1
|
Skalny AV, Aschner M, Zhang F, Guo X, Buha Djordevic A, Sotnikova TI, Korobeinikova TV, Domingo JL, Farsky SHP, Tinkov AA. Molecular mechanisms of environmental pollutant-induced cartilage damage: from developmental disorders to osteoarthritis. Arch Toxicol 2024; 98:2763-2796. [PMID: 38758407 DOI: 10.1007/s00204-024-03772-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
The objective of the present study was to review the molecular mechanisms of the adverse effects of environmental pollutants on chondrocytes and extracellular matrix (ECM). Existing data demonstrate that both heavy metals, including cadmium (Cd), lead (Pb), and arsenic (As), as well as organic pollutants, including polychlorinated dioxins and furans (PCDD/Fs) and polychlorinated biphenyls (PCB), bisphenol A, phthalates, polycyclic aromatic hydrocarbons (PAH), pesticides, and certain other organic pollutants that target cartilage ontogeny and functioning. Overall, environmental pollutants reduce chondrocyte viability through the induction apoptosis, senescence, and inflammatory response, resulting in cell death and impaired ECM production. The effects of organic pollutants on chondrocyte development and viability were shown to be mediated by binding to the aryl hydrocarbon receptor (AhR) signaling and modulation of non-coding RNA expression. Adverse effects of pollutant exposures were observed in articular and growth plate chondrocytes. These mechanisms also damage chondrocyte precursors and subsequently hinder cartilage development. In addition, pollutant exposure was shown to impair chondrogenesis by inhibiting the expression of Sox9 and other regulators. Along with altered Runx2 signaling, these effects also contribute to impaired chondrocyte hypertrophy and chondrocyte-to-osteoblast trans-differentiation, resulting in altered endochondral ossification. Several organic pollutants including PCDD/Fs, PCBs and PAHs, were shown to induce transgenerational adverse effects on cartilage development and the resulting skeletal deformities. Despite of epidemiological evidence linking human environmental pollutant exposure to osteoarthritis or other cartilage pathologies, the data on the molecular mechanisms of adverse effects of environmental pollutant exposure on cartilage tissue were obtained from studies in laboratory rodents, fish, or cell cultures and should be carefully extrapolated to humans, although they clearly demonstrate that cartilage should be considered a putative target for environmental pollutant toxicity.
Collapse
Affiliation(s)
- Anatoly V Skalny
- IM Sechenov First Moscow State Medical University (Sechenov University), 119435, Moscow, Russia
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Health Science Center, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Health Science Center, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Aleksandra Buha Djordevic
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, 11000, Belgrade, Serbia
| | - Tatiana I Sotnikova
- IM Sechenov First Moscow State Medical University (Sechenov University), 119435, Moscow, Russia
- City Clinical Hospital N. a. S.P. Botkin of the Moscow City Health Department, 125284, Moscow, Russia
| | - Tatiana V Korobeinikova
- IM Sechenov First Moscow State Medical University (Sechenov University), 119435, Moscow, Russia
| | - Jose L Domingo
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, 4320, Reus, Catalonia, Spain
| | - Sandra H P Farsky
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, 005508-000, Brazil
| | - Alexey A Tinkov
- IM Sechenov First Moscow State Medical University (Sechenov University), 119435, Moscow, Russia.
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, 150003, Yaroslavl, Russia.
| |
Collapse
|
2
|
Espadas I, Wingfield JL, Nakahata Y, Chanda K, Grinman E, Ghosh I, Bauer KE, Raveendra B, Kiebler MA, Yasuda R, Rangaraju V, Puthanveettil S. Synaptically-targeted long non-coding RNA SLAMR promotes structural plasticity by increasing translation and CaMKII activity. Nat Commun 2024; 15:2694. [PMID: 38538603 PMCID: PMC10973417 DOI: 10.1038/s41467-024-46972-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in maintaining cell homeostasis and function. However, it remains largely unknown whether and how neuronal activity impacts the transcriptional regulation of lncRNAs, or if this leads to synapse-related changes and contributes to the formation of long-term memories. Here, we report the identification of a lncRNA, SLAMR, which becomes enriched in CA1-hippocampal neurons upon contextual fear conditioning but not in CA3 neurons. SLAMR is transported along dendrites via the molecular motor KIF5C and is recruited to the synapse upon stimulation. Loss of function of SLAMR reduces dendritic complexity and impairs activity-dependent changes in spine structural plasticity and translation. Gain of function of SLAMR, in contrast, enhances dendritic complexity, spine density, and translation. Analyses of the SLAMR interactome reveal its association with CaMKIIα protein through a 220-nucleotide element also involved in SLAMR transport. A CaMKII reporter reveals a basal reduction in CaMKII activity with SLAMR loss-of-function. Furthermore, the selective loss of SLAMR function in CA1 disrupts the consolidation of fear memory in male mice, without affecting their acquisition, recall, or extinction, or spatial memory. Together, these results provide new molecular and functional insight into activity-dependent changes at the synapse and consolidation of contextual fear.
Collapse
Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna L Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Karl E Bauer
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
| |
Collapse
|
3
|
Cintrón-Rivera LG, Burns N, Patel R, Plavicki JS. Exposure to the aryl hydrocarbon receptor agonist dioxin disrupts formation of the muscle, nerves, and vasculature in the developing jaw. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122499. [PMID: 37660771 DOI: 10.1016/j.envpol.2023.122499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
Human exposure to environmental pollutants can disrupt embryonic development and impact juvenile and adult health outcomes by adversely affecting cell and organ function. Notwithstanding, environmental contamination continues to increase due to industrial development, insufficient regulations, and the mobilization of pollutants as a result of extreme weather events. Dioxins are a class of structurally related persistent organic pollutants that are highly toxic, carcinogenic, and teratogenic. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent dioxin compound and has been shown to induce toxic effects in developing organisms by activating the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor targeted by multiple persistent organic pollutants. Contaminant-induced AHR activation results in malformations of the craniofacial cartilages and neurocranium; however, the mechanisms mediating these phenotypes are not well understood. In this study, we utilized the optically transparent zebrafish model to elucidate novel cellular targets and potential transcriptional targets underlying TCDD-induced craniofacial malformations. To this end, we exposed zebrafish embryos at 4 h post fertilization to TCDD and employed a mixed-methods approach utilizing immunohistochemistry staining, transgenic reporter lines, fixed and in vivo confocal imaging, and timelapse microscopy to determine the targets mediating TCDD-induced craniofacial phenotypes. Our data indicate that embryonic TCDD exposure reduced jaw and pharyngeal arch Sox10+ chondrocytes and Tcf21+ pharyngeal mesoderm progenitors. Exposure to TCDD correspondingly led to a reduction in collagen type II deposition in Sox10+ domains. Embryonic TCDD exposure impaired development of tissues derived from or guided by Tcf21+ progenitors, namely: nerves, muscle, and vasculature. Specifically, TCDD exposure disrupted development of the hyoid and mandibular arch muscles, decreased neural innervation of the jaw, resulted in compression of cranial nerves V and VII, and led to jaw vasculature malformations. Collectively, these findings reveal novel structural targets and potential transcriptional targets of TCDD-induced toxicity, showcasing how contaminant exposures lead to congenital craniofacial malformations.
Collapse
Affiliation(s)
- Layra G Cintrón-Rivera
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Nicole Burns
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Ratna Patel
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Jessica S Plavicki
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA.
| |
Collapse
|
4
|
Alluli A, Rijnbout St James W, Eidelman DH, Baglole CJ. Dynamic relationship between the aryl hydrocarbon receptor and long noncoding RNA balances cellular and toxicological responses. Biochem Pharmacol 2023; 216:115745. [PMID: 37597813 DOI: 10.1016/j.bcp.2023.115745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor activated by endogenous ligands and xenobiotic chemicals. Once the AhR is activated, it translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT) and binds to xenobiotic response elements (XRE) to promote gene transcription, notably the cytochrome P450 CYP1A1. The AhR not only mediates the toxic effects of environmental chemicals, but also has numerous putative physiological functions. This dichotomy in AhR biology may be related to reciprocal regulation of long non-coding RNA (lncRNA). lncRNA are defined as transcripts more than 200 nucleotides in length that do not encode a protein but are implicated in many physiological processes such as cell differentiation, cell proliferation, and apoptosis. lncRNA are also linked to disease pathogenesis, particularly the development of cancer. Recent studies have revealed that AhR activation by environmental chemicals affects the expression and function of lncRNA. In this article, we provide an overview of AhR signaling pathways activated by diverse ligands and highlight key differences in the putative biological versus toxicological response of AhR activation. We also detail the functions of lncRNA and provide current data on their regulation by the AhR. Finally, we outline how overlap in function between AhR and lncRNA may be one way in which AhR can be both a regulator of endogenous functions but also a mediator of toxicological responses to environmental chemicals. Overall, more research is still needed to fully understand the dynamic interplay between the AhR and lncRNA.
Collapse
Affiliation(s)
- Aeshah Alluli
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - Willem Rijnbout St James
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - David H Eidelman
- Meakins-Christie Laboratories, McGill University, Canada; Department of Medicine, McGill University, Canada
| | - Carolyn J Baglole
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada; Department of Medicine, McGill University, Canada; Department of Pharmacology and Therapeutics, McGill University, Canada.
| |
Collapse
|
5
|
Opitz CA, Holfelder P, Prentzell MT, Trump S. The complex biology of aryl hydrocarbon receptor activation in cancer and beyond. Biochem Pharmacol 2023; 216:115798. [PMID: 37696456 PMCID: PMC10570930 DOI: 10.1016/j.bcp.2023.115798] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
The aryl hydrocarbon receptor (AHR) signaling pathway is a complex regulatory network that plays a critical role in various biological processes, including cellular metabolism, development, and immune responses. The complexity of AHR signaling arises from multiple factors, including the diverse ligands that activate the receptor, the expression level of AHR itself, and its interaction with the AHR nuclear translocator (ARNT). Additionally, the AHR crosstalks with the AHR repressor (AHRR) or other transcription factors and signaling pathways and it can also mediate non-genomic effects. Finally, posttranslational modifications of the AHR and its interaction partners, epigenetic regulation of AHR and its target genes, as well as AHR-mediated induction of enzymes that degrade AHR-activating ligands may contribute to the context-specificity of AHR activation. Understanding the complexity of AHR signaling is crucial for deciphering its physiological and pathological roles and developing therapeutic strategies targeting this pathway. Ongoing research continues to unravel the intricacies of AHR signaling, shedding light on the regulatory mechanisms controlling its diverse functions.
Collapse
Affiliation(s)
- Christiane A Opitz
- German Cancer Research Center (DKFZ), Heidelberg, Division of Metabolic Crosstalk in Cancer and the German Cancer Consortium (DKTK), DKFZ Core Center Heidelberg, 69120 Heidelberg, Germany; Neurology Clinic and National Center for Tumor Diseases, 69120 Heidelberg, Germany.
| | - Pauline Holfelder
- German Cancer Research Center (DKFZ), Heidelberg, Division of Metabolic Crosstalk in Cancer and the German Cancer Consortium (DKTK), DKFZ Core Center Heidelberg, 69120 Heidelberg, Germany; Faculty of Bioscience, Heidelberg University, 69120 Heidelberg, Germany
| | - Mirja Tamara Prentzell
- German Cancer Research Center (DKFZ), Heidelberg, Division of Metabolic Crosstalk in Cancer and the German Cancer Consortium (DKTK), DKFZ Core Center Heidelberg, 69120 Heidelberg, Germany; Faculty of Bioscience, Heidelberg University, 69120 Heidelberg, Germany
| | - Saskia Trump
- Molecular Epidemiology Unit, Berlin Institute of Health at Charité and the German Cancer Consortium (DKTK), Partner Site Berlin, a partnership between DKFZ and Charité -Universitätsmedizin Berlin, 10117 Berlin, Germany
| |
Collapse
|
6
|
Shankar P, Villeneuve DL. AOP Report: Aryl Hydrocarbon Receptor Activation Leads to Early-Life Stage Mortality via Sox9 Repression-Induced Craniofacial and Cardiac Malformations. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:2063-2077. [PMID: 37341548 PMCID: PMC10772968 DOI: 10.1002/etc.5699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/22/2023]
Abstract
The aryl hydrocarbon receptors (Ahrs) are evolutionarily conserved ligand-dependent transcription factors that are activated by structurally diverse endogenous compounds as well as environmental chemicals such as polycyclic aromatic hydrocarbons and halogenated aromatic hydrocarbons. Activation of the Ahr leads to several transcriptional changes that can cause developmental toxicity resulting in mortality. Evidence was assembled and evaluated for two novel adverse outcome pathways (AOPs) which describe how Ahr activation (molecular initiating event) can lead to early-life stage mortality (adverse outcome), via either SOX9-mediated craniofacial malformations (AOP 455) or cardiovascular toxicity (AOP 456). Using a key event relationship (KER)-by-KER approach, we collected evidence using both a narrative search and a systematic review based on detailed search terms. Weight of evidence for each KER was assessed to inform overall confidence of the AOPs. The AOPs link to previous descriptions of Ahr activation and connect them to two novel key events (KEs), increase in slincR expression, a newly characterized long noncoding RNA with regulatory functions, and suppression of SOX9, a critical transcription factor implicated in chondrogenesis and cardiac development. In general, confidence levels for KERs ranged between medium and strong, with few inconsistencies, as well as several opportunities for future research identified. While the majority of KEs have only been demonstrated in zebrafish with 2,3,7,8-tetrachlorodibenzo-p-dioxin as an Ahr activator, evidence suggests that the two AOPs likely apply to most vertebrates and many Ahr-activating chemicals. Addition of the AOPs into the AOP-Wiki (https://aopwiki.org/) helps expand the growing Ahr-related AOP network to 19 individual AOPs, of which six are endorsed or in progress and the remaining 13 relatively underdeveloped. Environ Toxicol Chem 2023;42:2063-2077. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Collapse
Affiliation(s)
- Prarthana Shankar
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota, USA
- University of Wisconsin Madison Sea Grant Fellow at Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota, USA
| | - Daniel L. Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota, USA
| |
Collapse
|
7
|
Elson DJ, Nguyen BD, Korjeff NA, Wilferd SF, Puig-Sanvicens V, Sang Jang H, Bernales S, Chakravarty S, Belmar S, Ureta G, Finlay D, Plaisier CL, Kolluri SK. Suppression of Ah Receptor (AhR) increases the aggressiveness of TNBC cells and 11-Cl-BBQ-activated AhR inhibits their growth. Biochem Pharmacol 2023; 215:115706. [PMID: 37506922 DOI: 10.1016/j.bcp.2023.115706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Triple-negative breast cancer (TNBC) represents around 15% of the 2.26 million breast cancers diagnosed worldwide annually and has the worst outcome. Despite recent therapeutic advances, there remains a lack of targeted therapies for this breast cancer subtype. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor with biological roles in regulating development, xenobiotic metabolism, cell cycle progression and cell death. AhR activation by select ligands can promote tumor suppression in multiple cancer types. AhR can negatively regulate the activity of different oncogenic signaling pathways and can directly upregulate tumor suppressor genes such as p27Kip1. To determine the role of AhR in TNBC, we generated AhR-deficient cancer cells and investigated the impact of AhR loss on TNBC cell growth phenotypes. We found that AhR-deficient MDA-MB-468 TNBC cells have increased proliferation and formed significantly more colonies compared to AhR expressing cells. These cells without AhR expression grew aggressively in vivo. To determine the molecular targets driving this phenotype, we performed transcriptomic profiling in AhR expressing and AhR knockout MDA-MB-468 cells and identified tyrosine receptor kinases, as well as other genes involved in proliferation, survival and clonogenicity that are repressed by AhR. In order to determine therapeutic targeting of AhR in TNBC, we investigated the anti-cancer effects of the novel AhR ligand 11-chloro-7H-benzimidazo[2,1-a]benzo[de]iso-quinolin-7-one (11-Cl-BBQ), which belongs to a class of high affinity, rapidly metabolized AhR ligands called benzimidazoisoquinolines (BBQs). 11-Cl-BBQ induced AhR-dependent cancer cell-selective growth inhibition and strongly inhibited colony formation in TNBC cells.
Collapse
Affiliation(s)
- Daniel J Elson
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, United States
| | - Bach D Nguyen
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, United States
| | - Nicholas A Korjeff
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, United States
| | - Sierra F Wilferd
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, United States
| | - Veronica Puig-Sanvicens
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, United States
| | - Hyo Sang Jang
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, United States
| | - Sebastian Bernales
- Praxis Biotech, San Francisco, CA 94158, United States; Fundación Ciencia & Vida, Centro Científico y Tecnológico Ciencia & Vida, Avda. Del valle Norte 725, Santiago, Chile
| | | | - Sebastián Belmar
- Praxis Biotech, San Francisco, CA 94158, United States; Merken Biotech, Avda. Del valle Norte 725, Santiago, Chile
| | - Gonzalo Ureta
- Praxis Biotech, San Francisco, CA 94158, United States; Merken Biotech, Avda. Del valle Norte 725, Santiago, Chile
| | - Darren Finlay
- Sanford Burnham Prebys Medical Discovery Institute, NCI Designated Cancer Center, La Jolla, CA 92037, United States
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, United States
| | - Siva K Kolluri
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, United States; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, United States.
| |
Collapse
|
8
|
Dasgupta S, LaDu JK, Garcia GR, Li S, Tomono-Duval K, Rericha Y, Huang L, Tanguay RL. A CRISPR-Cas9 mutation in sox9b long intergenic noncoding RNA (slincR) affects zebrafish development, behavior, and regeneration. Toxicol Sci 2023; 194:153-166. [PMID: 37220911 PMCID: PMC10375313 DOI: 10.1093/toxsci/kfad050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
The role of long noncoding RNAs (lncRNAs) regulators of toxicological responses to environmental chemicals is gaining prominence. Previously, our laboratory discovered an lncRNA, sox9b long intergenic noncoding RNA (slincR), that is activated by multiple ligands of aryl hydrocarbon receptor (AHR). Within this study, we designed a CRISPR-Cas9-mediated slincR zebrafish mutant line to better understand its biological function in presence or absence of a model AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The slincRosu3 line contains an 18 bp insertion within the slincR sequence that changes its predicted mRNA secondary structure. Toxicological profiling showed that slincRosu3 is equally or more sensitive to TCDD for morphological and behavioral phenotypes. Embryonic mRNA-sequencing showed differential responses of 499 or 908 genes in slincRosu3 in absence or presence of TCDD Specifically, unexposed slincRosu3 embryos showed disruptions in metabolic pathways, suggesting an endogenous role for slincR. slincRosu3 embryos also had repressed mRNA levels of sox9b-a transcription factor that slincR is known to negatively regulate. Hence, we studied cartilage development and regenerative capacity-both processes partially regulated by sox9b. Cartilage development was disrupted in slincRosu3 embryos both in presence and absence of TCDD. slincRosu3 embryos also displayed a lack of regenerative capacity of amputated tail fins, accompanied by a lack of cell proliferation. In summary, using a novel slincR mutant line, we show that a mutation in slincR can have widespread impacts on gene expression and structural development endogenously and limited, but significant impacts in presence of AHR induction that further highlights its importance in the developmental process.
Collapse
Affiliation(s)
- Subham Dasgupta
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333, USA
| | - Jane K LaDu
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333, USA
| | - Gloria R Garcia
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333, USA
| | - Sizhen Li
- Department of Electrical Engineering and Computer Science, College of Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Konoha Tomono-Duval
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333, USA
| | - Yvonne Rericha
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333, USA
| | - Liang Huang
- Department of Electrical Engineering and Computer Science, College of Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Robyn L Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333, USA
| |
Collapse
|
9
|
Espadas I, Wingfield J, Grinman E, Ghosh I, Chanda K, Nakahata Y, Bauer K, Raveendra B, Kiebler M, Yasuda R, Rangaraju V, Puthanveettil S. SLAMR, a synaptically targeted lncRNA, facilitates the consolidation of contextual fear memory. RESEARCH SQUARE 2023:rs.3.rs-2489387. [PMID: 36993323 PMCID: PMC10055528 DOI: 10.21203/rs.3.rs-2489387/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
LncRNAs are involved in critical processes for cell homeostasis and function. However, it remains largely unknown whether and how the transcriptional regulation of long noncoding RNAs results in activity-dependent changes at the synapse and facilitate formation of long-term memories. Here, we report the identification of a novel lncRNA, SLAMR, that becomes enriched in CA1- but not in CA3-hippocampal neurons upon contextual fear conditioning. SLAMR is transported to dendrites via the molecular motor KIF5C and recruited to the synapse in response to stimulation. Loss of function of SLAMR reduced dendritic complexity and impaired activity dependent changes in spine structural plasticity. Interestingly, gain of function of SLAMR enhanced dendritic complexity, and spine density through enhanced translation. Analyses of the SLAMR interactome revealed its association with CaMKIIα protein through a 220-nucleotide element and its modulation of CaMKIIα activity. Furthermore, loss-of-function of SLAMR in CA1 selectively impairs consolidation but neither acquisition, recall, nor extinction of fear memory and spatial memory. Together, these results establish a new mechanism for activity dependent changes at the synapse and consolidation of contextual fear.
Collapse
Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute, Jupiter, FL, USA
| | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Karl Bauer
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael Kiebler
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | | | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| |
Collapse
|
10
|
Kossack ME, Manz KE, Martin NR, Pennell KD, Plavicki J. Environmentally relevant uptake, elimination, and metabolic changes following early embryonic exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin in zebrafish. CHEMOSPHERE 2023; 310:136723. [PMID: 36241106 PMCID: PMC9835613 DOI: 10.1016/j.chemosphere.2022.136723] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 06/03/2023]
Abstract
Dioxin and dioxin-like compounds are ubiquitous environmental contaminants that induce toxicity by binding to the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor. The zebrafish model has been used to define the developmental toxicity observed following exposure to exogenous AHR ligands such as the potent agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin, TCDD). While the model has successfully identified cellular targets of TCDD and molecular mechanisms mediating TCDD-induced phenotypes, fundamental information such as the body burden produced by standard exposure models is still unknown. We performed targeted gas chromatography (GC) high-resolution mass spectrometry (HRMS) in tandem with non-targeted liquid chromatography (LC) HRMS to quantify TCDD uptake, model the elimination dynamics of TCDD, and determine how TCDD exposure affects the zebrafish metabolome. We found that 50 ppt, 10 ppb, and 1 ppb waterborne exposures to TCDD during early embryogenesis produced environmentally relevant body burdens: 38 ± 4.34, 26.6 ± 1.2, and 8.53 ± 0.341 pg/embryo, respectively, at 24 hours post fertilization. TCDD exposure was associated with the dysregulation of metabolic pathways that are associated with the AHR signaling pathway as well as pathways shown to be affected in mammals following TCDD exposure. In addition, we discovered that TCDD exposure affected several metabolic pathways that are critical for brain development and function including glutamate metabolism, chondroitin sulfate biosynthesis, and tyrosine metabolism. Together, these data demonstrate that existing exposure methods produce environmentally relevant body burdens of TCDD in zebrafish and provide insight into the biochemical pathways impacted by toxicant-induced AHR activation.
Collapse
Affiliation(s)
- Michelle E Kossack
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Katherine E Manz
- School of Engineering, Brown University, 184 Hope St, Box D, Providence, RI, 02903, USA
| | - Nathan R Martin
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Kurt D Pennell
- School of Engineering, Brown University, 184 Hope St, Box D, Providence, RI, 02903, USA
| | - Jessica Plavicki
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA.
| |
Collapse
|
11
|
Shankar P, Garcia GR, LaDu JK, Sullivan CM, Dunham CL, Goodale BC, Waters KM, Stanisheuski S, Maier CS, Thunga P, Reif DM, Tanguay RL. The Ahr2-Dependent wfikkn1 Gene Influences Zebrafish Transcriptome, Proteome, and Behavior. Toxicol Sci 2022; 187:325-344. [PMID: 35377459 DOI: 10.1093/toxsci/kfac037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is required for vertebrate development and is also activated by exogenous chemicals, including polycyclic aromatic hydrocarbons (PAHs) and TCDD. AHR activation is well-understood, but roles of downstream molecular signaling events are largely unknown. From previous transcriptomics in 48-hours post fertilization (hpf) zebrafish exposed to several PAHs and TCDD, we found wfikkn1 was highly co-expressed with cyp1a (marker for AHR activation). Thus, we hypothesized wfikkn1's role in AHR signaling, and showed that wfikkn1 expression was Ahr2 (zebrafish ortholog of human AHR)-dependent in developing zebrafish exposed to TCDD. To functionally characterize wfikkn1, we made a CRISPR-Cas9 mutant line with a 16-bp deletion in wfikkn1's exon, and exposed wildtype and mutants to DMSO or TCDD. 48-hpf mRNA sequencing revealed over 700 genes that were differentially expressed (p < 0.05, log2FC > 1) between each pair of treatment combinations, suggesting an important role for wfikkn1 in altering both the 48-hpf transcriptome and TCDD-induced expression changes. Mass spectrometry-based proteomics of 48-hpf wildtype and mutants revealed 325 significant differentially expressed proteins. Functional enrichment demonstrated wfikkn1 was involved in skeletal muscle development and played a role in neurological pathways after TCDD exposure. Mutant zebrafish appeared morphologically normal but had significant behavior deficiencies at all life stages, and absence of Wfikkn1 did not significantly alter TCDD-induced behavior effects at all life stages. In conclusion, wfikkn1 did not appear to be significantly involved in TCDD's overt toxicity but is likely a necessary functional member of the AHR signaling cascade.
Collapse
Affiliation(s)
- Prarthana Shankar
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Gloria R Garcia
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Jane K LaDu
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Christopher M Sullivan
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Cheryl L Dunham
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Britton C Goodale
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756 USA
| | - Katrina M Waters
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331.,Biological Sciences Division, Pacific Northwest Laboratory, 902 Battelle Boulevard, Richland, P.O. Box 999, USA WA 99352
| | | | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR, 97330, USA
| | - Preethi Thunga
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - David M Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Robyn L Tanguay
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| |
Collapse
|
12
|
Hammond CL, Roztocil E, Gupta V, Feldon SE, Woeller CF. More than Meets the Eye: The Aryl Hydrocarbon Receptor is an Environmental Sensor, Physiological Regulator and a Therapeutic Target in Ocular Disease. FRONTIERS IN TOXICOLOGY 2022; 4:791082. [PMID: 35295218 PMCID: PMC8915869 DOI: 10.3389/ftox.2022.791082] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/08/2022] [Indexed: 12/22/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor originally identified as an environmental sensor of xenobiotic chemicals. However, studies have revealed that the AHR regulates crucial aspects of cell growth and metabolism, development and the immune system. The importance of the AHR and AHR signaling in eye development, toxicology and disease is now being uncovered. The AHR is expressed in many ocular tissues including the retina, choroid, cornea and the orbit. A significant role for the AHR in age-related macular degeneration (AMD), autoimmune uveitis, and other ocular diseases has been identified. Ligands for the AHR are structurally diverse organic molecules from exogenous and endogenous sources. Natural AHR ligands include metabolites of tryptophan and byproducts of the microbiome. Xenobiotic AHR ligands include persistent environmental pollutants such as dioxins, benzo (a) pyrene [B (a) P] and polychlorinated biphenyls (PCBs). Pharmaceutical agents including the proton pump inhibitors, esomeprazole and lansoprazole, and the immunosuppressive drug, leflunomide, activate the AHR. In this review, we highlight the role of the AHR in the eye and discuss how AHR signaling is involved in responding to endogenous and environmental stimuli. We also present the emerging concept that the AHR is a promising therapeutic target for eye disease.
Collapse
Affiliation(s)
| | | | | | | | - Collynn F. Woeller
- Flaum Eye Institute, Rochester, NY, United States
- Department of Environmental Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
- *Correspondence: Collynn F. Woeller,
| |
Collapse
|
13
|
Cannon AS, Nagarkatti PS, Nagarkatti M. Targeting AhR as a Novel Therapeutic Modality against Inflammatory Diseases. Int J Mol Sci 2021; 23:288. [PMID: 35008717 PMCID: PMC8745713 DOI: 10.3390/ijms23010288] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 12/12/2022] Open
Abstract
For decades, activation of Aryl Hydrocarbon Receptor (AhR) was excluded from consideration as a therapeutic approach due to the potential toxic effects of AhR ligands and the induction of the cytochrome P450 enzyme, Cyp1a1, following AhR activation. However, it is now understood that AhR activation not only serves as an environmental sensor that regulates the effects of environmental toxins, but also as a key immunomodulator where ligands induce a variety of cellular and epigenetic mechanisms to attenuate inflammation. Thus, the emergence of further in-depth research into diverse groups of compounds capable of activating this receptor has prompted reconsideration of its use therapeutically. The aim of this review is to summarize the body of research surrounding AhR and its role in regulating inflammation. Specifically, evidence supporting the potential of targeting this receptor to modulate the immune response in inflammatory and autoimmune diseases will be highlighted. Additionally, the opportunities and challenges of developing AhR-based therapies to suppress inflammation will be discussed.
Collapse
Affiliation(s)
| | | | - Mitzi Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (A.S.C.); (P.S.N.)
| |
Collapse
|
14
|
Disner GR, Lopes-Ferreira M, Lima C. Where the Aryl Hydrocarbon Receptor Meets the microRNAs: Literature Review of the Last 10 Years. Front Mol Biosci 2021; 8:725044. [PMID: 34746229 PMCID: PMC8566438 DOI: 10.3389/fmolb.2021.725044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) is an environmentally responsive ligand-activated transcription factor, identified in the ‘70s for its toxic responses to halogenated polycyclic aromatic hydrocarbons, such as dioxin. Recently, AhR has been recognized as engaged in multiple physiological processes in health and diseases, particularly in the immune system, inflammatory response, tumorigenesis, and cellular differentiation by epigenetic mechanisms involving miRNAs. However, there is still scarce information about AhR-dependent miRNA regulation and miRNA-mediated epigenetic control in pathologies and therapies. In this review, we explore the mutual regulation of AhR and miRNA over the last decade of studies since many miRNAs have dioxin response elements (DRE) in their 3’ UTR, as well as AhR might contain binding sites of miRNAs. TCDD is the most used ligand to investigate the impact of AhR activation, and the immune system is one of the most sensitive of its targets. An association between TCDD-activated AhR and epigenetic mechanisms like post-transcriptional regulation by miRNAs, DNA methylation, or histone modification has already been confirmed. Besides, several studies have shown that AhR-induced miR-212/132 cluster suppresses cancers, attenuates autoimmune diseases, and has an anti-inflammatory role in different immune responses by regulating cytokine levels and immune cells. Together the ever-expanding new AhR roles and the miRNA therapeutics are a prominent segment among biopharmaceuticals. Additionally, AhR-activated miRNAs can serve as valuable biomarkers of diseases, notably cancer progression or suppression and chemical exposure. Once AhR-dependent gene expression may hinge on the ligand, cell type, and context singularity, the reviewed outcomes might help contextualize state of the art and support new trends and emerging opportunities in the field.
Collapse
Affiliation(s)
- Geonildo Rodrigo Disner
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICS/FAPESP), Butantan Institute, São Paulo, Brazil
| | - Monica Lopes-Ferreira
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICS/FAPESP), Butantan Institute, São Paulo, Brazil
| | - Carla Lima
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICS/FAPESP), Butantan Institute, São Paulo, Brazil
| |
Collapse
|
15
|
Shankar P, McClure RS, Waters KM, Tanguay RL. Gene co-expression network analysis in zebrafish reveals chemical class specific modules. BMC Genomics 2021; 22:658. [PMID: 34517816 PMCID: PMC8438978 DOI: 10.1186/s12864-021-07940-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify genes and biological pathways that Aryl Hydrocarbon Receptor 2 (AHR2) Activators and flame retardant chemicals (FRCs) alter in developing zebrafish. Taking advantage of a compendium of phenotypically-anchored RNA sequencing data collected from 48-h post fertilization (hpf) zebrafish, we inferred a co-expression network that grouped genes based on their transcriptional response. RESULTS Genes responding to the FRCs and AHR2 Activators localized to distinct regions of the network, with FRCs inducing a broader response related to neurobehavior. AHR2 Activators centered in one region related to chemical stress responses. We also discovered several highly co-expressed genes in this module, including cyp1a, and we subsequently show that these genes are definitively within the AHR2 signaling pathway. Systematic removal of the two chemical types from the data, and analysis of network changes identified neurogenesis associated with FRCs, and regulation of vascular development associated with both chemical classes. We also identified highly connected genes responding specifically to each class that are potential biomarkers of exposure. CONCLUSIONS Overall, we created the first zebrafish chemical-specific gene co-expression network illuminating how chemicals alter the transcriptome relative to each other. In addition to our conclusions regarding FRCs and AHR2 Activators, our network can be leveraged by other studies investigating chemical mechanisms of toxicity.
Collapse
Affiliation(s)
- Prarthana Shankar
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, 28645 East Highway 34, Oregon State University, Corvallis, OR, 97331, USA
| | - Ryan S McClure
- Biological Sciences Division, Pacific National Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA, 99352, USA
| | - Katrina M Waters
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, 28645 East Highway 34, Oregon State University, Corvallis, OR, 97331, USA.,Biological Sciences Division, Pacific National Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA, 99352, USA
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, 28645 East Highway 34, Oregon State University, Corvallis, OR, 97331, USA.
| |
Collapse
|
16
|
Bungsu I, Kifli N, Ahmad SR, Ghani H, Cunningham AC. Herbal Plants: The Role of AhR in Mediating Immunomodulation. Front Immunol 2021; 12:697663. [PMID: 34249001 PMCID: PMC8264659 DOI: 10.3389/fimmu.2021.697663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/08/2021] [Indexed: 12/25/2022] Open
Abstract
The prevalence of chronic inflammatory diseases including inflammatory bowel disease (IBD), autoimmunity and cancer have increased in recent years. Herbal-based compounds such as flavonoids have been demonstrated to contribute to the modulation of these diseases although understanding their mechanism of action remains limited. Flavonoids are able to interact with cellular immune components in a distinct way and influence immune responses at a molecular level. In this mini review, we highlight recent progress in our understanding of the modulation of immune responses by the aryl hydrocarbon receptor (AhR), a ligand-dependent transcription factor whose activity can be regulated by diverse molecules including flavonoids. We focus on the role of AhR in integrating signals from flavonoids to modulate inflammatory responses using in vitro and experimental animal models. We also summarize the limitations of these studies. Medicinal herbs have been widely used to treat inflammatory disorders and may offer a valuable therapeutic strategy to treat aberrant inflammatory responses by modulation of the AhR pathway.
Collapse
Affiliation(s)
- Izzah Bungsu
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB), Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
| | - Nurolaini Kifli
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB), Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
| | - Siti Rohaiza Ahmad
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB), Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
| | - Hazim Ghani
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB), Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
| | - Anne Catherine Cunningham
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB), Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
| |
Collapse
|
17
|
Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
Collapse
|
18
|
Shankar P, Dasgupta S, Hahn ME, Tanguay RL. A Review of the Functional Roles of the Zebrafish Aryl Hydrocarbon Receptors. Toxicol Sci 2020; 178:215-238. [PMID: 32976604 PMCID: PMC7706399 DOI: 10.1093/toxsci/kfaa143] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the last 2 decades, the zebrafish (Danio rerio) has emerged as a stellar model for unraveling molecular signaling events mediated by the aryl hydrocarbon receptor (AHR), an important ligand-activated receptor found in all eumetazoan animals. Zebrafish have 3 AHRs-AHR1a, AHR1b, and AHR2, and studies have demonstrated the diversity of both the endogenous and toxicological functions of the zebrafish AHRs. In this contemporary review, we first highlight the evolution of the zebrafish ahr genes, and the characteristics of the receptors including developmental and adult expression, their endogenous and inducible roles, and the predicted ligands from homology modeling studies. We then review the toxicity of a broad spectrum of AHR ligands across multiple life stages (early stage, and adult), discuss their transcriptomic and epigenetic mechanisms of action, and report on any known interactions between the AHRs and other signaling pathways. Through this article, we summarize the promising research that furthers our understanding of the complex AHR pathway through the extensive use of zebrafish as a model, coupled with a large array of molecular techniques. As much of the research has focused on the functions of AHR2 during development and the mechanism of TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) toxicity, we illustrate the need to address the considerable knowledge gap in our understanding of both the mechanistic roles of AHR1a and AHR1b, and the diverse modes of toxicity of the various AHR ligands.
Collapse
Affiliation(s)
- Prarthana Shankar
- Department of Environmental and Molecular Toxicology, The Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, Oregon 97331
| | - Subham Dasgupta
- Department of Environmental and Molecular Toxicology, The Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, Oregon 97331
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, The Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, Oregon 97331
| |
Collapse
|
19
|
Lawrence EA, Hammond CL, Blain EJ. Potential of zebrafish as a model to characterise MicroRNA profiles in mechanically mediated joint degeneration. Histochem Cell Biol 2020; 154:521-531. [PMID: 32935147 PMCID: PMC7609428 DOI: 10.1007/s00418-020-01918-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2020] [Indexed: 12/19/2022]
Abstract
Mechanically mediated joint degeneration and cartilage dyshomeostasis is implicated in highly prevalent diseases such as osteoarthritis. Increasingly, MicroRNAs are being associated with maintaining the normal state of cartilage, making them an exciting and potentially key contributor to joint health and disease onset. Here, we present a summary of current in vitro and in vivo models which can be used to study the role of mechanical load and MicroRNAs in joint degeneration, including: non-invasive murine models of PTOA, surgical models which involve ligament transection, and unloading models based around immobilisation of joints or removal of load from the joint through suspension. We also discuss how zebrafish could be used to advance this field, namely through the availability of transgenic lines relevant to cartilage homeostasis and the ability to accurately map strain through the cartilage, enabling the response of downstream MicroRNA targets to be followed dynamically at a cellular level in areas of high and low strain.
Collapse
Affiliation(s)
- Elizabeth A Lawrence
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK.
| | - Chrissy L Hammond
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Emma J Blain
- Biomechanics and Bioengineering Centre Versus Arthritis, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| |
Collapse
|
20
|
Gumna J, Zok T, Figurski K, Pachulska-Wieczorek K, Szachniuk M. RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis. PLoS One 2020; 15:e0239287. [PMID: 33002005 PMCID: PMC7529196 DOI: 10.1371/journal.pone.0239287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/03/2020] [Indexed: 12/18/2022] Open
Abstract
RNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experimental data, for example, chemical probing information that can define pseudo-energy constraints for RNA folding algorithms. At the same time, diverse computational tools have been developed to facilitate analysis and visualization of data from RNA structure probing experiments followed by capillary electrophoresis or next-generation sequencing. RNAthor, a new software tool for the fully automated normalization of SHAPE and DMS probing data resolved by capillary electrophoresis, has recently joined this collection. RNAthor automatically identifies unreliable probing data. It normalizes the reactivity information to a uniform scale and uses it in the RNA secondary structure prediction. Our web server also provides tools for fast and easy RNA probing data visualization and statistical analysis that facilitates the comparison of multiple data sets. RNAthor is freely available at http://rnathor.cs.put.poznan.pl/.
Collapse
Affiliation(s)
- Julita Gumna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Kacper Figurski
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
- * E-mail: (KPW); (MS)
| |
Collapse
|
21
|
Nijoukubo D, Adachi H, Kitazawa T, Teraoka H. Blood vessels are primary targets for 2,3,7,8-tetrachlorodibenzo-p-dioxin in pre-cardiac edema formation in larval zebrafish. CHEMOSPHERE 2020; 254:126808. [PMID: 32339801 DOI: 10.1016/j.chemosphere.2020.126808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 05/07/2023]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) has adverse effects on the development and function of the heart in zebrafish eleutheroembryos (embryos and larvae). We previously reported that TCDD reduced blood flow in the mesencephalic vein of zebrafish eleutheroembryos long before inducing pericardial edema. In the present study, we compared early edema (pre-cardiac edema), reduction of deduced cardiac output and reduction of blood flow in the dorsal aorta and cardinal vein caused by TCDD. In the same group of eleutheroembryos, TCDD (1.0 ppb) caused pre-cardiac edema and circulation failure at the cardinal vein in the central trunk region with the similar time courses from 42 to 54 h post fertilization (hpf), while the same concentration of TCDD did not significantly affect aortic circulation in the central trunk region or cardiac output. The dependence of pre-cardiac edema on TCDD concentration (0-2.0 ppb) at 55 hpf correlated well with the dependence of blood flow through the cardinal vein on TCDD concentration. Several treatments that markedly inhibited TCDD-induced pre-cardiac edema such as knockdown of aryl hydrocarbon receptor nuclear translocator-1 (ARNT1) and treatment with ascorbic acid, an antioxidant, did not significantly prevent the reduction of cardiac output at 55 hpf caused by 2.0 ppb TCDD. TCDD caused hemorrhage and extravasation of Evans blue that was intravascularly injected with bovine serum albumin, suggesting an increase in endothelium permeability to serum protein induced by TCDD. The results suggest that the blood vessels are primary targets of TCDD in edema formation in larval zebrafish.
Collapse
Affiliation(s)
- Daisuke Nijoukubo
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Hikaru Adachi
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Takio Kitazawa
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan.
| |
Collapse
|
22
|
Song H, Park KH. Regulation and function of SOX9 during cartilage development and regeneration. Semin Cancer Biol 2020; 67:12-23. [PMID: 32380234 DOI: 10.1016/j.semcancer.2020.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 09/23/2019] [Accepted: 04/26/2020] [Indexed: 12/21/2022]
Abstract
Chondrogenesis is a highly coordinated event in embryo development, adult homeostasis, and repair of the vertebrate cartilage. Fate decisions and differentiation of chondrocytes accompany differential expression of genes critical for each step of chondrogenesis. SOX9 is a master transcription factor that participates in sequential events in chondrogenesis by regulating a series of downstream factors in a stage-specific manner. SOX9 either works alone or in combination with downstream SOX transcription factors, SOX5 and SOX6 as chondrogenic SOX Trio. SOX9 is reduced in the articular cartilage of patients with osteoarthritis while highly maintained during tumorigenesis of cartilage and bone. Gene therapy using viral and non-viral vectors accompanied by tissue engineering (scaffolds) is a promising tool to regenerate impaired cartilage. Delivery of SOX9 or chondrogenic SOX Trio into cells produces efficient therapeutic effects on chondrogenesis and this event is facilitated by scaffolds. Non-viral vector-guided delivery systems encapsulated or loaded in mechanically stable solid scaffolds are useful for the regeneration of articular cartilage. Here we review major milestones and most recent studies focusing on regulation and function of chondrogenic SOX Trio, during chondrogenesis and cartilage regeneration, and on the development of advanced technologies in gene delivery with tissue engineering to improve efficiency of cartilage repair process.
Collapse
Affiliation(s)
- Haengseok Song
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea
| | - Keun-Hong Park
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea.
| |
Collapse
|
23
|
Shrestha R, Lieberth J, Tillman S, Natalizio J, Bloomekatz J. Using Zebrafish to Analyze the Genetic and Environmental Etiologies of Congenital Heart Defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:189-223. [PMID: 32304074 DOI: 10.1007/978-981-15-2389-2_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Congenital heart defects (CHDs) are among the most common human birth defects. However, the etiology of a large proportion of CHDs remains undefined. Studies identifying the molecular and cellular mechanisms that underlie cardiac development have been critical to elucidating the origin of CHDs. Building upon this knowledge to understand the pathogenesis of CHDs requires examining how genetic or environmental stress changes normal cardiac development. Due to strong molecular conservation to humans and unique technical advantages, studies using zebrafish have elucidated both fundamental principles of cardiac development and have been used to create cardiac disease models. In this chapter we examine the unique toolset available to zebrafish researchers and how those tools are used to interrogate the genetic and environmental contributions to CHDs.
Collapse
Affiliation(s)
- Rabina Shrestha
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Jaret Lieberth
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Savanna Tillman
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Joseph Natalizio
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | | |
Collapse
|
24
|
The aryl hydrocarbon receptor: an environmental sensor integrating immune responses in health and disease. Nat Rev Immunol 2019; 19:184-197. [PMID: 30718831 DOI: 10.1038/s41577-019-0125-8] [Citation(s) in RCA: 638] [Impact Index Per Article: 127.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The environment, diet, microbiota and body's metabolism shape complex biological processes in health and disease. However, our understanding of the molecular pathways involved in these processes is still limited. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that integrates environmental, dietary, microbial and metabolic cues to control complex transcriptional programmes in a ligand-specific, cell-type-specific and context-specific manner. In this Review, we summarize our current knowledge of AHR and the transcriptional programmes it controls in the immune system. Finally, we discuss the role of AHR in autoimmune and neoplastic diseases of the central nervous system, with a special focus on the gut immune system, the gut-brain axis and the therapeutic potential of targeting AHR in neurological disorders.
Collapse
|
25
|
lncRNAs: function and mechanism in cartilage development, degeneration, and regeneration. Stem Cell Res Ther 2019; 10:344. [PMID: 31753016 PMCID: PMC6873685 DOI: 10.1186/s13287-019-1458-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/17/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
With the increasing incidence of cartilage-related diseases such as osteoarthritis (OA) and intervertebral disc degeneration (IDD), heavier financial and social burdens need to be faced. Unfortunately, there is no satisfactory clinical method to target the pathophysiology of cartilage-related diseases. Many gene expressions, signaling pathways, and biomechanical dysregulations were involved in cartilage development, degeneration, and regeneration. However, the underlying mechanism was not clearly understood. Recently, lots of long non-coding RNAs (lncRNAs) were identified in the biological processes, including cartilage development, degeneration, and regeneration. It is clear that lncRNAs were important in regulating gene expression and maintaining chondrocyte phenotypes and homeostasis. In this review, we summarize the recent researches studying lncRNAs’ expression and function in cartilage development, degeneration, and regeneration and illustrate the potential mechanism of how they act in the pathologic process. With continued efforts, regulating lncRNA expression in the cartilage regeneration may be a promising biological treatment approach.
Collapse
|
26
|
Qiao J, Du Y, Yu J, Guo J. MicroRNAs as Potential Biomarkers of Insecticide Exposure: A Review. Chem Res Toxicol 2019; 32:2169-2181. [PMID: 31625722 DOI: 10.1021/acs.chemrestox.9b00236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Insecticides are key weapons for the control of pests. Large scale use of insecticides is harmful to the ecosystem, which is made up of a wide range of species and environments. MicroRNAs (miRNAs) are a class of endogenous single-stranded noncoding small RNAs in length of 20-24 nucleotides (nt), which extensively regulate expression of genes at transcriptional and post-transcriptional levels. The current research on miRNA-induced insecticide resistance reveals that dysregulated miRNAs cause significant changes in detoxification genes, particularly cytochrome P450s. Meanwhile, insecticide-induced changes in miRNAs are related to the decline of honeybees and threatened the development of zebrafish and other animals. Additionally, miRNAs are involved in insecticide-induced cytotoxicity, and dysregulated miRNAs are associated with human occupational and environmental exposure to insecticides. Therefore, miRNAs are valuable novel biomarkers of insecticide exposure, and they are potential factors to explain the toxicological effects of insecticides.
Collapse
Affiliation(s)
- Jiakai Qiao
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| | - Yuting Du
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| | - Junjie Yu
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| | - Jiangfeng Guo
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| |
Collapse
|
27
|
Minzaghi D, Pavel P, Dubrac S. Xenobiotic Receptors and Their Mates in Atopic Dermatitis. Int J Mol Sci 2019; 20:E4234. [PMID: 31470652 PMCID: PMC6747412 DOI: 10.3390/ijms20174234] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023] Open
Abstract
Atopic dermatitis (AD) is the most common inflammatory skin disease worldwide. It is a chronic, relapsing and pruritic skin disorder which results from epidermal barrier abnormalities and immune dysregulation, both modulated by environmental factors. AD is strongly associated with asthma and allergic rhinitis in the so-called 'atopic march.' Xenobiotic receptors and their mates are ligand-activated transcription factors expressed in the skin where they control cellular detoxification pathways. Moreover, they regulate the expression of genes in pathways involved in AD in epithelial cells and immune cells. Activation or overexpression of xenobiotic receptors in the skin can be deleterious or beneficial, depending on context, ligand and activation duration. Moreover, their impact on skin might be amplified by crosstalk among xenobiotic receptors and their mates. Because they are activated by a broad range of endogenous molecules, drugs and pollutants owing to their promiscuous ligand affinity, they have recently crystalized the attention of researchers, including in dermatology and especially in the AD field. This review examines the putative roles of these receptors in AD by critically evaluating the conditions under which the proteins and their ligands have been studied. This information should provide new insights into AD pathogenesis and ways to develop new therapeutic interventions.
Collapse
Affiliation(s)
- Deborah Minzaghi
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Petra Pavel
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sandrine Dubrac
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| |
Collapse
|
28
|
GC-MS Chemical Characterization and In Vitro Evaluation of Antioxidant and Toxic Effects Using Drosophila melanogaster Model of the Essential Oil of Lantana montevidensis (Spreng) Briq. ACTA ACUST UNITED AC 2019; 55:medicina55050194. [PMID: 31126036 PMCID: PMC6572660 DOI: 10.3390/medicina55050194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/27/2019] [Accepted: 05/15/2019] [Indexed: 11/17/2022]
Abstract
Background and objectives: Natural products such as essential oils with antioxidant potential can reduce the level of oxidative stress and prevent the oxidation of biomolecules. In the present study, we investigated the antioxidant potential of Lantana montevidensis leaf essential oil (EOLM) in chemical and biological models using Drosophila melanogaster. Materials and methods: in addition, the chemical components of the oil were identified and quantified by gas chromatography coupled to mass spectrometry (GC-MS), and the percentage compositions were obtained from electronic integration measurements using flame ionization detection (FID). Results: our results demonstrated that EOLM is rich in terpenes with Germacrene-D (31.27%) and β-caryophyllene (28.15%) as the major components. EOLM (0.12-0.48 g/mL) was ineffective in scavenging DPPH radical, and chelating Fe(II), but showed reducing activity at 0.24 g/mL and 0.48 g/mL. In in vivo studies, exposure of D. melanogaster to EOLM (0.12-0.48 g/mL) for 5 h resulted in 10% mortality; no change in oxidative stress parameters such as total thiol, non-protein thiol, and malondialdehyde contents, in comparison to control (p > 0.05). Conclusions: taken together, our results indicate EOLM may not be toxic at the concentrations tested, and thus may not be suitable for the development of new botanical insecticides, such as fumigants or spray-type control agents against Drosophila melanogaster.
Collapse
|
29
|
Yoshioka W, Tohyama C. Mechanisms of Developmental Toxicity of Dioxins and Related Compounds. Int J Mol Sci 2019; 20:E617. [PMID: 30708991 PMCID: PMC6387164 DOI: 10.3390/ijms20030617] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 12/20/2022] Open
Abstract
Dioxins and related compounds induce morphological abnormalities in developing animals in an aryl hydrocarbon receptor (AhR)-dependent manner. Here we review the studies in which 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is used as a prototypical compound to elucidate the pathogenesis of morphological abnormalities. TCDD-induced cleft palate in fetal mice involves a delay in palatogenesis and dissociation of fused palate shelves. TCDD-induced hydronephrosis, once considered to be caused by the anatomical obstruction of the ureter, is now separated into TCDD-induced obstructive and non-obstructive hydronephrosis, which develops during fetal and neonatal periods, respectively. In the latter, a prostaglandin E₂ synthesis pathway and urine concentration system are involved. TCDD-induced abnormal development of prostate involves agenesis of the ventral lobe. A suggested mechanism is that AhR activation in the urogenital sinus mesenchyme by TCDD modulates the wingless-type MMTV integration site family (WNT)/β-catenin signaling cascade to interfere with budding from urogenital sinus epithelium. TCDD exposure to zebrafish embryos induces loss of epicardium progenitor cells and heart malformation. AHR2-dependent downregulation of Sox9b expression in cardiomyocytes is a suggested underlying mechanism. TCDD-induced craniofacial malformation in zebrafish is considered to result from the AHR2-dependent reduction in SRY-box 9b (SOX9b), probably partly via the noncoding RNA slincR, resulting in the underdevelopment of chondrocytes and cartilage.
Collapse
Affiliation(s)
- Wataru Yoshioka
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Chiharu Tohyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| |
Collapse
|
30
|
Dempsey J, Zhang A, Cui JY. Coordinate regulation of long non-coding RNAs and protein-coding genes in germ-free mice. BMC Genomics 2018; 19:834. [PMID: 30463508 PMCID: PMC6249886 DOI: 10.1186/s12864-018-5235-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are increasingly recognized as regulators of tissue-specific cellular functions and have been shown to regulate transcriptional and translational processes, acting as signals, decoys, guides, and scaffolds. It has been suggested that some lncRNAs act in cis to regulate the expression of neighboring protein-coding genes (PCGs) in a mechanism that fine-tunes gene expression. Gut microbiome is increasingly recognized as a regulator of development, inflammation, host metabolic processes, and xenobiotic metabolism. However, there is little known regarding whether the gut microbiome modulates lncRNA gene expression in various host metabolic organs. The goals of this study were to 1) characterize the tissue-specific expression of lncRNAs and 2) identify and annotate lncRNAs differentially regulated in the absence of gut microbiome. RESULTS Total RNA was isolated from various tissues (liver, duodenum, jejunum, ileum, colon, brown adipose tissue, white adipose tissue, and skeletal muscle) from adult male conventional and germ-free mice (n = 3 per group). RNA-Seq was conducted and reads were mapped to the mouse reference genome (mm10) using HISAT. Transcript abundance and differential expression was determined with Cufflinks using the reference databases NONCODE 2016 for lncRNAs and UCSC mm10 for PCGs. Although the constitutive expression of lncRNAs was ubiquitous within the enterohepatic (liver and intestine) and the peripheral metabolic tissues (fat and muscle) in conventional mice, differential expression of lncRNAs by lack of gut microbiota was highly tissue specific. Interestingly, the majority of gut microbiota-regulated lncRNAs were in jejunum. Most lncRNAs were co-regulated with neighboring PCGs. STRING analysis showed that differentially expressed PCGs in proximity to lncRNAs form tissue-specific networks, suggesting that lncRNAs may interact with gut microbiota/microbial metabolites to regulate tissue-specific functions. CONCLUSIONS This study is among the first to demonstrate that gut microbiota critically regulates the expression of lncRNAs not only locally in intestine but also remotely in other metabolic organs, suggesting that common transcriptional machinery may be shared to transcribe lncRNA-PCG pairs, and lncRNAs may interact with PCGs to regulate tissue-specific pathways.
Collapse
Affiliation(s)
- Joseph Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Seattle, WA, 98105, USA
| | - Angela Zhang
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Seattle, WA, 98105, USA
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Seattle, WA, 98105, USA.
| |
Collapse
|
31
|
Shinde R, McGaha TL. The Aryl Hydrocarbon Receptor: Connecting Immunity to the Microenvironment. Trends Immunol 2018; 39:1005-1020. [PMID: 30409559 DOI: 10.1016/j.it.2018.10.010] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytoplasmic receptor and transcription factor activated through cognate ligand binding. It is an important factor in immunity and tissue homeostasis, and structurally diverse compounds from the environment, diet, microbiome, and host metabolism can induce AhR activity. Emerging evidence suggests that AhR is a key sensor allowing immune cells to adapt to environmental conditions and changes in AhR activity have been associated with autoimmune disorders and cancer. Furthermore, AhR agonists or antagonists can impact immune disease outcomes identifying AhR as a potentially actionable target for immunotherapy. In this review, we describe known ligands stimulating AhR activity, downstream proinflammatory and suppressive mechanisms potentiated by AhR, and how this understanding is being applied to immunopathology to help control disease outcomes.
Collapse
Affiliation(s)
- Rahul Shinde
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Tracy L McGaha
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
32
|
Garcia GR, Shankar P, Dunham CL, Garcia A, La Du JK, Truong L, Tilton SC, Tanguay RL. Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA ( slincR) Using the Zebrafish Model. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:117002. [PMID: 30398377 PMCID: PMC6371766 DOI: 10.1289/ehp3281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND A structurally diverse group of chemicals, including dioxins [e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)] and polycyclic aromatic hydrocarbons (PAHs), can xenobiotically activate the aryl hydrocarbon receptor (AHR) and contribute to adverse health effects in humans and wildlife. In the zebrafish model, repression of sox9b has a causal role in several AHR-mediated toxic responses, including craniofacial cartilage malformations; however, the mechanism of sox9b repression remains unknown. We previously identified a long noncoding RNA, sox9b long intergenic noncoding RNA (slincR), which is increased (in an AHR-dependent manner) by multiple AHR ligands and is required for the AHR-activated repression of sox9b. OBJECTIVE Using the zebrafish model, we aimed to enhance our understanding of the signaling events downstream of AHR activation that contribute to toxic responses by identifying: a) whether slincR is enriched on the sox9b locus, b) slincR's functional contributions to TCDD-induced toxicity, c) PAHs that increase slincR expression, and d) mammalian orthologs of slincR. METHODS We used capture hybridization analysis of RNA targets (CHART), qRT-PCR, RNA sequencing, morphometric analysis of cartilage structures, and hemorrhaging screens. RESULTS The slincR transcript was enriched at the 5' untranslated region (UTR) of the sox9b locus. Transcriptome profiling and human ortholog analyses identified processes related to skeletal and cartilage development unique to TCDD-exposed controls, and angiogenesis and vasculature development unique to TCDD-exposed zebrafish that were injected with a splice-blocking morpholino targeting slincR. In comparison to TCDD exposed control morphants, slincR morphants exposed to TCDD resulted in abnormal cartilage structures and a smaller percentage of animals displaying the hemorrhaging phenotype. In addition, slincR expression was significantly increased in six out of the sixteen PAHs we screened. CONCLUSION Our study establishes that in zebrafish, slincR is recruited to the sox9b 5' UTR to repress transcription, can regulate cartilage development, has a causal role in the TCDD-induced hemorrhaging phenotype, and is up-regulated by multiple environmentally relevant PAHs. These findings have important implications for understanding the ligand-specific mechanisms of AHR-mediated toxicity. https://doi.org/10.1289/EHP3281.
Collapse
Affiliation(s)
- Gloria R Garcia
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Prarthana Shankar
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Cheryl L Dunham
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Abraham Garcia
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Jane K La Du
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Lisa Truong
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Susan C Tilton
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
33
|
sox9b is required in cardiomyocytes for cardiac morphogenesis and function. Sci Rep 2018; 8:13906. [PMID: 30224706 PMCID: PMC6141582 DOI: 10.1038/s41598-018-32125-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/03/2018] [Indexed: 12/18/2022] Open
Abstract
The high mobility group transcription factor SOX9 is expressed in stem cells, progenitor cells, and differentiated cell-types in developing and mature organs. Exposure to a variety of toxicants including dioxin, di(2-ethylhexyl) phthalate, 6:2 chlorinated polyfluorinated ether sulfonate, and chlorpyrifos results in the downregulation of tetrapod Sox9 and/or zebrafish sox9b. Disruption of Sox9/sox9b function through environmental exposures or genetic mutations produce a wide range of phenotypes and adversely affect organ development and health. We generated a dominant-negative sox9b (dnsox9b) to inhibit sox9b target gene expression and used the Gal4/UAS system to drive dnsox9b specifically in cardiomyocytes. Cardiomyocyte-specific inhibition of sox9b function resulted in a decrease in ventricular cardiomyocytes, an increase in atrial cardiomyocytes, hypoplastic endothelial cushions, and impaired epicardial development, ultimately culminating in heart failure. Cardiomyocyte-specific dnsox9b expression significantly reduced end diastolic volume, which corresponded with a decrease in stroke volume, ejection fraction, and cardiac output. Further analysis of isolated cardiac tissue by RT-qPCR revealed cardiomyocyte-specific inhibition of sox9b function significantly decreased the expression of the critical cardiac development genes nkx2.5, nkx2.7, and myl7, as well as c-fos, an immediate early gene necessary for cardiomyocyte progenitor differentiation. Together our studies indicate sox9b transcriptional regulation is necessary for cardiomyocyte development and function.
Collapse
|
34
|
Gutiérrez-Vázquez C, Quintana FJ. Regulation of the Immune Response by the Aryl Hydrocarbon Receptor. Immunity 2018; 48:19-33. [PMID: 29343438 DOI: 10.1016/j.immuni.2017.12.012] [Citation(s) in RCA: 573] [Impact Index Per Article: 95.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/04/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is activated by small molecules provided by the diet, microorganisms, metabolism, and pollutants. AhR is expressed by a number of immune cells, and thus AhR signaling provides a molecular pathway that integrates the effects of the environment and metabolism on the immune response. Studies have shown that AhR signaling plays important roles in the immune system in health and disease. As its activity is regulated by small molecules, AhR also constitutes a potential target for therapeutic immunomodulation. In this review we discuss the role of AhR in the regulation of the immune response in the context of autoimmunity, infection, and cancer, as well as the potential opportunities and challenges of developing AhR-targeted therapeutics.
Collapse
Affiliation(s)
- Cristina Gutiérrez-Vázquez
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
35
|
Procházková J, Strapáčová S, Svržková L, Andrysík Z, Hýžďalová M, Hrubá E, Pěnčíková K, Líbalová H, Topinka J, Kléma J, Espinosa JM, Vondráček J, Machala M. Adaptive changes in global gene expression profile of lung carcinoma A549 cells acutely exposed to distinct types of AhR ligands. Toxicol Lett 2018; 292:162-174. [PMID: 29704546 DOI: 10.1016/j.toxlet.2018.04.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/28/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
Abstract
Exposure to persistent ligands of aryl hydrocarbon receptor (AhR) has been found to cause lung cancer in experimental animals, and lung adenocarcinomas are often associated with enhanced AhR expression and aberrant AhR activation. In order to better understand the action of toxic AhR ligands in lung epithelial cells, we performed global gene expression profiling and analyze TCDD-induced changes in A549 transcriptome, both sensitive and non-sensitive to CH223191 co-treatment. Comparison of our data with results from previously reported microarray and ChIP-seq experiments enabled us to identify candidate genes, which expression status reflects exposure of lung cancer cells to TCDD, and to predict processes, pathways (e.g. ER stress, Wnt/β-cat, IFNɣ, EGFR/Erbb1), putative TFs (e.g. STAT, AP1, E2F1, TCF4), which may be implicated in adaptive response of lung cells to TCDD-induced AhR activation. Importantly, TCDD-like expression fingerprint of selected genes was observed also in A549 cells exposed acutely to both toxic (benzo[a]pyrene, benzo[k]fluoranthene) and endogenous AhR ligands (2-(1H-Indol-3-ylcarbonyl)-4-thiazolecarboxylic acid methyl ester and 6-formylindolo[3,2-b]carbazole). Overall, our results suggest novel cellular candidates, which could help to improve monitoring of AhR-dependent transcriptional activity during acute exposure of lung cells to distinct types of environmental pollutants.
Collapse
Affiliation(s)
- Jiřina Procházková
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Simona Strapáčová
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Lucie Svržková
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Zdeněk Andrysík
- 1 Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Martina Hýžďalová
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Eva Hrubá
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Kateřina Pěnčíková
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Helena Líbalová
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Topinka
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Kléma
- Department of Computer Science, Czech Technical University in Prague, Czech Republic
| | - Joaquín M Espinosa
- 1 Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Machala
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic.
| |
Collapse
|
36
|
Garcia GR, Bugel SM, Truong L, Spagnoli S, Tanguay RL. AHR2 required for normal behavioral responses and proper development of the skeletal and reproductive systems in zebrafish. PLoS One 2018; 13:e0193484. [PMID: 29494622 PMCID: PMC5832240 DOI: 10.1371/journal.pone.0193484] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/12/2018] [Indexed: 01/24/2023] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a conserved ligand-activated transcription factor required for proper vertebrate development and homeostasis. The inappropriate activation of AHR by ubiquitous pollutants can lead to adverse effects on wildlife and human health. The zebrafish is a powerful model system that provides a vertebrate data stream that anchors hypothesis at the genetic and cellular levels to observations at the morphological and behavioral level, in a high-throughput format. In order to investigate the endogenous functions of AHR, we generated an AHR2 (homolog of human AHR)-null zebrafish line (ahr2osu1) using the clustered, regulatory interspaced, short palindromic repeats (CRISPR)-Cas9 precision genome editing method. In zebrafish, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) mediated toxicity requires AHR2. The AHR2-null line was resistant to TCDD-induced toxicity, indicating the line can be used to investigate the biological and toxicological functions of AHR2. The AHR2-null zebrafish exhibited decreased survival and fecundity compared to the wild type line. At 36 weeks, histological evaluations of the AHR2-null ovaries revealed a reduction of mature follicles when compared to wild type ovaries, suggesting AHR2 regulates follicle growth in zebrafish. AHR2-null adults had malformed cranial skeletal bones and severely damaged fins. Our data suggests AHR2 regulates some aspect(s) of neuromuscular and/or sensory system development, with impaired behavioral responses observed in larval and adult AHR2-null zebrafish. This study increases our understanding of the endogenous functions of AHR, which may help foster a better understanding of the target organs and molecular mechanisms involved in AHR-mediated toxicities.
Collapse
Affiliation(s)
- Gloria R. Garcia
- Department of Environmental & Molecular Toxicology, Environmental Health Sciences Center, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States of America
| | - Sean M. Bugel
- Department of Environmental & Molecular Toxicology, Environmental Health Sciences Center, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States of America
| | - Lisa Truong
- Department of Environmental & Molecular Toxicology, Environmental Health Sciences Center, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States of America
| | - Sean Spagnoli
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Environmental Health Sciences Center, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States of America
| |
Collapse
|
37
|
The aryl hydrocarbon receptor regulates the expression of TIPARP and its cis long non-coding RNA, TIPARP-AS1. Biochem Biophys Res Commun 2018; 495:2356-2362. [DOI: 10.1016/j.bbrc.2017.12.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022]
|
38
|
Aluru N, Karchner SI, Krick KS, Zhu W, Liu J. Role of DNA methylation in altered gene expression patterns in adult zebrafish ( Danio rerio) exposed to 3, 3', 4, 4', 5-pentachlorobiphenyl (PCB 126). ENVIRONMENTAL EPIGENETICS 2018; 4:dvy005. [PMID: 29686887 PMCID: PMC5905506 DOI: 10.1093/eep/dvy005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/09/2018] [Accepted: 03/08/2018] [Indexed: 05/08/2023]
Abstract
There is growing evidence that environmental toxicants can affect various physiological processes by altering DNA methylation patterns. However, very little is known about the impact of toxicant-induced DNA methylation changes on gene expression patterns. The objective of this study was to determine the genome-wide changes in DNA methylation concomitant with altered gene expression patterns in response to 3, 3', 4, 4', 5-pentachlorobiphenyl (PCB126) exposure. We used PCB126 as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. Adult zebrafish were exposed to 10 nM PCB126 for 24 h (water-borne exposure) and brain and liver tissues were sampled at 7 days post-exposure in order to capture both primary and secondary changes in DNA methylation and gene expression. We used enhanced Reduced Representation Bisulfite Sequencing and RNAseq to quantify DNA methylation and gene expression, respectively. Enhanced reduced representation bisulfite sequencing analysis revealed 573 and 481 differentially methylated regions in the liver and brain, respectively. Most of the differentially methylated regions are located more than 10 kilobases upstream of transcriptional start sites of the nearest neighboring genes. Gene Ontology analysis of these genes showed that they belong to diverse physiological pathways including development, metabolic processes and regeneration. RNAseq results revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and energy metabolism in response to polychlorinated biphenyl exposure. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting that the relationship between methylation and gene expression is dynamic and complex, involving multiple layers of regulation.
Collapse
Affiliation(s)
- Neelakanteswar Aluru
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Correspondence address. Department of Biology, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02543, USA. Tel: 508-289-3607; Fax: 508-457-2134; E-mail:
| | - Sibel I Karchner
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Keegan S Krick
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Wei Zhu
- CAS Key Laboratory of Genomic Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing 100101, China
| | - Jiang Liu
- CAS Key Laboratory of Genomic Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing 100101, China
| |
Collapse
|