of the role of GxE in both gene regulation and complex traits. The richness and complexity of these datasets also required parallel efforts to develop robust and sensitive statistical and computational approaches. Although our understanding of the genetic architecture of molecular and complex traits has been maturing, a large proportion of complex trait heritability remains unexplained. Furthermore, there are increasing efforts to characterize the effect of environmental exposure on human health. We therefore review GxE in human gene regulation and complex traits, advocating for a comprehensive approach that jointly considers genetic and environmental factors in human health and disease.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Ali Ranjbaran
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, US.
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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Filer DL, Hoffman K, Sargis RM, Trasande L, Kassotis CD. On the Utility of ToxCast-Based Predictive Models to Evaluate Potential Metabolic Disruption by Environmental Chemicals. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:57005. [PMID: 35533074 PMCID: PMC9084331 DOI: 10.1289/ehp6779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/19/2022] [Accepted: 04/06/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Research suggests environmental contaminants can impact metabolic health; however, high costs prohibit in vivo screening of putative metabolic disruptors. High-throughput screening programs, such as ToxCast, hold promise to reduce testing gaps and prioritize higher-order (in vivo) testing. OBJECTIVES We sought to a) examine the concordance of in vitro testing in 3T3-L1 cells to a targeted literature review for 38 semivolatile environmental chemicals, and b) assess the predictive utility of various expert models using ToxCast data against the set of 38 reference chemicals. METHODS Using a set of 38 chemicals with previously published results in 3T3-L1 cells, we performed a metabolism-targeted literature review to determine consensus activity determinations. To assess ToxCast predictive utility, we used two published ToxPi models: a) the 8-Slice model published by Janesick et al. (2016) and b) the 5-Slice model published by Auerbach et al. (2016). We examined the performance of the two models against the Janesick in vitro results and our own 38-chemical reference set. We further evaluated the predictive performance of various modifications to these models using cytotoxicity filtering approaches and validated our best-performing model with new chemical testing in 3T3-L1 cells. RESULTS The literature review revealed relevant publications for 30 out of the 38 chemicals (the remaining 8 chemicals were only examined in our previous 3T3-L1 testing). We observed a balanced accuracy (average of sensitivity and specificity) of 0.86 comparing our previous in vitro results to the literature-derived calls. ToxPi models provided balanced accuracies ranging from 0.55 to 0.88, depending on the model specifications and reference set. Validation chemical testing correctly predicted 29 of 30 chemicals as per 3T3-L1 testing, suggesting good adipogenic prediction performance for our best adapted model. DISCUSSION Using the most recent ToxCast data and an updated ToxPi model, we found ToxCast performed similarly to that of our own 3T3-L1 testing in predicting consensus calls. Furthermore, we provide the full ranked list of largely untested chemicals with ToxPi scores that predict adipogenic activity and that require further investigation. https://doi.org/10.1289/EHP6779.
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Affiliation(s)
- Dayne L. Filer
- Department of Genetics, School of Medicine, and Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kate Hoffman
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Robert M. Sargis
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Leonardo Trasande
- Department of Pediatrics, New York University (NYU) School of Medicine, New York, New York, USA
- Department of Environmental Medicine, New York University (NYU) School of Medicine, New York, New York, USA
- Department of Population Health, New York University (NYU) School of Medicine, New York, New York, USA
- NYU College of Global Public Health, New York University, New York, New York, USA
| | - Christopher D. Kassotis
- Institute of Environmental Health Sciences and Department of Pharmacology, School of Medicine, Wayne State University, Detroit, Michigan, USA
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Tse ACK, Lau KYT, Ge W, Wu RSS. A rapid screening test for endocrine disrupting chemicals using primary cell culture of the marine medaka. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 144-145:50-58. [PMID: 24140634 DOI: 10.1016/j.aquatox.2013.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/16/2013] [Accepted: 09/22/2013] [Indexed: 06/02/2023]
Abstract
While endocrine disrupting chemicals (EDCs) pose a significant threat to wildlife worldwide, their diverse chemical structures present a major challenge to their detection, particularly since they are present at very low concentrations in the environment. We here report the development of an in vitro system for rapid screening of EDCs, using primary cell cultures (pituitary, ovarian follicular and testicular cells) of the marine medaka (Oryzias melastigma). Pituitary, testis and ovary cell cultures were developed and challenged by environmentally relevant concentrations of three well known EDCs (viz. estradiol, 2,2',4,4'-tetrabromodiphenyl ether, and 4-n-nonylphenol) as well as hypoxia (which has been shown to be a potent endocrine disruptor). In general, the mRNA expression levels of gonadotropins, their receptors and steroidogenic enzymes exhibited dose response relationships to the four endocrine disruptors in different tissues. The sensitivity and responses were also comparable to in vivo responses of whole fish and in vitro responses of the H295R human adrenocortical cell line. Our results suggest that the use of marine medaka primary cultured cells can serve as a cost effective tool for rapid screening of EDCs in the marine environment, and at the same time, sheds light on the underlying mechanisms of EDCs by deciphering their specific target sites along the hypothalamus-pituitary-gonad axis of vertebrates.
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Affiliation(s)
- Anna C K Tse
- School of Biological Sciences, The University of Hong Kong, Hong Kong
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Kentner AC, Miguelez M, James JS, Bielajew C. Behavioral and physiological effects of a single injection of rat interferon-alpha on male Sprague-Dawley rats: a long-term evaluation. Brain Res 2006; 1095:96-106. [PMID: 16712809 DOI: 10.1016/j.brainres.2006.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 03/31/2006] [Accepted: 04/04/2006] [Indexed: 12/31/2022]
Abstract
Interferon-alpha (IFN-alpha) is a cytokine used as a first line of defense against diseases such as cancer and hepatitis C. However, reports indicate that its effectiveness as a treatment is countered by central nervous system (CNS) disruptions in patients. Our work explored the possibility that it may also cause long-term behavioral disruptions by chronicling the behavioral and physiological disturbances associated with a single injection of vehicle, 10, 100, or 1,000 units of IFN-alpha in male Sprague-Dawley rats (n = 5/dose). Following 1 day of locomotor baseline collection, we monitored sickness behaviors (ptosis, piloerection, lethargy, and sleep), food and water intake, body weight, temperature, and motor activity. Observations were recorded 4 days prior to and 4 days following the IFN-alpha injection. Temperature and sickness behaviors were recorded three times daily at 9:00, 15:00, and 21:00 h, and all other indices, once daily. On the injection day, temperature values were highest in the animals receiving the 10-unit IFN-alpha dose 15 min and 13 h post-injection. In the case of sickness behaviors, a significant increase was observed in piloerection in all IFN-alpha groups at each time point measured, while the scores of the rats in the vehicle condition remained unchanged between pre- and post-injection days. Analyses of overall sickness behaviors during morning and night observation periods indicated increased scores in all IFN-alpha groups following injection. Cumulatively, these data suggest that a single IFN-alpha exposure may elicit long-term behavioral disruptions and that its consequences should be thoroughly investigated for its use in clinical populations.
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Affiliation(s)
- A C Kentner
- School of Psychology, University of Ottawa, 11 Marie Curie, Room 108, Ottawa, Canada K1N 6N5.
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Teeguarden JG, Barton HA. Computational modeling of serum-binding proteins and clearance in extrapolations across life stages and species for endocrine active compounds. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2004; 24:751-70. [PMID: 15209943 DOI: 10.1111/j.0272-4332.2004.00473.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
One measure of the potency of compounds that lead to the effects through ligand-dependent gene transcription is the relative affinity for the critical receptor. Endocrine active compounds that are presumed to act principally through binding to the estrogen receptor (e.g., estradiol, genistein, bisphenol A, and octylphenol) comprise one class of such compounds. For making simple comparisons, receptor-binding affinity has been equated to in vivo potency, which consequently defines the dose-response characteristics for the compound. Direct extrapolation of in vitro estimated affinities to the corresponding in vivo system and to specific species or life stages (e.g., neonatal, pregnancy) can be misleading. Accurate comparison of the potency of endocrine active compounds requires characterization of biochemical and pharmacokinetic factors that affect their free concentration. Quantitative in vitro and in vivo models were developed for integrating pharmacokinetics factors (e.g., serum protein and receptor-binding affinities, clearance) that affect potency. Data for parameterizing these models for several estrogenic compounds were evaluated and the models exercised. While simulations of adult human or rat sera were generally successful, difficulties in describing early life stages were identified. Exogenous compounds were predicted to be largely ineffective at competing estradiol off serum-binding proteins, suggesting this was unlikely to be physiologically significant. Discrepancies were identified between relative potencies based upon modeling in vitro receptor-binding activity versus in vivo activity in the presence of clearance and serum-binding proteins. The examples illustrate the utility of this approach for integrating available experimental data from in vitro and in vivo studies to estimate the relative potency of these compounds.
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Diener LC, Schulte PM, Dixon DG, Greenberg BM. Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceran Daphnia magna. ENVIRONMENTAL TOXICOLOGY 2004; 19:179-190. [PMID: 15101033 DOI: 10.1002/tox.20010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Research on toxicant-responsive genes is providing new and important bioindicators for environmental biologists. Identifying genes whose expression is modulated by toxicant exposure provides important clues into the mechanisms underlying toxicity. In addition, toxicant-responsive genes can be developed as molecular end points that are likely to be sensitive tools for environmental assessment. Differential display polymerase chain reaction (ddPCR) is a useful approach for screening and analyzing the expression of genes. A ddPCR protocol was optimized to investigate gene expression in the cladoceran Daphnia magna. The modified protocol requires submicrogram quantities of total RNA (from <10 animals) and utilizes a sensitive fluorescent tagging system. By reverse-transcribing total RNA with arbitrary 18-nucleotide primers and PCR-amplifying the cDNA using the same arbitrary primers under low-stringency conditions, reproducible and consistent ddPCR profiles were generated. Minimal variability was introduced by reaction differences or biological variability. A trial stress (starvation) was found to generate modest differences in the ddPCR profiles. This technique promises to significantly advance knowledge regarding gene expression during toxicant insult. Furthermore, this represents the first step in the development of a novel gene fingerprinting technique that can be applied to any compound and organism of interest.
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Affiliation(s)
- Lara C Diener
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada
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Slikker W, Scallet AC, Doerge DR, Ferguson SA. Gender-based differences in rats after chronic dietary exposure to genistein. Int J Toxicol 2001; 20:175-9. [PMID: 11488560 DOI: 10.1080/109158101317097764] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Gender-based differences can be observed from pharmacokinetic, behavioral, or anatomical assessments. No single assessment tool will provide a complete answer, but the use of a variety of indices, each with known gender-related outcome differences, can reveal agent-induced gender-based alterations. In a series of initial range-finding studies in rats conducted at the National Center for Toxicological Research (NCTR), the effects of dietary exposure to the weak estrogen, genistein, have been assessed using a number of techniques with validated gender-related outcome measures. The findings indicated that (1) the internal dose of genistein was higher in females than males after equivalent dietary exposure and this was consistent with the faster rate of genistein elimination in males; (2) in behavioral assessments, males and females in the high-dose dietary genistein group consumed more of a sodium-flavored solution; however, no genistein-related changes were observed in open field or running wheel activity, play behavior, or intake of a saccharin-flavored solution; and (3) dose-related alterations of the volume of the sexually dimorphic nucleus of the medial preoptic area were observed in genistein-exposed male rats but not females. These observations describe the utility of a variety of gender-based assessment tools and indicate that dose-related effects of developmental and chronic dietary exposure to genistein can be observed in the rodent. Additional studies, perhaps in nonhuman primates, are necessary to further predict the effect(s) of genistein on human gender-based development.
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Affiliation(s)
- W Slikker
- Division of Neurotoxicology, National Center for Toxicological Research/Food and Drug Administration, Jefferson, Arkansas 72079-9502, USA.
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Ahmed SA. The immune system as a potential target for environmental estrogens (endocrine disrupters): a new emerging field. Toxicology 2000; 150:191-206. [PMID: 10996675 DOI: 10.1016/s0300-483x(00)00259-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It is now well known that natural (17beta-estradiol) and synthetic (e.g. diethylstilbestrol) estrogens not only affect the reproductive system, but also markedly influence the immune system. Recently, a new class of estrogens that is abundant in the environment (in industrial chemicals, pesticides, and surfactants) has been recognized. Some of these estrogenic chemicals (which are a large subgroup of endocrine disrupters) have also been shown to influence the immune system. This review assimilates growing evidence in wildlife, laboratory animals and to a limited extent in humans, which suggests that environmental chemicals may also affect the immune system. Further studies are needed to ascertain the immunological consequences of exposure to environmental estrogens, especially in humans. At the present time, it is not known whether the human immune system responds to a low dose of environmental estrogens or if environmental estrogens influence certain subsets of human populations, rather than the general population. Conceivably, an alteration of the immune system by environmental estrogens could affect the individuals' ability to mount well-regulated immune responses to microbial and vaccine antigens, allergens, self and tumor antigens. Possible changes in the immune system must be investigated routinely in toxicity studies. A comprehensive mechanistic understanding of potential immunomodulatory chemicals is needed. In this regard, relevant laboratory animals may be especially useful in identifying susceptible periods of life, whether both genders are equally affected, in analysis of changes in target lymphoid organs, and to determine the immunological effects of mixtures of chemicals.
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Affiliation(s)
- S A Ahmed
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, 1410, Prices Fork Road, Virginia, USA.
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