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Ho MF, Zhang C, Moon I, Biernacka J, Coombes B, Ngo Q, Skillon C, Skime M, Oesterle T, Croarkin PE, Karpyak VM, Li H, Weinshilboum RM. Epigenetic regulation of GABA catabolism in iPSC-derived neurons: The molecular links between FGF21 and histone methylation. Mol Metab 2023; 77:101798. [PMID: 37689244 PMCID: PMC10514449 DOI: 10.1016/j.molmet.2023.101798] [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: 04/26/2023] [Revised: 06/27/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023] Open
Abstract
OBJECTIVE Fibroblast growth factor 21 (FGF21) analogs have been tested as potential therapeutics for substance use disorders. Prior research suggests that FGF21 administration might affect alcohol consumption and reward behaviors. Our recent report showed that plasma FGF21 levels were positively correlated with alcohol use in patients with alcohol use disorder (AUD). FGF21 has a short half-life (0.5-2 h) and crosses the blood-brain barrier. Therefore, we set out to identify molecular mechanisms for both the naïve form of FGF21 and a long-acting FGF21 molecule (PF-05231023) in induced pluripotent stem cell (iPSC)-derived forebrain neurons. METHODS We performed RNA-seq in iPSC-derived forebrain neurons treated with naïve FGF21 or PF-05231023 at physiologically relevant concentrations. We obtained plasma levels of FGF21 and GABA from our previous AUD clinical trial (n = 442). We performed ELISA for FGF21 in both iPSC-derived forebrain neurons and forebrain organoids. We determined protein interactions using co-immunoprecipitation. Finally, we applied ChIP assays to confirm the occupancy of REST, EZH2 and H3K27me3 by FGF21 using iPSC-derived forebrain neurons with and without drug exposure. RESULTS We identified 4701 and 1956 differentially expressed genes in response to naïve FGF21 or PF-05231023, respectively (FDR < 0.05). Notably, 974 differentially expressed genes overlapped between treatment with naïve FGF21 and PF-05231023. REST was the most important upstream regulator of differentially expressed genes. The GABAergic synapse pathway was the most significant pathway identified using the overlapping genes. We also observed a significant positive correlation between plasma FGF21 and GABA concentrations in AUD patients. In parallel, FGF21 and PF-05231023 significantly induced GABA levels in iPSC-derived neurons. Finally, functional genomics studies showed a drug-dependent occupancy of REST, EZH2, and H3K27me3 in the promoter regions of genes involved in GABA catabolism which resulted in transcriptional repression. CONCLUSIONS Our results highlight a significant role in the epigenetic regulation of genes involved in GABA catabolism related to FGF21 action. (The ClinicalTrials.gov Identifier: NCT00662571).
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Affiliation(s)
- Ming-Fen Ho
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
| | - Cheng Zhang
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Irene Moon
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Joanna Biernacka
- Division of Computational Biology, Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Brandon Coombes
- Division of Computational Biology, Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Quyen Ngo
- Hazelden Betty Ford Foundation, Center City, MN, USA
| | | | - Michelle Skime
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Tyler Oesterle
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Paul E Croarkin
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Victor M Karpyak
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Richard M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
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Huifang L, Jie G, Yi F. Neuro-immune-endocrine mechanisms with poor adherence to aromatase inhibitor therapy in breast cancer. Front Oncol 2022; 12:1054086. [PMID: 36578931 PMCID: PMC9791186 DOI: 10.3389/fonc.2022.1054086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
As the most commonly used endocrine therapy regimen for patients with hormone receptor-positive (HR+) breast cancer (BC) at present, aromatase inhibitors (AIs) reduce the risk of localized and distant recurrence, contralateral BC and secondary cancer, and prolong disease-free survival. Clinical data show that poor adherence during AI treatment is mainly attributed to muscle and joint pain, fatigue, anxiety, depression and sleep disturbances during treatment. The rapid decline of estrogen caused by AIs in a short period of time enhances sympathetic activity, activates T cells in the body, produces inflammatory factors such as tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ) and interleukin (IL)-17A, and promotes the occurrence of inflammation and bone loss. This article reviewed the mechanism of poor dependence on AIs in BC patients from the neuro-immuno-endocrine (NIE) perspective and provided clues for clinical intervention against poor adherence.
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Affiliation(s)
- Li Huifang
- Department of Anesthesiology, Peking University People’s Hospital, Beijing, China
| | - Gao Jie
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Feng Yi
- Department of Anesthesiology, Peking University People’s Hospital, Beijing, China,*Correspondence: Feng Yi,
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Schneider KM, Kim J, Bahnsen K, Heuckeroth RO, Thaiss CA. Environmental perception and control of gastrointestinal immunity by the enteric nervous system. Trends Mol Med 2022; 28:989-1005. [PMID: 36208986 DOI: 10.1016/j.molmed.2022.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/25/2022] [Accepted: 09/07/2022] [Indexed: 12/12/2022]
Abstract
The enteric nervous system (ENS) forms a versatile sensory system along the gastrointestinal tract that interacts with most cell types in the bowel. Herein, we portray host-environment interactions at the intestinal mucosal surface through the lens of the enteric nervous system. We describe local cellular interactions as well as long-range circuits between the enteric, central, and peripheral nervous systems. Additionally, we discuss recently discovered mechanisms by which enteric neurons and glia respond to biotic and abiotic environmental changes and how they regulate intestinal immunity and inflammation. The enteric nervous system emerges as an integrative sensory system with manifold immunoregulatory functions under both homeostatic and pathophysiological conditions.
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Affiliation(s)
- Kai Markus Schneider
- Microbiology Department, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, PA, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Jihee Kim
- Microbiology Department, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, PA, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Klaas Bahnsen
- Microbiology Department, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, PA, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Robert O Heuckeroth
- Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph A Thaiss
- Microbiology Department, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, PA, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, PA, USA.
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Ho MF, Zhang C, Moon I, Coombes BJ, Biernacka J, Skime M, Choi DS, Croarkin PE, Frye MA, Ngo Q, Skillon C, Oesterle TS, Karpyak VM, Li H, Weinshilboum RM. Plasma TNFSF10 levels associated with acamprosate treatment response in patients with alcohol use disorder. Front Pharmacol 2022; 13:986238. [PMID: 36120372 PMCID: PMC9475292 DOI: 10.3389/fphar.2022.986238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Acamprosate is an anti-craving drug used in alcohol use disorder (AUD) pharmacotherapy. However, only a subset of patients achieves optimal treatment outcomes. The identification of predictive biomarkers of acamprosate treatment response in patients with AUD would be a substantial advance in addiction medicine. We designed this study to use proteomics data as a quantitative biological trait as a step toward identifying inflammatory modulators that might be associated with acamprosate treatment outcomes. The NIAAA-funded Mayo Clinic Center for the Individualized Treatment of Alcoholism study had previously recruited 442 AUD patients who received 3 months of acamprosate treatment. However, only 267 subjects returned for the 3-month follow-up visit and, as a result, had treatment outcome information available. Baseline alcohol craving intensity was the most significant predictor of acamprosate treatment outcomes. We performed plasma proteomics using the Olink target 96 inflammation panel and identified that baseline plasma TNF superfamily member 10 (TNFSF10) concentration was associated with alcohol craving intensity and variation in acamprosate treatment outcomes among AUD patients. We also performed RNA sequencing using baseline peripheral blood mononuclear cells from AUD patients with known acamprosate treatment outcomes which revealed that inflammation-related pathways were highly associated with relapse to alcohol use during the 3 months of acamprosate treatment. These observations represent an important step toward advancing our understanding of the pathophysiology of AUD and molecular mechanisms associated with acamprosate treatment response. In conclusion, applying omics-based approaches may be a practical approach for identifying biologic markers that could potentially predict alcohol craving intensity and acamprosate treatment response.
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Affiliation(s)
- Ming-Fen Ho
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Irene Moon
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Brandon J. Coombes
- Division of Computational Biology, Quantitative Health Sciences, Rochester, MN, United States
| | - Joanna Biernacka
- Division of Computational Biology, Quantitative Health Sciences, Rochester, MN, United States
| | - Michelle Skime
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Doo-Sup Choi
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Paul E. Croarkin
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Quyen Ngo
- Hazelden Betty Ford Foundation, Mayo Clinic, Center City, MN, United States
| | - Cedric Skillon
- Hazelden Betty Ford Foundation, Mayo Clinic, Center City, MN, United States
| | - Tyler S. Oesterle
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Victor M. Karpyak
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
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Ma L, Geng J, Chen W, Qin M, Wang L, Zeng Y. Effects of TLR9/NF-κB on oxidative stress and inflammation in IPEC-J2 cells. Genes Genomics 2022; 44:1149-1158. [PMID: 35900696 DOI: 10.1007/s13258-022-01271-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/10/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Oxidative stress is one of the most important factors affecting large-scale breeding, especially the performance of pigs. Oxidative stress plays a role by affecting various genes in pigs, which can cause serious body damage, functional degradation and reduce production performance. OBJECTIVE The purpose of this study was to investigate the effect of Toll like receptor 9 (TLR9) pathway on IPEC-J2 cells under oxidative stress and to provide reference for the growth development of Dapulian pigs. METHODS In this study, Diquat was used as a source of oxidative stress to study the effects on Dapulian pigs by detecting relevant indicators. Then the IPEC-J2 cells were selected to verify the TLR9 signaling pathway in oxidative stress. RESULTS Compared with the control group, superoxide dismutase (SOD) in experimental group decreased significantly, malondialdehyde (MDA) was significantly increased, accompanied by inflammatory reaction, and inflammatory factors were significantly increased in the experimental group. Oxidative stress model was constructed by H2O2 incubating IPEC-J2 cells. The interference and overexpression vectors of TLR9 and myeloid differentiation primary response protein 88 (MyD88) were constructed to detect the activity of antioxidant enzymes and related proteins. The results showed that overexpression of TLR9 enhanced the activity of antioxidant enzymes, decreased the secretion of inflammatory factors, and decreased the activity of MDA,reactive oxygen species (ROS); the results were opposite after TLR9 interference. This study also showed that H2O2 can activate the nuclear factor-κB (NF-κB) pathway and promote the translocation of NF-κB into the nucleus. After co-transfection with TLR9 and MyD88, the results showed that TLR9 regulated the expression of NF-κB through MyD88. CONCLUSION The study showed that TLR9 pathway had a significant positive effect on antioxidant.
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Affiliation(s)
- Lixia Ma
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an City, 271018, Shandong Province, China
| | - Jinhong Geng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an City, 271018, Shandong Province, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an City, 271018, Shandong Province, China
| | - Ming Qin
- Institute of Animal Science and Veterinary Medicine, Yantai Academy of Agricultural Sciences, Yantai City, 265599, Shandong Province, China
| | - Lixue Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an City, 271018, Shandong Province, China
| | - Yongqing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an City, 271018, Shandong Province, China.
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Chen X, Xu J, Zeng F, Yang C, Sun W, Yu T, Zhang H, Li Y. Inferring Cell Subtypes and LncRNA Function by a Cell-Specific CeRNA Network in Breast Cancer. Front Oncol 2021; 11:656675. [PMID: 33987091 PMCID: PMC8111082 DOI: 10.3389/fonc.2021.656675] [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: 01/21/2021] [Accepted: 03/30/2021] [Indexed: 12/11/2022] Open
Abstract
Single-cell RNA sequencing is a powerful tool to explore the heterogeneity of breast cancer. The identification of the cell subtype that responds to estrogen has profound significance in breast cancer research and treatment. The transcriptional regulation of estrogen is an intricate network involving crosstalk between protein-coding and non-coding RNAs, which is still largely unknown, particularly at the single cell level. Therefore, we proposed a novel strategy to specify cell subtypes based on a cell-specific ceRNA network (CCN). The CCN was constructed by integrating a cell-specific RNA-RNA co-expression network (RCN) with an existing ceRNA network. The cell-specific RCN was built based on single cell expression profiles with predefined reference cells. Heterogeneous cell subtypes were inferred by enriching RNAs in CCN to the estrogen response hallmark. Edge biomarkers were identified in the early estrogen response subtype. Topological analysis revealed that NEAT1 was a hub lncRNA for the early response subtype, and its ceRNAs could predict patient survival. Another hub lncRNA, DLEU2, could potentially be involved in GPCR signaling, based on CCN. The CCN method that we proposed here facilitates the inference of cell subtypes from a network perspective and explores the function of hub lncRNAs, which are promising targets for RNA-based therapeutics.
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Affiliation(s)
- Xin Chen
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Jing Xu
- Department of Oncology, Changhai Hospital, The Naval Military Medical University, Shanghai, China
| | - Feng Zeng
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Chao Yang
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Weijun Sun
- School of Automation, Guangdong University of Technology, Guangzhou, China.,Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Tao Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haokun Zhang
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Yan Li
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
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7
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Zayas J, Qin S, Yu J, Ingle JN, Wang L. Functional genomics based on germline genome-wide association studies of endocrine therapy for breast cancer. Pharmacogenomics 2020; 21:615-625. [PMID: 32539536 DOI: 10.2217/pgs-2019-0191] [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] [Indexed: 11/21/2022] Open
Abstract
Breast cancer is the most common invasive cancer in women worldwide. Functional follow-up of breast cancer genome-wide association studies has led to the discovery of genes that regulate endocrine therapy response in a SNP- and drug-dependent manner. Here, we will present four examples in which functional genomic studies from breast cancer clinical trials led to novel pharmacogenomic insights and molecular mechanisms of selective estrogen receptor modulators and aromatase inhibitors. The approach utilized for studying genetic variability described in this review offers substantial potential for meaningful discoveries that move the field toward precision medicine for patients.
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Affiliation(s)
- Jacqueline Zayas
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine & Mayo Clinic Medical Scientist Training Program, Rochester, MN 55905, USA
| | - Sisi Qin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - James N Ingle
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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Neavin DR, Lee JH, Liu D, Ye Z, Li H, Wang L, Ordog T, Weinshilboum RM. Single Nucleotide Polymorphisms at a Distance from Aryl Hydrocarbon Receptor (AHR) Binding Sites Influence AHR Ligand-Dependent Gene Expression. Drug Metab Dispos 2019; 47:983-994. [PMID: 31292129 PMCID: PMC7184190 DOI: 10.1124/dmd.119.087312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/07/2019] [Indexed: 12/17/2022] Open
Abstract
Greater than 90% of significant genome-wide association study (GWAS) single-nucleotide polymorphisms (SNPs) are in noncoding regions of the genome, but only 25.6% are known expression quantitative trait loci (eQTLs). Therefore, the function of many significant GWAS SNPs remains unclear. We have identified a novel type of eQTL for which SNPs distant from ligand-activated transcription factor (TF) binding sites can alter target gene expression in a SNP genotype-by-ligand–dependent fashion that we refer to as pharmacogenomic eQTLs (PGx-eQTLs)—loci that may have important pharmacotherapeutic implications. In the present study, we integrated chromatin immunoprecipitation-seq with RNA-seq and SNP genotype data for a panel of lymphoblastoid cell lines to identify 10 novel cis PGx-eQTLs dependent on the ligand-activated TF aryl hydrocarbon receptor (AHR)—a critical environmental sensor for xenobiotic (drug) and immune response. Those 10 cis PGx-eQTLs were eQTLs only after AHR ligand treatment, even though the SNPs did not create/destroy an AHR response element—the DNA sequence motif recognized and bound by AHR. Additional functional studies in multiple cell lines demonstrated that some cis PGx-eQTLs are functional in multiple cell types, whereas others displayed SNP-by-ligand–dependent effects in just one cell type. Furthermore, four of those cis PGx-eQTLs had previously been associated with clinical phenotypes, indicating that those loci might have the potential to inform clinical decisions. Therefore, SNPs across the genome that are distant from TF binding sites for ligand-activated TFs might function as PGx-eQTLs and, as a result, might have important clinical implications for interindividual variation in drug response.
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Affiliation(s)
- Drew R Neavin
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Jeong-Heon Lee
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Zhenqing Ye
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Hu Li
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Tamas Ordog
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
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Wang W, Aweya JJ, Su H, Zhao X, Zhong M, Zhang Y. Identification and immune-related analysis of SNPs in Litopenaeus vannamei Toll3 receptor. Immunol Lett 2018; 206:19-27. [PMID: 30550739 DOI: 10.1016/j.imlet.2018.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/15/2018] [Accepted: 12/10/2018] [Indexed: 11/26/2022]
Abstract
Tolls and Toll-like receptors (TLRs), as innate immune-recognition receptors that recognize molecular patterns associated with microbial pathogens, play a critical role in antimicrobial immune responses. Here, we report on single nucleotide polymorphisms (SNPs) of Litopenaeus vannamei Toll3 (LvToll3). Multiple sequence alignment of the L. vannamei Toll3 Leucine rich repeat C-terminal domain (LvToll3-LRR-CT) with other L. vannamei Tolls LRR-CT domains showed 39.23% - 43.96% homology at the nucleic acid level and 20.31% - 30.00% identity at the amino acid level. Analysis of different shrimp tissues by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) revealed that LvToll3-LRR-CT had genetic polymorphisms at both the genomic deoxyribonucleic acid (gDNA) and complementary deoxyribonucleic acid (cDNA) levels. Further, high-throughput sequencing analysis confirmed the presence of 8 non-synonymous SNP (nsSNP) and 1 nsSNPs with frequency greater than 1% at the gDNA level, while 13 nsSNPs and 2 nsSNPs with frequency greater than 1% at the cDNA level. In silico analysis revealed that the α-helix secondary structure and tertiary structure of LvToll3 changed when 3 SNPs (C2039T, T2041C, T2228C) were mutated. Interestingly, 2 novel bands on PCR-DGGE, which were identified as 2 nsSNPs (C2140A, T2186A) were observed following challenge with Streptococcus iniae but not with Vibrio parahaemolyticus or White spot syndrome virus (WSSV). Moreover, the secondary and tertiary structures of LvToll3 changed when the nsSNP T2186A was mutated. The present findings therefore provide novel insight into the molecular basis of shrimp innate immune response to pathogens through the generation of specific SNPs.
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Affiliation(s)
- Wei Wang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Jude Juventus Aweya
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Huimin Su
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Xianliang Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Mingqi Zhong
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China.
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10
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Neavin DR, Liu D, Ray B, Weinshilboum RM. The Role of the Aryl Hydrocarbon Receptor (AHR) in Immune and Inflammatory Diseases. Int J Mol Sci 2018; 19:ijms19123851. [PMID: 30513921 PMCID: PMC6321643 DOI: 10.3390/ijms19123851] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a nuclear receptor that modulates the response to environmental stimuli. It was recognized historically for its role in toxicology but, in recent decades, it has been increasingly recognized as an important modulator of disease—especially for its role in modulating immune and inflammatory responses. AHR has been implicated in many diseases that are driven by immune/inflammatory processes, including major depressive disorder, multiple sclerosis, rheumatoid arthritis, asthma, and allergic responses, among others. The mechanisms by which AHR has been suggested to impact immune/inflammatory diseases include targeted gene expression and altered immune differentiation. It has been suggested that single nucleotide polymorphisms (SNPs) that are near AHR-regulated genes may contribute to AHR-dependent disease mechanisms/pathways. Further, we have found that SNPs that are outside of nuclear receptor binding sites (i.e., outside of AHR response elements (AHREs)) may contribute to AHR-dependent gene regulation in a SNP- and ligand-dependent manner. This review will discuss the evidence and mechanisms of AHR contributions to immune/inflammatory diseases and will consider the possibility that SNPs that are outside of AHR binding sites might contribute to AHR ligand-dependent inter-individual variation in disease pathophysiology and response to pharmacotherapeutics.
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Affiliation(s)
- Drew R Neavin
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55902, USA.
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55902, USA.
| | - Balmiki Ray
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55902, USA.
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55902, USA.
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11
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Ho MF, Lummertz da Rocha E, Zhang C, Ingle JN, Goss PE, Shepherd LE, Kubo M, Wang L, Li H, Weinshilboum RM. TCL1A, a Novel Transcription Factor and a Coregulator of Nuclear Factor κB p65: Single Nucleotide Polymorphism and Estrogen Dependence. J Pharmacol Exp Ther 2018; 365:700-710. [PMID: 29592948 DOI: 10.1124/jpet.118.247718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/19/2018] [Indexed: 01/10/2023] Open
Abstract
T-cell leukemia 1A (TCL1A) single-nucleotide polymorphisms (SNPs) have been associated with aromatase inhibitor-induced musculoskeletal adverse events. We previously demonstrated that TCL1A is inducible by estradiol (E2) and plays a critical role in the regulation of cytokines, chemokines, and Toll-like receptors in a TCL1A SNP genotype and estrogen-dependent fashion. Furthermore, TCLIA SNP-dependent expression phenotypes can be "reversed" by exposure to selective estrogen receptor modulators such as 4-hydroxytamoxifen (4OH-TAM). The present study was designed to comprehensively characterize the role of TCL1A in transcriptional regulation across the genome by performing RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) assays with lymphoblastoid cell lines. RNA-seq identified 357 genes that were regulated in a TCL1A SNP- and E2-dependent fashion with expression patterns that were 4OH-TAM reversible. ChIP-seq for the same cells identified 57 TCL1A binding sites that could be regulated by E2 in a SNP-dependent fashion. Even more striking, nuclear factor-κB (NF-κB) p65 bound to those same DNA regions. In summary, TCL1A is a novel transcription factor with expression that is regulated in a SNP- and E2-dependent fashion-a pattern of expression that can be reversed by 4OH-TAM. Integrated RNA-seq and ChIP-seq results suggest that TCL1A also acts as a transcriptional coregulator with NF-κB p65, an important immune system transcription factor.
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Affiliation(s)
- Ming-Fen Ho
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Edroaldo Lummertz da Rocha
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Cheng Zhang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - James N Ingle
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Paul E Goss
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Lois E Shepherd
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Michiaki Kubo
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Hu Li
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (M.H., E.L.d.R., C.Z., L.W., H.L., R.M.W.), and Division of Medical Oncology, Department of Oncology (J.N.I.), Mayo Clinic, Rochester, Minnesota; Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts (P.E.G.); Canadian Cancer Trials Group, Kingston, Ontario, Canada (L.E.S.); and RIKEN Center for Integrative Medical Science, Yokohama, Japan (M.K.)
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12
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Danger R, Royer PJ, Reboulleau D, Durand E, Loy J, Tissot A, Lacoste P, Roux A, Reynaud-Gaubert M, Gomez C, Kessler R, Mussot S, Dromer C, Brugière O, Mornex JF, Guillemain R, Dahan M, Knoop C, Botturi K, Foureau A, Pison C, Koutsokera A, Nicod LP, Brouard S, Magnan A. Blood Gene Expression Predicts Bronchiolitis Obliterans Syndrome. Front Immunol 2018; 8:1841. [PMID: 29375549 PMCID: PMC5768645 DOI: 10.3389/fimmu.2017.01841] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/05/2017] [Indexed: 12/14/2022] Open
Abstract
Bronchiolitis obliterans syndrome (BOS), the main manifestation of chronic lung allograft dysfunction, leads to poor long-term survival after lung transplantation. Identifying predictors of BOS is essential to prevent the progression of dysfunction before irreversible damage occurs. By using a large set of 107 samples from lung recipients, we performed microarray gene expression profiling of whole blood to identify early biomarkers of BOS, including samples from 49 patients with stable function for at least 3 years, 32 samples collected at least 6 months before BOS diagnosis (prediction group), and 26 samples at or after BOS diagnosis (diagnosis group). An independent set from 25 lung recipients was used for validation by quantitative PCR (13 stables, 11 in the prediction group, and 8 in the diagnosis group). We identified 50 transcripts differentially expressed between stable and BOS recipients. Three genes, namely POU class 2 associating factor 1 (POU2AF1), T-cell leukemia/lymphoma protein 1A (TCL1A), and B cell lymphocyte kinase, were validated as predictive biomarkers of BOS more than 6 months before diagnosis, with areas under the curve of 0.83, 0.77, and 0.78 respectively. These genes allow stratification based on BOS risk (log-rank test p < 0.01) and are not associated with time posttransplantation. This is the first published large-scale gene expression analysis of blood after lung transplantation. The three-gene blood signature could provide clinicians with new tools to improve follow-up and adapt treatment of patients likely to develop BOS.
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Affiliation(s)
- Richard Danger
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Pierre-Joseph Royer
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Damien Reboulleau
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Eugénie Durand
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Jennifer Loy
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Adrien Tissot
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Philippe Lacoste
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Antoine Roux
- Pneumology, Adult Cystic Fibrosis Center and Lung Transplantation Department, Foch Hospital, Suresnes, France.,Universite Versailles Saint-Quentin-en-Yvelines, UPRES EA220, Suresnes, France
| | - Martine Reynaud-Gaubert
- Service de Pneumologie et Transplantation Pulmonaire, CHU Nord de Marseille, Aix-Marseille Université, Marseille, France
| | - Carine Gomez
- Service de Pneumologie et Transplantation Pulmonaire, CHU Nord de Marseille, Aix-Marseille Université, Marseille, France
| | - Romain Kessler
- Groupe de Transplantation Pulmonaire des Hôpitaux universitaires de Strasbourg, Strasbourg, France
| | - Sacha Mussot
- Hôpital Marie Lannelongue, Service de Chirurgie Thoracique, Vasculaire et Transplantation Cardiopulmonaire, Le Plessis Robinson, France
| | | | - Olivier Brugière
- Hôpital Bichat, Service de Pneumologie et Transplantation Pulmonaire, Paris, France
| | | | | | | | | | - Karine Botturi
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Aurore Foureau
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
| | - Christophe Pison
- Clinique Universitaire Pneumologie, Pôle Thorax et Vaisseaux, CHU de Grenoble, Université de Grenoble, INSERM U1055, Grenoble, France
| | - Angela Koutsokera
- Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Laurent P Nicod
- Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Sophie Brouard
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Antoine Magnan
- UMR S 1087 CNRS UMR 6291, l'Institut du Thorax, Université de Nantes, CHU Nantes, Nantes, France
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13
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Wang L, Ingle J, Weinshilboum R. Pharmacogenomic Discovery to Function and Mechanism: Breast Cancer as a Case Study. Clin Pharmacol Ther 2017; 103:243-252. [PMID: 29052219 PMCID: PMC5760458 DOI: 10.1002/cpt.915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/03/2017] [Accepted: 10/07/2017] [Indexed: 12/22/2022]
Abstract
Biomedical research is undergoing rapid change, with the development of a series of analytical omics techniques that are capable of generating Biomedical Big Data. These developments provide an unprecedented opportunity to gain novel insight into disease pathophysiology and mechanisms of drug action and response-but they also present significant challenges. Pharmacogenomics is a discipline within Clinical Pharmacology that has been at the forefront in defining, taking advantage of, and dealing with the opportunities and challenges of this aspect of the Post-Genome Project world. This overview will describe the evolution of germline pharmacogenomic research strategies as we have moved from an era of candidate genes to agnostic genome-wide association studies (GWAS) coupled with the functional and mechanistic pursuit of GWAS signals. Germline pharmacogenomic studies of breast cancer endocrine therapy will be used to illustrate research strategies that are being applied broadly to omics studies of drug response phenotypes.
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Affiliation(s)
- Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - James Ingle
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Richard Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
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14
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Liu D, Ho MF, Schaid DJ, Scherer SE, Kalari K, Liu M, Biernacka J, Yee V, Evans J, Carlson E, Goetz MP, Kubo M, Wickerham DL, Wang L, Ingle JN, Weinshilboum RM. Breast cancer chemoprevention pharmacogenomics: Deep sequencing and functional genomics of the ZNF423 and CTSO genes. NPJ Breast Cancer 2017; 3:30. [PMID: 28856246 PMCID: PMC5566425 DOI: 10.1038/s41523-017-0036-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 07/01/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022] Open
Abstract
Our previous GWAS using samples from the NSABP P-1 and P-2 selective estrogen receptor modulator (SERM) breast cancer prevention trials identified SNPs in ZNF423 and near CTSO that were associated with breast cancer risk during SERM chemoprevention. We have now performed Next Generation DNA sequencing to identify additional SNPs that might contribute to breast cancer risk and to extend our observation that SNPs located hundreds of bp from estrogen response elements (EREs) can alter estrogen receptor alpha (ERα) binding in a SERM-dependent fashion. Our study utilized a nested case-control cohort selected from patients enrolled in the original GWAS, with 199 cases who developed breast cancer during SERM therapy and 201 matched controls who did not. We resequenced approximately 500 kb across both ZNF423 and CTSO, followed by functional genomic studies. We identified 4079 SNPs across ZNF423 and 3876 across CTSO, with 9 SNPs in ZNF423 and 12 in CTSO with p < 1E-02 that were within 500 bp of an ERE motif. The rs746157 (p = 8.44E-04) and rs12918288 SNPs (p = 3.43E-03) in intron 5 of ZNF423, were in linkage equilibrium and were associated with alterations in ER-binding to an ERE motif distant from these SNPs. We also studied all nonsynonymous SNPs in both genes and observed that one nsSNP in ZNF423 displayed decreased protein expression. In conclusion, we identified additional functional SNPs in ZNF423 that were associated with SNP and SERM-dependent alternations in ER binding and transcriptional regulation for an ERE at a distance from the SNPs, thus providing novel insight into mechanisms of SERM effect.
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Affiliation(s)
- Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Ming-Fen Ho
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Krishna Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Mohan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Joanna Biernacka
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Vivien Yee
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH USA
| | - Jared Evans
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Erin Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Matthew P Goetz
- Division of Medical Oncology, Mayo Clinic, Rochester, MN USA
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - D Lawrence Wickerham
- Section of Cancer Genetics and Prevention, Allegheny General Hospital and the National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, PA USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - James N Ingle
- Division of Medical Oncology, Mayo Clinic, Rochester, MN USA
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
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15
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Ho MF, Weinshilboum RM. Immune Mediator Pharmacogenomics: TCL1A SNPs and Estrogen-Dependent Regulation of Inflammation. JOURNAL OF NATURE AND SCIENCE 2017; 3:e416. [PMID: 28868359 PMCID: PMC5578609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This review describes the important functional implications of TCL1A single nucleotide polymorphisms (SNPs) discovered during pharmacogenomic studies of aromatase inhibitor-induced musculoskeletal adverse events that were subsequently shown to influence the expression of cytokines, chemokines, toll-like receptors (TLR), and NF-κB in a SNP and estrogen-dependent fashion. Functional genomic studies of these SNPs led to the discovery of novel mechanisms that may contribute to disease pathophysiology and which may also increase our understanding of pharmacogenomic aspects of regulation of the expression of inflammatory mediators. Specifically, TCL1A expression was induced by estrogens in a SNP-dependent fashion, resulting in downstream effects on the expression of immune mediators that included IL17RA, IL17A, CCR6, CCL20 TLR2, TLR7, TLR9, TLR10 and NF-κB. These observations have potential implications for inflammatory diseases such as rheumatoid arthritis-a disease for which two thirds of patients are women. Strikingly, this genomic phenomenon could be "reversed" by estrogen receptor antagonist treatment-once again in a SNP-dependent, i.e., in a pharmacogenomic fashion. Specifically, differential SNP-dependent effects on estrogen receptor binding to estrogen response elements before and after estrogen receptor blockade might be associated with mechanisms underlying the SNP genotype and estrogen-dependent regulation of TCL1A and the expression of downstream immune mediators. Furthermore, this SNP and estrogen-dependent phenotypic response could be "reversed" by SERM treatment. These observations could potentially open the way to understand, predict and even pharmacologically manipulate the expression of selected immune mediators in a SNP-dependent fashion.
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Affiliation(s)
- Ming-Fen Ho
- Correspondence and reprint request to Ming-Fen Ho, Ph.D. Mayo Clinic 200 First Street S.W., Rochester, MN 55905, USA.
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