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Yu J, Li L, Tao X, Chen Y, Dong D. Metabolic interactions of host-gut microbiota: New possibilities for the precise diagnosis and therapeutic discovery of gastrointestinal cancer in the future-A review. Crit Rev Oncol Hematol 2024; 203:104480. [PMID: 39154670 DOI: 10.1016/j.critrevonc.2024.104480] [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: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024] Open
Abstract
Gastrointestinal (GI) cancer continues to pose a significant global health challenge. Recent advances in our understanding of the complex relationship between the host and gut microbiota have shed light on the critical role of metabolic interactions in the pathogenesis and progression of GI cancer. In this study, we examined how microbiota interact with the host to influence signalling pathways that impact the formation of GI tumours. Additionally, we investigated the potential therapeutic approach of manipulating GI microbiota for use in clinical settings. Revealing the complex molecular exchanges between the host and gut microbiota facilitates a deeper understanding of the underlying mechanisms that drive cancer development. Metabolic interactions hold promise for the identification of microbial signatures or metabolic pathways associated with specific stages of cancer. Hence, this study provides potential strategies for the diagnosis, treatment and management of GI cancers to improve patient outcomes.
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Affiliation(s)
- Jianing Yu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; College of Pharmacy, Dalian Medical University, China
| | - Lu Li
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Xufeng Tao
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
| | - Yanwei Chen
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
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2
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Zhang W, Xue Z, Cao Q, Zong Y, Li X, Ma Y, Jia C, Liu C, Ding N, Wang R. Characterization of medaka (Oryzias latipes) AHRs and the comparison of two model fishes-Medaka vs. zebrafish: The subform-specific sensitivity to dioxin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174136. [PMID: 38901578 DOI: 10.1016/j.scitotenv.2024.174136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Dioxins and the emerging dioxin-like compounds (DLCs) have recruited increasing concerns about their environmental contamination, toxicity, health impacts, and mechanisms. Based on the structural similarity of dioxins and many DLCs, their toxicity was predominantly mediated by the dioxin receptor (aryl hydrocarbon receptor, AHR) in animals (including human), which can be different in expression and function among species and then possibly produce the species-specific risk or toxicity. To date, characterizing the AHR of additional species other than human and rodents can increase the accuracy of toxicity/risk evaluation and increase knowledge about AHR biology. As a key model, the medaka AHR has not been clearly characterized. Through genome survey and phylogenetic analysis, we identified four AHRs (olaAHR1a, olaAHR1b, olaAHR2a, and olaAHR2b) and two ARNTs (olaARNT1 and olaARNT2). The medaka AHR pathway was conserved in expression in nine tested tissues, of which olaAHR2a represented the predominant subform with greater abundance. Medaka AHRs and ARNTs were functional and could be efficiently transactivated by the classical dioxin congener 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), although olaAHR1a did not seem to cooperate with olaARNT2. In terms of function/sensitivity, the EC50 values of medaka olaAHR1a (9.01 ± 1.43 nM), olaAHR1b (4.00 ± 1.10 nM), olaAHR2a (8.75 ± 3.34 nM), and olaAHR2b (3.06 ± 0.81 nM) showed slight differences; however, they were all at the nM level. The sensitivity of four medaka AHRs to TCDD was similar to that of zebrafish dreAHR2 (the dominant form, EC50 = 3.14 ± 4.19 nM), but these medaka AHRs were more sensitive than zebrafish dreAHR1b (EC50 = 27.05 ± 18.51 nM). The additional comparison also indicated that the EC50 values in various species were usually within the nM range, but AHRs of certain subforms/species can vary by one or two orders of magnitude. In summary, the present study will enhance the understanding of AHR and help improve research on the ecotoxicity of dioxins/DLCs.
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Affiliation(s)
- Wanglong Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China.
| | - Zhenhong Xue
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Qining Cao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Yanjiao Zong
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Xingyang Li
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Yongchao Ma
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chuanxing Jia
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Chunchen Liu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Ning Ding
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China.
| | - Renjun Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
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3
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Jindra M, Tumova S, Bittova L, Tuma R, Sedlak D. Agonist-dependent action of the juvenile hormone receptor. CURRENT OPINION IN INSECT SCIENCE 2024; 65:101234. [PMID: 39025365 DOI: 10.1016/j.cois.2024.101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Juvenile hormone (JH) signaling is realized at the gene regulatory level by receptors of the bHLH-PAS transcription factor family. The sesquiterpenoid hormones and their synthetic mimics are agonist ligands of a unique JH receptor (JHR) protein, methoprene-tolerant (MET). Upon binding an agonist to its PAS-B cavity, MET dissociates from a cytoplasmic chaperone complex including HSP83 and concomitantly switches to a bHLH-PAS partner taiman, forming a nuclear, transcriptionally active JHR heterodimer. This course of events resembles the vertebrate aryl hydrocarbon receptor (AHR), activated by a plethora of endogenous and synthetic compounds. Like in AHR, the pliable PAS-B cavity of MET adjusts to diverse ligands and binds them through similar mechanisms. Despite recent progress, we only begin to discern agonist-induced conformational shifts within the PAS-B domain, with the ultimate goal of understanding how these localized changes stimulate the assembly of the active JHR complex and, thus, fully grasp the mechanism of JHR signaling.
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Affiliation(s)
- Marek Jindra
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic.
| | - Sarka Tumova
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic
| | - Lenka Bittova
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic
| | - Roman Tuma
- Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic
| | - David Sedlak
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic
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4
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Zhuang J, Shang Q, Rastinejad F, Wu D. Decoding Allosteric Control in Hypoxia-Inducible Factors. J Mol Biol 2024; 436:168352. [PMID: 37935255 DOI: 10.1016/j.jmb.2023.168352] [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: 08/15/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The mammalian family of basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors possess the ability to sense and respond to diverse environmental and physiological cues. These proteins all share a common structural framework, comprising a bHLH domain, two PAS domains, and transcriptional activation or repression domain. To function effectively as transcription factors, members of the family must form dimers, bringing together bHLH segments to create a functional unit that allows for DNA response element binding. The significance of bHLH-PAS family is underscored by their involvement in many major human diseases, offering potential avenues for therapeutic intervention. Notably, the clear identification of ligand-binding cavities within their PAS domains enables the development of targeted small molecules. Two examples are Belzutifan, targeting hypoxia-inducible factor (HIF)-2α, and Tapinarof, targeting the aryl hydrocarbon receptor (AHR), both of which have gained regulatory approval recently. Here, we focus on the HIF subfamily. The crystal structures of all three HIF-α proteins have been elucidated, revealing their bHLH and tandem PAS domains are used to engage their dimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT, also called HIF-1β). A broad range of recent findings point to a shared allosteric modulation mechanism among these proteins, whereby small-molecules at the PAS-B domains exert direct influence over the HIF-α transcriptional functions. As our understanding of the architectural and allosteric mechanisms of bHLH-PAS proteins continues to advance, the possibility of discovering new therapeutic drugs becomes increasingly promising.
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Affiliation(s)
- Jingjing Zhuang
- Marine College, Shandong University, Weihai 264209, China; Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford OX3 7FZ, UK.
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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5
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Bonati L, Motta S, Callea L. The AhR Signaling Mechanism: A Structural Point of View. J Mol Biol 2024; 436:168296. [PMID: 37797832 DOI: 10.1016/j.jmb.2023.168296] [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: 07/28/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
The Aryl hydrocarbon Receptor (AhR) is a well-known sensor of xenobiotics; moreover, it is considered a promising drug target as it is involved in the regulation of many patho-physiological processes. For these reasons the study of its ligand-activated transcription mechanism has stimulated several studies for over twenty years. In this review we highlight the key role of molecular structural information in understanding the different steps of the signaling mechanism. The architecture of the AhR cytosolic complex, encompassing the hsp90 chaperone protein and the XAP2 and p23 co-chaperones, has become available in the last year thanks to Cryo-EM experiments. The structure of the AhR ligand-binding (PAS-B) domain has remained elusive for a long time; it has been predicted by homology modelling, based on known PAS systems, and its ligand-bound forms were modelled through ligand molecular docking. Although very recently some structural information on this domain has become available, considerable efforts are still needed to determine the binding geometries of the AhR key ligands by experimental high-resolution studies. On the other hand, the dimeric structure of AhR with the ARNT protein, bound to the specific DNA responsive element, was partially determined by X-ray crystallography and it was completed by homology modelling. On the whole the current structural knowledge of the main protein complexes that form over the AhR mechanism opens the way to confirm and further investigate the main steps of the proposed ligand-activated transcription mechanism of the AhR.
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Affiliation(s)
- Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Lara Callea
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
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Ramal M, Corral S, Kalisz M, Lapi E, Real FX. The urothelial gene regulatory network: understanding biology to improve bladder cancer management. Oncogene 2024; 43:1-21. [PMID: 37996699 DOI: 10.1038/s41388-023-02876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
The urothelium is a stratified epithelium composed of basal cells, one or more layers of intermediate cells, and an upper layer of differentiated umbrella cells. Most bladder cancers (BLCA) are urothelial carcinomas. Loss of urothelial lineage fidelity results in altered differentiation, highlighted by the taxonomic classification into basal and luminal tumors. There is a need to better understand the urothelial transcriptional networks. To systematically identify transcription factors (TFs) relevant for urothelial identity, we defined highly expressed TFs in normal human bladder using RNA-Seq data and inferred their genomic binding using ATAC-Seq data. To focus on epithelial TFs, we analyzed RNA-Seq data from patient-derived organoids recapitulating features of basal/luminal tumors. We classified TFs as "luminal-enriched", "basal-enriched" or "common" according to expression in organoids. We validated our classification by differential gene expression analysis in Luminal Papillary vs. Basal/Squamous tumors. Genomic analyses revealed well-known TFs associated with luminal (e.g., PPARG, GATA3, FOXA1) and basal (e.g., TP63, TFAP2) phenotypes and novel candidates to play a role in urothelial differentiation or BLCA (e.g., MECOM, TBX3). We also identified TF families (e.g., KLFs, AP1, circadian clock, sex hormone receptors) for which there is suggestive evidence of their involvement in urothelial differentiation and/or BLCA. Genomic alterations in these TFs are associated with BLCA. We uncover a TF network involved in urothelial cell identity and BLCA. We identify novel candidate TFs involved in differentiation and cancer that provide opportunities for a better understanding of the underlying biology and therapeutic intervention.
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Affiliation(s)
- Maria Ramal
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Corral
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- CIBERONC, Madrid, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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7
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Cheng YC, Ma WC, Li YH, Wu J, Liang KW, Lee WJ, Liu HC, Sheu WHH, Lee IT. Plasma aryl hydrocarbon receptor associated with epicardial adipose tissue in men: a cross-sectional study. Diabetol Metab Syndr 2023; 15:188. [PMID: 37749614 PMCID: PMC10519097 DOI: 10.1186/s13098-023-01166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Epicardial adipose tissue (EAT) is a type of ectopic fat with endocrine and paracrine functions. Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that responds to environmental stimuli. AhR expression is associated with obesity. In this cross-sectional study, we aimed to determine the relationship between circulating AhR concentrations and EAT. METHODS A total of 30 men with obesity and 23 age-matched men as healthy controls were enrolled. Plasma AhR concentrations were determined at fasting. The EAT thickness was measured on the free wall of the right ventricle from the basal short-axis plane by magnetic resonance imaging. RESULTS The participants with obesity had a higher plasma AhR level than the controls (81.0 ± 24.5 vs. 65.1 ± 16.4 pg/mL, P = 0.010). The plasma AhR level was positively correlated with EAT thickness (correlation coefficient = 0.380, P = 0.005). After adjusting for fasting glucose levels, plasma AhR levels were still significantly associated with EAT thickness (95% CI 0.458‒5.357, P = 0.021) but not with body mass index (P = 0.168). CONCLUSION Plasma AhR concentrations were positively correlated with EAT thickness on the free wall of the right ventricle in men. Further investigations are needed to evaluate the causal effects and underlying mechanisms between AhR and EAT.
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Affiliation(s)
- Yu-Cheng Cheng
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Sect. 4, Taichung, 40705, Taiwan
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Wei-Chun Ma
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Feng Yuan Hospital, Ministry of Health and Welfare, Taichung, 42055, Taiwan
| | - Yu-Hsuan Li
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Sect. 4, Taichung, 40705, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Department of Computer Science & Information Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - Junyi Wu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Sect. 4, Taichung, 40705, Taiwan
| | - Kae-Woei Liang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, School of Medicine, National Chung Hsing University, Taichung, 402204, Taiwan
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, 40705, Taiwan
| | - Hsiu-Chen Liu
- Department of Nursing, Taichung Veterans General Hospital, Taichung, 40705, Taiwan
| | | | - I-Te Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Sect. 4, Taichung, 40705, Taiwan.
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
- School of Medicine, Chung Shan Medical University, Taichung, 40201, Taiwan.
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8
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Chong ZX, Yong CY, Ong AHK, Yeap SK, Ho WY. Deciphering the roles of aryl hydrocarbon receptor (AHR) in regulating carcinogenesis. Toxicology 2023; 495:153596. [PMID: 37480978 DOI: 10.1016/j.tox.2023.153596] [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: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
Aryl hydrocarbon receptor (AHR) is a ligand-dependent receptor that belongs to the superfamily of basic helix-loop-helix (bHLH) transcription factors. The activation of the canonical AHR signaling pathway is known to induce the expression of cytochrome P450 enzymes, facilitating the detoxification metabolism in the human body. Additionally, AHR could interact with various signaling pathways such as epidermal growth factor receptor (EGFR), signal transducer and activator of transcription 3 (STAT3), hypoxia-inducible factor-1α (HIF-1α), nuclear factor ekappa B (NF-κβ), estrogen receptor (ER), and androgen receptor (AR) signaling pathways. Over the past 30 years, several studies have reported that various chemical, physical, or biological agents, such as tobacco, hydrocarbon compounds, industrial and agricultural chemical wastes, drugs, UV, viruses, and other toxins, could affect AHR expression or activity, promoting cancer development. Thus, it is valuable to overview how these factors regulate AHR-mediated carcinogenesis. Current findings have reported that many compounds could act as AHR ligands to drive the expressions of AHR-target genes, such as CYP1A1, CYP1B1, MMPs, and AXL, and other targets that exert a pro-proliferation or anti-apoptotic effect, like XIAP. Furthermore, some other physical and chemical agents, such as UV and 3-methylcholanthrene, could promote AHR signaling activities, increasing the signaling activities of a few oncogenic pathways, such as the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) pathways. Understanding how various factors regulate AHR-mediated carcinogenesis processes helps clinicians and scientists plan personalized therapeutic strategies to improve anti-cancer treatment efficacy. As many studies that have reported the roles of AHR in regulating carcinogenesis are preclinical or observational clinical studies that did not explore the detailed mechanisms of how different chemical, physical, or biological agents promote AHR-mediated carcinogenesis processes, future studies should focus on conducting large-scale and functional studies to unravel the underlying mechanism of how AHR interacts with different factors in regulating carcinogenesis processes.
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Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia
| | - Chean Yeah Yong
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Alan Han Kiat Ong
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000 Kajang, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
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Wen Z, Zhang Y, Zhang B, Hang Y, Xu L, Chen Y, Xie Q, Zhao Q, Zhang L, Li G, Zhao B, Sun F, Zhai Y, Zhu Y. Cryo-EM structure of the cytosolic AhR complex. Structure 2023; 31:295-308.e4. [PMID: 36649707 DOI: 10.1016/j.str.2022.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/24/2022] [Accepted: 12/21/2022] [Indexed: 01/17/2023]
Abstract
Aryl hydrocarbon receptor (AhR) is an important ligand-activated transcription factor involved in the regulation of various important physiological functions. Here, we report the cryo-EM structures of the Hsp90-AhR-p23 complex with or without bound XAP2, where the structure of the mouse AhR PAS-B domain is resolved. A highly conserved bridge motif of AhR is responsible for the interaction with the Hsp90 dimeric lumen. The ligand-free AhR PAS-B domain is attached to the Hsp90 dimer and is stabilized in the complex with bound XAP2. In addition, the DE-loop and a group of conserved pocket inner residues in the AhR PAS-B domain are found to be important for ligand binding. These results reveal the structural basis of the biological functions of AhR. Moreover, the protein purification method presented here allows the isolation of stable mouse AhR protein, which could be used to develop high-sensitivity biosensors for environmental pollutant detection.
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Affiliation(s)
- Zuoling Wen
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Beirong Zhang
- University of Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yumo Hang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yangsheng Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China.
| | - Yujia Zhai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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10
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Gruszczyk J, Grandvuillemin L, Lai-Kee-Him J, Paloni M, Savva CG, Germain P, Grimaldi M, Boulahtouf A, Kwong HS, Bous J, Ancelin A, Bechara C, Barducci A, Balaguer P, Bourguet W. Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex. Nat Commun 2022; 13:7010. [PMID: 36385050 PMCID: PMC9668932 DOI: 10.1038/s41467-022-34773-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including pollutants, natural products and metabolites. However, the scarcity of structural data precludes understanding of how AHR is activated by such diverse compounds. Our 2.85 Å structure of the human indirubin-bound AHR complex with the chaperone Hsp90 and the co-chaperone XAP2, reported herein, reveals a closed conformation Hsp90 dimer with AHR threaded through its lumen and XAP2 serving as a brace. Importantly, we disclose the long-awaited structure of the AHR PAS-B domain revealing a unique organisation of the ligand-binding pocket and the structural determinants of ligand-binding specificity and promiscuity of the receptor. By providing structural details of the molecular initiating event leading to AHR activation, our study rationalises almost forty years of biochemical data and provides a framework for future mechanistic studies and structure-guided drug design.
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Affiliation(s)
- Jakub Gruszczyk
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
| | - Loïc Grandvuillemin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Josephine Lai-Kee-Him
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Christos G Savva
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester, UK
| | - Pierre Germain
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Marina Grimaldi
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - Abdelhay Boulahtouf
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - Hok-Sau Kwong
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Julien Bous
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Aurélie Ancelin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Cherine Bechara
- IGF, University of Montpellier, CNRS, Inserm, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Alessandro Barducci
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Patrick Balaguer
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - William Bourguet
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
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11
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Grishanova AY, Perepechaeva ML. Aryl Hydrocarbon Receptor in Oxidative Stress as a Double Agent and Its Biological and Therapeutic Significance. Int J Mol Sci 2022; 23:6719. [PMID: 35743162 PMCID: PMC9224361 DOI: 10.3390/ijms23126719] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/02/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) has long been implicated in the induction of a battery of genes involved in the metabolism of xenobiotics and endogenous compounds. AhR is a ligand-activated transcription factor necessary for the launch of transcriptional responses important in health and disease. In past decades, evidence has accumulated that AhR is associated with the cellular response to oxidative stress, and this property of AhR must be taken into account during investigations into a mechanism of action of xenobiotics that is able to activate AhR or that is susceptible to metabolic activation by enzymes encoded by the genes that are under the control of AhR. In this review, we examine various mechanisms by which AhR takes part in the oxidative-stress response, including antioxidant and prooxidant enzymes and cytochrome P450. We also show that AhR, as a participant in the redox balance and as a modulator of redox signals, is being increasingly studied as a target for a new class of therapeutic compounds and as an explanation for the pathogenesis of some disorders.
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Affiliation(s)
| | - Maria L. Perepechaeva
- Federal Research Center of Fundamental and Translational Medicine, Institute of Molecular Biology and Biophysics, Timakova Str. 2, 630117 Novosibirsk, Russia;
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12
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Current Therapeutic Landscape and Safety Roadmap for Targeting the Aryl Hydrocarbon Receptor in Inflammatory Gastrointestinal Indications. Cells 2022; 11:cells11101708. [PMID: 35626744 PMCID: PMC9139855 DOI: 10.3390/cells11101708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/30/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Target modulation of the AhR for inflammatory gastrointestinal (GI) conditions holds great promise but also the potential for safety liabilities both within and beyond the GI tract. The ubiquitous expression of the AhR across mammalian tissues coupled with its role in diverse signaling pathways makes development of a “clean” AhR therapeutically challenging. Ligand promiscuity and diversity in context-specific AhR activation further complicates targeting the AhR for drug development due to limitations surrounding clinical translatability. Despite these concerns, several approaches to target the AhR have been explored such as small molecules, microbials, PROTACs, and oligonucleotide-based approaches. These various chemical modalities are not without safety liabilities and require unique de-risking strategies to parse out toxicities. Collectively, these programs can benefit from in silico and in vitro methodologies that investigate specific AhR pathway activation and have the potential to implement thresholding parameters to categorize AhR ligands as “high” or “low” risk for sustained AhR activation. Exploration into transcriptomic signatures for AhR safety assessment, incorporation of physiologically-relevant in vitro model systems, and investigation into chronic activation of the AhR by structurally diverse ligands will help address gaps in our understanding regarding AhR-dependent toxicities. Here, we review the role of the AhR within the GI tract, novel therapeutic modality approaches to target the AhR, key AhR-dependent safety liabilities, and relevant strategies that can be implemented to address drug safety concerns. Together, this review discusses the emerging therapeutic landscape of modalities targeting the AhR for inflammatory GI indications and offers a safety roadmap for AhR drug development.
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13
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Zhang W, Xie HQ, Li Y, Zhou M, Zhou Z, Wang R, Hahn ME, Zhao B. The aryl hydrocarbon receptor: A predominant mediator for the toxicity of emerging dioxin-like compounds. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128084. [PMID: 34952507 PMCID: PMC9039345 DOI: 10.1016/j.jhazmat.2021.128084] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/29/2021] [Accepted: 12/12/2021] [Indexed: 06/01/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has broad biological functions. Early after the identification of the AHR, most studies focused on its roles in regulating the expression of drug-metabolizing enzymes and mediating the toxicity of dioxins and dioxin-like compounds (DLCs). Currently, more diverse functions of AHR have been identified, indicating that AHR is not just a dioxin receptor. Dioxins and DLCs occur ubiquitously and have diverse health/ecological risks. Additional research is required to identify both shared and compound-specific mechanisms, especially for emerging DLCs such as polyhalogenated carbazoles (PHCZs), polychlorinated diphenyl sulfides (PCDPSs), and others, of which only a few investigations have been performed at present. Many of the toxic effects of emerging DLCs were observed to be predominantly mediated by the AHR because of their structural similarity as dioxins, and the in vitro TCDD-relative potencies of certain emerging DLC congeners are comparable to or even greater than the WHO-TEFs of OctaCDD, OctaCDF, and most coplanar PCBs. Due to the close relationship between AHR biology and environmental science, this review begins by providing novel insights into AHR signaling (canonical and non-canonical), AHR's biochemical properties (AHR structure, AHR-ligand interaction, AHR-DNA binding), and the variations during AHR transactivation. Then, AHR ligand classification and the corresponding mechanisms are discussed, especially the shared and compound-specific, AHR-mediated effects and mechanisms of emerging DLCs. Accordingly, a series of in vivo and in vitro toxicity evaluation methods based on the AHR signaling pathway are reviewed. In light of current advances, future research on traditional and emerging DLCs will enhance our understanding of their mechanisms, toxicity, potency, and ecological impacts.
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Affiliation(s)
- Wanglong Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Heidi Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunping Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingxi Zhou
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zhiguang Zhou
- State Environmental Protection Key Laboratory of Dioxin Pollution Control, National Research Center for Environmental Analysis and Measurement, Beijing 100029, China
| | - Renjun Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA; Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Lu CL, Liao CH, Wu WB, Zheng CM, Lu KC, Ma MC. Uremic Toxin Indoxyl Sulfate Impairs Hydrogen Sulfide Formation in Renal Tubular Cells. Antioxidants (Basel) 2022; 11:antiox11020361. [PMID: 35204244 PMCID: PMC8868407 DOI: 10.3390/antiox11020361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
Hydrogen sulfide (H2S) was the third gasotransmitter to be recognized as a cytoprotectant. A recent study demonstrated that exogenous supplementation of H2S ameliorates functional insufficiency in chronic kidney disease (CKD). However, how the H2S system is impaired by CKD has not been elucidated. The uremic toxin indoxyl sulfate (IS) is known to accumulate in CKD patients and harm the renal tubular cells. This study therefore treated the proximal tubular cells, LLC-PK1, with IS to see how IS affects H2S formation. Our results showed that H2S release from LLC-PK1 cells was markedly attenuated by IS when compared with control cells. The H2S donors NaHS and GYY-4137 significantly attenuated IS-induced tubular damage, indicating that IS impairs H2S formation. Interestingly, IS downregulated the H2S-producing enzymes cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and 3-mercaptopyruvate sulfurtransferase (3-MST), and these effects could be reversed by inhibition of the IS receptor, aryl hydrocarbon receptor (AhR). As transcription factor specificity protein 1 (Sp1) regulates the gene expression of H2S-producing enzymes, we further showed that IS significantly decreased the DNA binding activity of Sp1 but not its protein expression. Blockade of AhR reversed low Sp1 activity caused by IS. Moreover, exogenous H2S supplementation attenuated IS-mediated superoxide formation and depletion of the cellular glutathione content. These results clearly indicate that IS activates AhR, which then attenuates Sp1 function through the regulation of H2S-producing enzyme expression. The attenuation of H2S formation contributes to the low antioxidant defense of glutathione in uremic toxin-mediated oxidative stress, causing tubular cell damage.
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Affiliation(s)
- Chien-Lin Lu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242062, Taiwan; (C.-L.L.); (C.-H.L.); (W.-B.W.)
- Division of Nephrology, Department of Internal Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City 243089, Taiwan;
| | - Chun-Hou Liao
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242062, Taiwan; (C.-L.L.); (C.-H.L.); (W.-B.W.)
- Divisions of Urology, Department of Surgery, Cardinal Tien Hospital, New Taipei City 231403, Taiwan
| | - Wen-Bin Wu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242062, Taiwan; (C.-L.L.); (C.-H.L.); (W.-B.W.)
| | - Cai-Mei Zheng
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Shuang Ho Hospital, New Taipei City 235041, Taiwan;
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Research Center of Urology and Kidney, Taipei Medical University, Taipei 110301, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Internal Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City 243089, Taiwan;
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231405, Taiwan
| | - Ming-Chieh Ma
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242062, Taiwan; (C.-L.L.); (C.-H.L.); (W.-B.W.)
- Correspondence:
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15
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The Aryl Hydrocarbon Receptor (AHR): A Novel Therapeutic Target for Pulmonary Diseases? Int J Mol Sci 2022; 23:ijms23031516. [PMID: 35163440 PMCID: PMC8836075 DOI: 10.3390/ijms23031516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 01/08/2023] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a cytoplasmic transcription factor that is well-known for regulating xenobiotic metabolism. Studies in knockout and transgenic mice indicate that the AHR plays a vital role in the development of liver and regulation of reproductive, cardiovascular, hematopoietic, and immune homeostasis. In this focused review on lung diseases associated with acute injury and alveolar development, we reviewed and summarized the current literature on the mechanistic role(s) and therapeutic potential of the AHR in acute lung injury, chronic obstructive pulmonary disease, and bronchopulmonary dysplasia (BPD). Pre-clinical studies indicate that endogenous AHR activation is necessary to protect neonatal and adult lungs against hyperoxia- and cigarette smoke-induced injury. Our goal is to provide insight into the high translational potential of the AHR in the meaningful management of infants and adults with these lung disorders that lack curative therapies.
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16
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Jindra M, McKinstry WJ, Nebl T, Bittova L, Ren B, Shaw J, Phan T, Lu L, Low JKK, Mackay JP, Sparrow LG, Lovrecz GO, Hill RJ. Purification of an insect juvenile hormone receptor complex enables insights into its post-translational phosphorylation. J Biol Chem 2021; 297:101387. [PMID: 34758356 PMCID: PMC8683598 DOI: 10.1016/j.jbc.2021.101387] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
Juvenile hormone (JH) plays vital roles in insect reproduction, development, and in many aspects of physiology. JH primarily acts at the gene-regulatory level through interaction with an intracellular receptor (JH receptor [JHR]), a ligand-activated complex of transcription factors consisting of the JH-binding protein methoprene-tolerant (MET) and its partner taiman (TAI). Initial studies indicated significance of post-transcriptional phosphorylation, subunit assembly, and nucleocytoplasmic transport of JHR in JH signaling. However, our knowledge of JHR regulation at the protein level remains rudimentary, partly because of the difficulty of obtaining purified and functional JHR proteins. Here, we present a method for high-yield expression and purification of JHR complexes from two insect species, the beetle T. castaneum and the mosquito Aedes aegypti. Recombinant JHR subunits from each species were coexpressed in an insect cell line using a baculovirus system. MET–TAI complexes were purified through affinity chromatography and anion exchange columns to yield proteins capable of binding both the hormonal ligand (JH III) and DNA bearing cognate JH-response elements. We further examined the beetle JHR complex in greater detail. Biochemical analyses and MS confirmed that T. castaneum JHR was a 1:1 heterodimer consisting of MET and Taiman proteins, stabilized by the JHR agonist ligand methoprene. Phosphoproteomics uncovered multiple phosphorylation sites in the MET protein, some of which were induced by methoprene treatment. Finally, we report a functional bipartite nuclear localization signal, straddled by phosphorylated residues, within the disordered C-terminal region of MET. Our present characterization of the recombinant JHR is an initial step toward understanding JHR structure and function.
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Affiliation(s)
- Marek Jindra
- Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.
| | | | - Thomas Nebl
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Lenka Bittova
- Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Bin Ren
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Jan Shaw
- CSIRO Health and Biosecurity, CSIRO, North Ryde, New South Wales, Australia
| | - Tram Phan
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Louis Lu
- CSIRO Manufacturing, CSIRO, Parkville, Victoria, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | | | - Ronald J Hill
- CSIRO Health and Biosecurity, CSIRO, North Ryde, New South Wales, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
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17
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Motta S, Pandini A, Fornili A, Bonati L. Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. J Chem Theory Comput 2021; 17:2080-2089. [PMID: 33780250 PMCID: PMC8047803 DOI: 10.1021/acs.jctc.0c01308] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Several experimental
studies indicated that large conformational
changes, including partial domain unfolding, have a role in the functional
mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription
factors. Recently, single-molecule atomic force microscopy (AFM) revealed
two distinct pathways for the mechanical unfolding of the ARNT PAS-B.
In this work we used steered molecular dynamics simulations to gain
new insights into this process at an atomistic level. To reconstruct
and classify pathways sampled in multiple simulations, we designed
an original approach based on the use of self-organizing maps (SOMs).
This led us to identify two types of unfolding pathways for the ARNT
PAS-B, which are in good agreement with the AFM findings. Analysis
of average forces mapped on the SOM revealed a stable conformation
of the PAS-B along one pathway, which represents a possible structural
model for the intermediate state detected by AFM. The approach here
proposed will facilitate the study of other signal transmission mechanisms
involving the folding/unfolding of PAS domains.
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Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge UB8 3PH, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
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18
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How do Uremic Toxins Affect the Endothelium? Toxins (Basel) 2020; 12:toxins12060412. [PMID: 32575762 PMCID: PMC7354502 DOI: 10.3390/toxins12060412] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Uremic toxins can induce endothelial dysfunction in patients with chronic kidney disease (CKD). Indeed, the structure of the endothelial monolayer is damaged in CKD, and studies have shown that the uremic toxins contribute to the loss of cell–cell junctions, increasing permeability. Membrane proteins, such as transporters and receptors, can mediate the interaction between uremic toxins and endothelial cells. In these cells, uremic toxins induce oxidative stress and activation of signaling pathways, including the aryl hydrocarbon receptor (AhR), nuclear factor kappa B (NF-κB), and mitogen-activated protein kinase (MAPK) pathways. The activation of these pathways leads to overexpression of proinflammatory (e.g., monocyte chemoattractant protein-1, E-selectin) and prothrombotic (e.g., tissue factor) proteins. Uremic toxins also induce the formation of endothelial microparticles (EMPs), which can lead to the activation and dysfunction of other cells, and modulate the expression of microRNAs that have an important role in the regulation of cellular processes. The resulting endothelial dysfunction contributes to the pathogenesis of cardiovascular diseases, such as atherosclerosis and thrombotic events. Therefore, uremic toxins as well as the pathways they modulated may be potential targets for therapies in order to improve treatment for patients with CKD.
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