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Thome T, Vugman NA, Stone LE, Wimberly K, Scali ST, Ryan TE. A tryptophan-derived uremic metabolite/Ahr/Pdk4 axis governs skeletal muscle mitochondrial energetics in chronic kidney disease. JCI Insight 2024; 9:e178372. [PMID: 38652558 PMCID: PMC11141944 DOI: 10.1172/jci.insight.178372] [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: 12/08/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Chronic kidney disease (CKD) causes accumulation of uremic metabolites that negatively affect skeletal muscle. Tryptophan-derived uremic metabolites are agonists of the aryl hydrocarbon receptor (AHR), which has been shown to be activated in CKD. This study investigated the role of the AHR in skeletal muscle pathology of CKD. Compared with controls with normal kidney function, AHR-dependent gene expression (CYP1A1 and CYP1B1) was significantly upregulated in skeletal muscle of patients with CKD, and the magnitude of AHR activation was inversely correlated with mitochondrial respiration. In mice with CKD, muscle mitochondrial oxidative phosphorylation (OXPHOS) was markedly impaired and strongly correlated with the serum level of tryptophan-derived uremic metabolites and AHR activation. Muscle-specific deletion of the AHR substantially improved mitochondrial OXPHOS in male mice with the greatest uremic toxicity (CKD + probenecid) and abolished the relationship between uremic metabolites and OXPHOS. The uremic metabolite/AHR/mitochondrial axis in skeletal muscle was verified using muscle-specific AHR knockdown in C57BL/6J mice harboring a high-affinity AHR allele, as well as ectopic viral expression of constitutively active mutant AHR in mice with normal renal function. Notably, OXPHOS changes in AHRmKO mice were present only when mitochondria were fueled by carbohydrates. Further analyses revealed that AHR activation in mice led to significantly increased pyruvate dehydrogenase kinase 4 (Pdk4) expression and phosphorylation of pyruvate dehydrogenase enzyme. These findings establish a uremic metabolite/AHR/Pdk4 axis in skeletal muscle that governs mitochondrial deficits in carbohydrate oxidation during CKD.
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Affiliation(s)
- Trace Thome
- Department of Applied Physiology and Kinesiology and
| | | | | | - Keon Wimberly
- Department of Applied Physiology and Kinesiology and
| | - Salvatore T. Scali
- Division of Vascular Surgery and Endovascular Therapy, University of Florida, Gainesville, Florida, USA
- Malcom Randall VA Medical Center, Gainesville, Florida, USA
| | - Terence E. Ryan
- Department of Applied Physiology and Kinesiology and
- Center for Exercise Science and
- Myology Institute, University of Florida, Gainesville, Florida, USA
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2
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Alvik K, Shao P, Hutin D, Baglole C, Grant DM, Matthews J. Increased sensitivity to chemically induced colitis in mice harboring a DNA-binding deficient aryl hydrocarbon receptor. Toxicol Sci 2023; 191:321-331. [PMID: 36519841 PMCID: PMC9936212 DOI: 10.1093/toxsci/kfac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR), a transcription factor best known for mediating toxic responses of environmental pollutants, also integrates metabolic signals to promote anti-inflammatory responses, intestinal homeostasis, and maintain barrier integrity. AHR regulates its target genes through direct DNA-binding to aryl hydrocarbon response elements (AHREs) but also through tethering to other transcription factors in a DNA-binding independent manner. However, it is not known if AHR's anti-inflammatory role in the gut requires its ability to bind to AHREs. To test this, we determined the sensitivity of Ahrdbd/dbd mice, a genetically modified mouse line that express an AHR protein incapable of binding to AHREs, to dextran sulfate sodium (DSS)-induced colitis. Ahrdbd/dbd mice exhibited more severe symptoms of intestinal inflammation than Ahr+/+ mice. None of the Ahrdbd/dbd mice survived after the 5-day DSS followed by 7-day washout period. By day 6, the Ahrdbd/dbd mice had severe body weight loss, shortening of the colon, higher disease index scores, enlarged spleens, and increased expression of several inflammation genes, including interleukin 1b (Il-1b), Il-6, Il-17, C-x-c motif chemokine ligand 1 (Cxcl1), Cxcl2, Prostaglandin-endoperoxide synthase (Ptgs2), and lipocalin-2. Our findings show that AHR's DNA-binding domain and ability to bind to AHREs are required to reduce inflammation, maintain a healthy intestinal environment, and protect against DSS-induced colitis.
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Affiliation(s)
- Karoline Alvik
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Peng Shao
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S1A8, Canada
| | - David Hutin
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S1A8, Canada
| | - Carolyn Baglole
- Department of Medicine, McGill University, Montreal H4A3J1, Canada.,Department of Pathology, McGill University, Montreal H4A3J1, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal H3G1Y6, Canada
| | - Denis M Grant
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S1A8, Canada
| | - Jason Matthews
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S1A8, Canada
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3
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In-depth analysis of the interactions of various aryl hydrocarbon receptor ligands from a computational perspective. J Mol Graph Model 2023; 118:108339. [PMID: 36183684 DOI: 10.1016/j.jmgm.2022.108339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/01/2022] [Accepted: 09/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that acts as a machinery that controls the expression of many genes, including cytochrome P450 CYP1A1, CYP1A2 and CYP1B1. It plays a principal role in numerous biological and toxicological functions, making it a promising target for developing therapeutic agents. Several novel small molecules targeting the AhR signaling pathway are currently under investigation as antitumor agents. Some have already advanced into clinical trials in patients with various tumors. Activation of AhR by diverse chemicals either endogenous or exogenous is initiated by the binding of these ligands to the PAS-B domain, which modulates AhR functions. There is, however, limited information about how various ligands interact with the PAS-B domain for activating or inhibiting the AhR. To better understand the mode of action of AhR agonists/antagonists. The current work proposes a combination of several computational tools to build dynamical models for the PAS-B domain bound to different ligands in mouse and human. Our findings reveal the essential roles of specific PAS-B residues (e.g., S365, V381& Q383), which mediate the AhR ligand-binding process. Our results also explain how these residues regulate the promiscuity of AhR in accommodating various chemicals in its binding PAS-B ligand-binding pocket.
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Jin J, Wahlang B, Thapa M, Head KZ, Hardesty JE, Srivastava S, Merchant ML, Rai SN, Prough RA, Cave MC. Proteomics and metabolic phenotyping define principal roles for the aryl hydrocarbon receptor in mouse liver. Acta Pharm Sin B 2021; 11:3806-3819. [PMID: 35024308 PMCID: PMC8727924 DOI: 10.1016/j.apsb.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022] Open
Abstract
Dioxin-like molecules have been associated with endocrine disruption and liver disease. To better understand aryl hydrocarbon receptor (AHR) biology, metabolic phenotyping and liver proteomics were performed in mice following ligand-activation or whole-body genetic ablation of this receptor. Male wild type (WT) and Ahr–/– mice (Taconic) were fed a control diet and exposed to 3,3′,4,4′,5-pentachlorobiphenyl (PCB126) (61 nmol/kg by gavage) or vehicle for two weeks. PCB126 increased expression of canonical AHR targets (Cyp1a1 and Cyp1a2) in WT but not Ahr–/–. Knockouts had increased adiposity with decreased glucose tolerance; smaller livers with increased steatosis and perilipin-2; and paradoxically decreased blood lipids. PCB126 was associated with increased hepatic triglycerides in Ahr–/–. The liver proteome was impacted more so by Ahr–/– genotype than ligand-activation, but top gene ontology (GO) processes were similar. The PCB126-associated liver proteome was Ahr-dependent. Ahr principally regulated liver metabolism (e.g., lipids, xenobiotics, organic acids) and bioenergetics, but it also impacted liver endocrine response (e.g., the insulin receptor) and function, including the production of steroids, hepatokines, and pheromone binding proteins. These effects could have been indirectly mediated by interacting transcription factors or microRNAs. The biologic roles of the AHR and its ligands warrant more research in liver metabolic health and disease.
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Key Words
- AHR
- AHR, aryl hydrocarbon receptor
- ALT, alanine transaminase
- ANOVA, analysis of variance
- AST, aspartate transaminase
- AUC, area under the curve
- CAR, constitutive androstane receptor
- CD36, cluster of differentiation 36
- CYP, cytochrome P450
- EPF, enrichment by protein function
- Endocrine disruption
- Environmental liver disease
- FDR, false discovery rate
- FGF21, fibroblast growth factor 21
- GCR, glucocorticoid receptor
- GO, gene ontology
- H&E, hematoxylin-eosin
- HDL, high-density lipoprotein
- HFD, high fat diet
- IGF1, insulin-like growth factor 1
- IL-6, interleukin 6
- IPF, interaction by protein function
- LDL, low-density lipoprotein
- MCP-1, monocyte chemoattractant protein-1
- MUP, major urinary protein
- NAFLD, non-alcoholic fatty liver disease
- NFKBIA, nuclear factor kappa-inhibitor alpha
- Nonalcoholic fatty liver disease
- PAI-1, plasminogen activator inhibitor-1
- PCB, polychlorinated biphenyl
- PCB126
- PLIN2, perilipin-2
- PNPLA3, patatin-like phospholipase domain-containing protein 3
- PPARα, peroxisome proliferator-activated receptor alpha
- PXR, pregnane-xenobiotic receptor
- Perilipin-2
- Pheromones
- SGK1, serum/glucocorticoid regulated kinase
- TAFLD, toxicant-associated fatty liver disease
- TASH, toxicant-associated steatohepatitis
- TAT, tyrosine aminotransferase
- TMT, tandem mass tag
- VLDL, very low-density lipoprotein
- WT, wild type
- ZFP125, zinc finger protein 125
- miR, microRNA
- nHDLc, non-HDL cholesterol
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Vazquez-Rivera E, Rojas B, Parrott JC, Shen AL, Xing Y, Carney PR, Bradfield CA. The aryl hydrocarbon receptor as a model PAS sensor. Toxicol Rep 2021; 9:1-11. [PMID: 34950569 PMCID: PMC8671103 DOI: 10.1016/j.toxrep.2021.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins containing PER-ARNT-SIM (PAS) domains are commonly associated with environmental adaptation in a variety of organisms. The PAS domain is found in proteins throughout Archaea, Bacteria, and Eukarya and often binds small-molecules, supports protein-protein interactions, and transduces input signals to mediate an adaptive physiological response. Signaling events mediated by PAS sensors can occur through induced phosphorelays or genomic events that are often dependent upon PAS domain interactions. In this perspective, we briefly discuss the diversity of PAS domain containing proteins, with particular emphasis on the prototype member, the aryl hydrocarbon receptor (AHR). This ligand-activated transcription factor acts as a sensor of the chemical environment in humans and many chordates. We conclude with the idea that since mammalian PAS proteins often act through PAS-PAS dimers, undocumented interactions of this type may link biological processes that we currently think of as independent. To support this idea, we present a framework to guide future experiments aimed at fully elucidating the spectrum of PAS-PAS interactions with an eye towards understanding how they might influence environmental sensing in human and wildlife populations.
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Affiliation(s)
- Emmanuel Vazquez-Rivera
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Brenda Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Jessica C. Parrott
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Anna L. Shen
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Yongna Xing
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Patrick R. Carney
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Christopher A. Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
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6
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Rubinstein CD, McLean DT, Lehman BP, Meudt JJ, Schomberg DT, Krentz KJ, Reichert JL, Meyer MB, Adams M, Konsitzke CM, Shanmuganayagam D. Assessment of Mosaicism and Detection of Cryptic Alleles in CRISPR/Cas9-Engineered Neurofibromatosis Type 1 and TP53 Mutant Porcine Models Reveals Overlooked Challenges in Precision Modeling of Human Diseases. Front Genet 2021; 12:721045. [PMID: 34630515 PMCID: PMC8495252 DOI: 10.3389/fgene.2021.721045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Genome editing in pigs has been made efficient, practical, and economically viable by the CRISPR/Cas9 platform, representing a promising new era in translational modeling of human disease for research and preclinical development of therapies and devices. Porcine embryo microinjection provides a universally available, efficient option over somatic-cell nuclear transfer, but requires that critical considerations be made in genotypic validation of the models that routinely go unaddressed. Accurate validation of genotypes is especially important when modeling genetic disorders, such as neurofibromatosis type 1 (NF1) that exhibits complex genotype–phenotypic relationships. NF1, an autosomal dominant disorder, is particularly hard to model as it manifests very differently across patients, and even within families, with over 3,000 disease-associated mutations of the neurofibromin 1 (NF1) gene identified. The precise nature of the mutations plays a role in the complex phenotypic presentation of the disorder that includes benign and malignant peripheral and central nervous system tumors, a variety of motor deficits and debilitating cognitive impairments and musculoskeletal, cardiovascular, and gastrointestinal disorders. NF1 can also often involve mutations in passenger genes such as TP53. In this manuscript, we describe the creation of three novel porcine models of NF1 and a model additionally harboring a mutation in TP53 by embryo microinjection of CRISPR/Cas9. We present the challenges encountered in validation of genotypes and the methodological strategies developed to counter the hurdles. We present simple options for quantifying level of mosaicism: a quantitative method (targeted amplicon sequencing) for small edits such as SNPs and indels and a semiquantitative method (competitive PCR) for large edits. Characterization of mosaicism allowed for strategic selection of founder pigs for rapid, economical expansion of genetically defined lines. We also present commonly observed unexpected DNA repair products (i.e., structural variants or cryptic alleles) that are refractory to PCR amplification and thus evade detection. We present the use of copy number variance assays to overcome hurdles in detecting cryptic alleles. The report provides a framework for genotypic validation of porcine models created by embryo microinjection and the expansion of lines in an efficient manner.
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Affiliation(s)
| | - Dalton T McLean
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Dominic T Schomberg
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kathy J Krentz
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jamie L Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Charles M Konsitzke
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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7
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Abstract
The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that is a member of the PER-ARNT-SIM superfamily of environmental sensors. This receptor has been a molecule of interest for many years in the field of toxicology, as it was originally discovered to mediate the toxic effects of certain environmental pollutants like benzo(a)pyrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin. While all animals express this protein, there is naturally occurring variability in receptor size and responsiveness to ligand. This naturally occurring variation, particularly in mice, has been an essential tool in the discovery and early characterization of the AHR. Genetic models including congenic mice and induced mutations at the Ahr locus have proven invaluable in further understanding the role of the AHR in adaptive metabolism and TCDD-induced toxicity. The creation and examination of Ahr null mice revealed an important physiological role for the AHR in vascular and hepatic development and mediation of the immune system. In this review, we attempt to provide an overview to many of the AHR models that have aided in the understanding of AHR biology thus far. We describe the naturally occurring polymorphisms, congenic models, induced mutations at the Ahr locus and at the binding partner Ah Receptor Nuclear Translocator and chaperone, Ah receptor associated 9 loci in mice, with a brief description of naturally occurring and induced mutations in rats.
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Affiliation(s)
- Rachel H Wilson
- Molecular and Environmental Toxicology Center, University of Wisconsin, Madison, WI, USA.,Department of Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Christopher A Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin, Madison, WI, USA.,Department of Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.,Biotechnology Center, University of Wisconsin, Madison, WI, USA
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