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Baker Frost D, da Silveira W, Hazard ES, Atanelishvili I, Wilson RC, Flume J, Day KL, Oates JC, Bogatkevich GS, Feghali-Bostwick C, Hardiman G, Ramos PS. Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis. Genes (Basel) 2021; 12:129. [PMID: 33498390 PMCID: PMC7909410 DOI: 10.3390/genes12020129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/20/2023] Open
Abstract
The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Reduced representation bisulfite sequencing (RRBS) was performed on primary dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. The dermal fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions while depleted in 5' UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. Gene set enrichment analysis (GSEA) and gene ontology (GO) analyses revealed an enrichment of pathways related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes' overexpression in patients but underexpression for lncRNA MGC12916. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.
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Affiliation(s)
- DeAnna Baker Frost
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Willian da Silveira
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - E. Starr Hazard
- Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Ilia Atanelishvili
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Robert C. Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Jonathan Flume
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | | | - James C. Oates
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Rheumatology Section, Ralph H. Johnson VA Medical Center, Charleston, SC 29425, USA
| | - Galina S. Bogatkevich
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Carol Feghali-Bostwick
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Gary Hardiman
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - Paula S. Ramos
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
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2
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Toomer KA, Yu M, Fulmer D, Guo L, Moore KS, Moore R, Drayton KD, Glover J, Peterson N, Ramos-Ortiz S, Drohan A, Catching BJ, Stairley R, Wessels A, Lipschutz JH, Delling FN, Jeunemaitre X, Dina C, Collins RL, Brand H, Talkowski ME, Del Monte F, Mukherjee R, Awgulewitsch A, Body S, Hardiman G, Hazard ES, da Silveira WA, Wang B, Leyne M, Durst R, Markwald RR, Le Scouarnec S, Hagege A, Le Tourneau T, Kohl P, Rog-Zielinska EA, Ellinor PT, Levine RA, Milan DJ, Schott JJ, Bouatia-Naji N, Slaugenhaupt SA, Norris RA. Primary cilia defects causing mitral valve prolapse. Sci Transl Med 2020; 11:11/493/eaax0290. [PMID: 31118289 PMCID: PMC7331025 DOI: 10.1126/scitranslmed.aax0290] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022]
Abstract
Mitral valve prolapse (MVP) affects 1 in 40 people and is the most common indication for mitral valve surgery. MVP can cause arrhythmias, heart failure, and sudden cardiac death, and to date, the causes of this disease are poorly understood. We now demonstrate that defects in primary cilia genes and their regulated pathways can cause MVP in familial and sporadic nonsyndromic MVP cases. Our expression studies and genetic ablation experiments confirmed a role for primary cilia in regulating ECM deposition during cardiac development. Loss of primary cilia during development resulted in progressive myxomatous degeneration and profound mitral valve pathology in the adult setting. Analysis of a large family with inherited, autosomal dominant nonsyndromic MVP identified a deleterious missense mutation in a cilia gene, DZIP1 A mouse model harboring this variant confirmed the pathogenicity of this mutation and revealed impaired ciliogenesis during development, which progressed to adult myxomatous valve disease and functional MVP. Relevance of primary cilia in common forms of MVP was tested using pathway enrichment in a large population of patients with MVP and controls from previously generated genome-wide association studies (GWAS), which confirmed the involvement of primary cilia genes in MVP. Together, our studies establish a developmental basis for MVP through altered cilia-dependent regulation of ECM and suggest that defects in primary cilia genes can be causative to disease phenotype in some patients with MVP.
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Affiliation(s)
- Katelynn A Toomer
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Mengyao Yu
- INSERM, UMR-970, Paris Cardiovascular Research Center, 75015 Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Faculty of Medicine, 75006 Paris, France
| | - Diana Fulmer
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Lilong Guo
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Kelsey S Moore
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Reece Moore
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Ka'la D Drayton
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Janiece Glover
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Neal Peterson
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Sandra Ramos-Ortiz
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Alex Drohan
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Breiona J Catching
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Rebecca Stairley
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Andy Wessels
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Joshua H Lipschutz
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.,Department of Medicine, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29401, USA
| | - Francesca N Delling
- Department of Medicine, Division of Cardiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xavier Jeunemaitre
- INSERM, UMR-970, Paris Cardiovascular Research Center, 75015 Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Faculty of Medicine, 75006 Paris, France.,Assistance Publique-Hôpitaux de Paris, Département de Génétique, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Christian Dina
- INSERM, CNRS, Univ Nantes, L'Institut du Thorax, Nantes 44093, France.,CHU Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes 44093, France
| | - Ryan L Collins
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital Research Institute, Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Harrison Brand
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital Research Institute, Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital Research Institute, Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Federica Del Monte
- Gazes Cardiac Research Institute, Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Rupak Mukherjee
- Gazes Cardiac Research Institute, Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Alexander Awgulewitsch
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | - Simon Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gary Hardiman
- Center for Genomic Medicine, Medical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, SC 29425, USA.,Faculty of Medicine, Health and Life Sciences School of Biological Sciences, Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, Northern Ireland, BT7 1NN, UK
| | - E Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, SC 29425, USA
| | - Willian A da Silveira
- Center for Genomic Medicine, Medical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, SC 29425, USA
| | - Baolin Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Maire Leyne
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital Research Institute, Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Ronen Durst
- Cardiology Division, Hadassah Hebrew University Medical Center, POB 12000, Jerusalem, Israel
| | - Roger R Markwald
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA
| | | | - Albert Hagege
- INSERM, UMR-970, Paris Cardiovascular Research Center, 75015 Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Faculty of Medicine, 75006 Paris, France.,Assistance Publique-Hôpitaux de Paris, Department of Cardiology, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Thierry Le Tourneau
- INSERM, CNRS, Univ Nantes, L'Institut du Thorax, Nantes 44093, France.,CHU Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes 44093, France
| | - Peter Kohl
- University Heart Center Freiburg, Bad Krozingen and Faculty of Medicine of the Albert-Ludwigs University Freiburg, Institute for Experimental Cardiovascular Medicine, Elsässerstr 2Q, 79110 Freiburg, Germany
| | - Eva A Rog-Zielinska
- University Heart Center Freiburg, Bad Krozingen and Faculty of Medicine of the Albert-Ludwigs University Freiburg, Institute for Experimental Cardiovascular Medicine, Elsässerstr 2Q, 79110 Freiburg, Germany
| | - Patrick T Ellinor
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital Research Institute, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Robert A Levine
- Cardiac Ultrasound Laboratory, Cardiology Division, Massachusetts General Hospital Research Institute, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - David J Milan
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital Research Institute, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA.,Leducq Foundation, 265 Franklin Street, Suite 1902, Boston, MA, 02110, USA
| | - Jean-Jacques Schott
- INSERM, CNRS, Univ Nantes, L'Institut du Thorax, Nantes 44093, France.,CHU Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes 44093, France
| | - Nabila Bouatia-Naji
- INSERM, UMR-970, Paris Cardiovascular Research Center, 75015 Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Faculty of Medicine, 75006 Paris, France
| | - Susan A Slaugenhaupt
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital Research Institute, Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Russell A Norris
- Cardiovascular Developmental Biology Center, Department of Regenerative Medicine and Cell Biology, College of Medicine, Children's Research Institute, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA.
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3
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Richards DJ, Li Y, Kerr CM, Yao J, Beeson GC, Coyle RC, Chen X, Jia J, Damon B, Wilson R, Starr Hazard E, Hardiman G, Menick DR, Beeson CC, Yao H, Ye T, Mei Y. Human cardiac organoids for the modelling of myocardial infarction and drug cardiotoxicity. Nat Biomed Eng 2020; 4:446-462. [PMID: 32284552 PMCID: PMC7422941 DOI: 10.1038/s41551-020-0539-4] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/20/2020] [Indexed: 12/27/2022]
Abstract
Environmental factors are the largest contributors to cardiovascular disease. Here we show that cardiac organoids that incorporate an oxygen-diffusion gradient and that are stimulated with the neurotransmitter noradrenaline model the structure of the human heart after myocardial infarction (by mimicking the infarcted, border and remote zones), and recapitulate hallmarks of myocardial infarction (in particular, pathological metabolic shifts, fibrosis and calcium handling) at the transcriptomic, structural and functional levels. We also show that the organoids can model hypoxia-enhanced doxorubicin cardiotoxicity. Human organoids that model diseases with non-genetic pathological factors could help with drug screening and development.
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Affiliation(s)
- Dylan J Richards
- Bioengineering Department, Clemson University, Clemson, SC, USA
- Immunology Translational Sciences, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Yang Li
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - Charles M Kerr
- Molecular Cell Biology and Pathology Program, Medical University of South Carolina, Charleston, SC, USA
| | - Jenny Yao
- Bioengineering Department, Clemson University, Clemson, SC, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Gyda C Beeson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Robert C Coyle
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - Xun Chen
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - Jia Jia
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - Brooke Damon
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - Robert Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - E Starr Hazard
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Gary Hardiman
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA
- Departments of Medicine and Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Donald R Menick
- Division of Cardiology, Department of Medicine, Gazes Cardiac Research Institute, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson Veterans Affairs Medical Center, Medical University of South Carolina, Charleston, SC, USA
| | - Craig C Beeson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Hai Yao
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - Tong Ye
- Bioengineering Department, Clemson University, Clemson, SC, USA.
| | - Ying Mei
- Bioengineering Department, Clemson University, Clemson, SC, USA.
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
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4
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Zimmerman KA, Huang J, He L, Revell DZ, Li Z, Hsu JS, Fitzgibbon WR, Hazard ES, Hardiman G, Mrug M, Bell PD, Yoder BK, Saigusa T. Interferon Regulatory Factor-5 in Resident Macrophage Promotes Polycystic Kidney Disease. ACTA ACUST UNITED AC 2020; 1:179-190. [PMID: 33490963 DOI: 10.34067/kid.0001052019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Autosomal dominant polycystic kidney disease is caused by genetic mutations in PKD1 or PKD2. Macrophages and their associated inflammatory cytokines promote cyst progression; however, transcription factors within macrophages that control cytokine production and cystic disease are unknown. Methods In these studies, we used conditional Pkd1 mice to test the hypothesis that macrophage-localized interferon regulatory factor-5 (IRF5), a transcription factor associated with production of cyst-promoting cytokines (TNFα, IL-6), is required for accelerated cyst progression in a unilateral nephrectomy (1K) model. Analyses of quantitative real-time PCR (qRT-PCR) and flow-cytometry data 3 weeks post nephrectomy, a time point before the onset of severe cystogenesis, indicate an accumulation of inflammatory infiltrating and resident macrophages in 1K Pkd1 mice compared with controls. qRT-PCR data from FACS cells at this time demonstrate that macrophages from 1K Pkd1 mice have increased expression of Irf5 compared with controls. To determine the importance of macrophage-localized Irf5 in cyst progression, we injected scrambled or IRF5 antisense oligonucleotide (ASO) in 1K Pkd1 mice and analyzed the effect on macrophage numbers, cytokine production, and renal cystogenesis 6 weeks post nephrectomy. Results Analyses of qRT-PCR and IRF5 ASO treatment significantly reduced macrophage numbers, Irf5 expression in resident-but not infiltrating-macrophages, and the severity of cystic disease. In addition, IRF5 ASO treatment in 1K Pkd1 mice reduced Il6 expression in resident macrophages, which was correlated with reduced STAT3 phosphorylation and downstream p-STAT3 target gene expression. Conclusions These data suggest that Irf5 promotes inflammatory cytokine production in resident macrophages resulting in accelerated cystogenesis.
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Affiliation(s)
- Kurt A Zimmerman
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jifeng Huang
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lan He
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Dustin Z Revell
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhang Li
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jung-Shan Hsu
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Wayne R Fitzgibbon
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - E Starr Hazard
- Academic Affairs Faculty and Computational Biology Resource Center, Medical University of South Carolina, Charleston, South Carolina
| | - Gary Hardiman
- School of Biological Sciences, Institute for Global Food Security, Queens University Belfast, Belfast, United Kingdom
| | - Michal Mrug
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
| | - P Darwin Bell
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Takamitsu Saigusa
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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5
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Bisese EC, Ciuba CM, Davidson AL, Kaushik A, Mullen SM, Barth JL, Hazard ES, Wilson RC, Hardiman G, Hollis DM. The acute transcriptome response of the midbrain/diencephalon to injury in the adult mummichog (Fundulus heteroclitus). Mol Brain 2019; 12:119. [PMID: 31888716 PMCID: PMC6937918 DOI: 10.1186/s13041-019-0542-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/23/2019] [Indexed: 11/18/2022] Open
Abstract
Adult fish produce new cells throughout their central nervous system during the course of their lives and maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in adult fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received little attention. We sought to examine differential gene expression in the midbrain/diencephalon in response to injury in the adult fish using RNA-seq. Using the mummichog (Fundulus heteroclitus), we administered a mechanical lesion to the midbrain/diencephalon and examined differentially expressed genes (DEGs) at an acute recovery time of 1 h post-injury. Comparisons of whole transcriptomes derived from isolated RNA of intact and injured midbrain/diencephalic tissue identified 404 DEGs with the vast majority being upregulated. Using qPCR, we validated the upregulation of DEGs pim-2-like, syndecan-4-like, and cd83. Based on genes both familiar and novel regarding the adult brain response to injury, these data provide an extensive molecular profile giving insight into a range of cellular processes involved in the injury response of a brain regenerative-capable vertebrate.
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Affiliation(s)
- Eleanor C Bisese
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Chandler M Ciuba
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Amelia L Davidson
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Akanksha Kaushik
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Sabrina M Mullen
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA
| | - Jeremy L Barth
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA
| | - E Starr Hazard
- Computational Biology Resource Center, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA
| | - Robert C Wilson
- Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA.,School of Biological Sciences & Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, BT9 5DL, UK
| | - David M Hollis
- Department of Biology, Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, USA.
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6
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Yoshida A, Bu Y, Qie S, Wrangle J, Camp ER, Hazard ES, Hardiman G, de Leeuw R, Knudsen KE, Diehl JA. SLC36A1-mTORC1 signaling drives acquired resistance to CDK4/6 inhibitors. Sci Adv 2019; 5:eaax6352. [PMID: 31555743 PMCID: PMC6750908 DOI: 10.1126/sciadv.aax6352] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/21/2019] [Indexed: 06/03/2023]
Abstract
The cyclin-dependent kinase 4/6 (CDK4/6) kinase is dysregulated in melanoma, highlighting it as a potential therapeutic target. CDK4/6 inhibitors are being evaluated in trials for melanoma and additional cancers. While beneficial, resistance to therapy is a concern, and the molecular mechanisms of such resistance remain undefined. We demonstrate that reactivation of mammalian target of rapamycin 1 (mTORC1) signaling through increased expression of the amino acid transporter, solute carrier family 36 member 1 (SLC36A1), drives resistance to CDK4/6 inhibitors. Increased expression of SLC36A1 reflects two distinct mechanisms: (i) Rb loss, which drives SLC36A1 via reduced suppression of E2f; (ii) fragile X mental retardation syndrome-associated protein 1 overexpression, which promotes SLC36A1 translation and subsequently mTORC1. Last, we demonstrate that a combination of a CDK4/6 inhibitor with an mTORC1 inhibitor has increased therapeutic efficacy in vivo, providing an important avenue for improved therapeutic intervention in aggressive melanoma.
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Affiliation(s)
- Akihiro Yoshida
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yiwen Bu
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shuo Qie
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - John Wrangle
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - E. Ramsay Camp
- Department of Surgery, Medical University of South Carolina, Charleston, SC 29425, USA
| | - E. Starr Hazard
- Center for Genomic Medicine Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Center for Genomic Medicine Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Renée de Leeuw
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Karen E. Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - J. Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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7
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da Silveira WA, Hazard ES, Chung D, Hardiman G. Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses. Methods Mol Biol 2019; 1908:185-204. [PMID: 30649729 DOI: 10.1007/978-1-4939-9004-7_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNAseq is a powerful technique enabling global profiles of transcriptomes in healthy and diseased states. In this chapter we review pipelines to analyze the data generated by sequencing RNA, from raw data to a system level analysis. We first give an overview of workflow to generate mapped reads from FASTQ files, including quality control of FASTQ, filtering and trimming of reads, and alignment of reads to a genome. Then, we compare and contrast three popular options to determine differentially expressed (DE) transcripts (The Tuxedo Pipeline, DESeq2, and Limma/voom). Finally, we examine four tool sets to extrapolate biological meaning from the list of DE genes (Genecards, The Human Protein Atlas, GSEA, and ToppGene). We emphasize the need to ask a concise scientific question and to clearly under stand the strengths and limitations of the methods.
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Affiliation(s)
- Willian A da Silveira
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.,Institute for Global Food Security, Queens University Belfast, Belfast, UK
| | - E Starr Hazard
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.,Library Science and Informatics, Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - Gary Hardiman
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,Department of Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast, BT9 5AG, UK.
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8
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Huff M, da Silveira W, Starr Hazard E, Courtney SM, Renaud L, Hardiman G. Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol. Gen Comp Endocrinol 2019; 271:1-14. [PMID: 30563618 DOI: 10.1016/j.ygcen.2018.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 09/25/2018] [Accepted: 10/23/2018] [Indexed: 01/17/2023]
Abstract
Nonylphenol (NP) arises from the environmental degradation of nonylphenol ethoxylates. It is a ubiquitous environmental contaminant and has been detected at levels up to 167 nM in rivers in the United States. NP is an endocrine disruptor (ED) that can act as an agonist for estrogen receptors. The Adverse Outcome Pathway (AOP) framework defines an adverse outcome as the causal result of a series of molecular initiating events (MIEs) and key events (KEs) that lead to altered phenotypes. This study examined the liver transcriptome after a 21 day exposure to NP and 17β-estradiol (E2) by exploiting the zebrafish (Danio rerio) as a systems toxicology model. The goal of this study was to tease out non-estrogenic genomic signatures associated with NP exposure using DNA microarray and RNA sequencing. Our experimental design included E2 as a positive and potent estrogenic control in order to effectively compare and contrast the 2 compounds. This approach allowed us to identify hepatic transcriptomic perturbations that could serve as MIEs for adverse health outcomes in response to NP. Our results revealed that exposure to NP was associated with differential expression (DE) of genes associated with the development of steatosis, disruption of metabolism, altered immune response, and metabolism of reactive oxygen species, further highlighting NP as a chemical of emerging concern (CEC).
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Affiliation(s)
- Matthew Huff
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC 29415, United States; MS in Biomedical Sciences Program, Medical University of South Carolina, United States
| | - Willian da Silveira
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC 29415, United States; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, United States
| | - E Starr Hazard
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC 29415, United States
| | - Sean M Courtney
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC 29415, United States
| | - Ludivine Renaud
- Department of Medicine, Medical University of South Carolina, United States
| | - Gary Hardiman
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC 29415, United States; Department of Medicine, Medical University of South Carolina, United States; Department of Medicine, University of California San Diego, United States; Department of Public Health Sciences, Medical University of South Carolina, United States; Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, United States; Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
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9
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Renaud L, Agarwal N, Richards DJ, Falcinelli S, Hazard ES, Carnevali O, Hyde J, Hardiman G. Transcriptomic analysis of short-term 17α-ethynylestradiol exposure in two Californian sentinel fish species sardine (Sardinops sagax) and mackerel (Scomber japonicus). Environ Pollut 2019; 244:926-937. [PMID: 30469287 DOI: 10.1016/j.envpol.2018.10.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/24/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are substances which disrupt normal functioning of the endocrine system by interfering with hormone regulated physiological pathways. Aquatic environments provide the ultimate reservoir for many EDCs as they enter rivers and the ocean via effluent discharges and accumulate in sediments. One EDC widely dispersed in municipal wastewater effluent discharges is 17α-ethynylestradiol (EE2), which is one of the most widely prescribed medicines. EE2 is a bio-active estrogen employed in the majority of oral contraceptive pill formulations. As evidence of the health risks posed by EDCs mount, there is an urgent need to improve diagnostic tools for monitoring the effects of pollutants. As the cost of high throughput sequencing (HTS) diminishes, transcriptional profiling of an organism in response to EDC perturbation presents a cost-effective way of screening a wide range of endocrine responses. Coastal pelagic filter feeding fish species analyzed using HTS provide an excellent tool for EDC risk assessment in the marine environment. Unfortunately, there are limited genome sequence data and annotation for many of these species including Pacific sardine (Sardinops sagax) and chub mackerel (Scomber japonicus), which limits the utility of molecular tools such as HTS to interrogate the effects of endocrine disruption. In this study, we carried out RNA sequencing (RNAseq) of liver RNA harvested from wild sardine and mackerel exposed for 5 h under laboratory conditions to a concentration of 12.5 pM EE2 in the tank water. We developed an analytical framework for transcriptomic analyses of species with limited genomic information. EE2 exposure altered expression patterns of key genes involved in important metabolic and physiological processes. The systems approach presented here provides a powerful tool for obtaining a comprehensive picture of endocrine disruption in aquatic organisms.
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Affiliation(s)
- Ludivine Renaud
- Department of Medicine, Nephrology, Medical University of South Carolina, Charleston, SC, USA
| | - Nisha Agarwal
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA, USA
| | | | - Silvia Falcinelli
- Dipartimento di Scienze della Vita e Dell'Ambiente, Università Politecnica della Marche, 60131, Ancona, Italy
| | - E Starr Hazard
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA; Academic Affairs Faculty & Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC, USA
| | - Oliana Carnevali
- Dipartimento di Scienze della Vita e Dell'Ambiente, Università Politecnica della Marche, 60131, Ancona, Italy
| | - John Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Gary Hardiman
- Department of Medicine, Nephrology, Medical University of South Carolina, Charleston, SC, USA; Biomedical Informatics Research Center, San Diego State University, San Diego, CA, USA; MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA; Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC, USA; School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
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10
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Richards DJ, Renaud L, Agarwal N, Starr Hazard E, Hyde J, Hardiman G. De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. Genes (Basel) 2018; 9:genes9110521. [PMID: 30366465 PMCID: PMC6266404 DOI: 10.3390/genes9110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/17/2018] [Indexed: 12/31/2022] Open
Abstract
The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns. The marine environments contain many contaminants of anthropogenic origin that have sufficient similarities to steroid and thyroid hormones, to potentially disrupt normal endocrine physiology in humans, fish, and other animals. An appropriate understanding of the effects of these endocrine disrupting chemicals (EDCs) on forage fish (e.g., sardine, anchovy, mackerel) can lead to significant insight into how these contaminants may affect local ecosystems in addition to their potential impacts on human health. With advancements in molecular tools (e.g., high-throughput sequencing, HTS), a genomics approach offers a robust toolkit to discover putative genetic biomarkers in fish exposed to these chemicals. However, the lack of available sequence information for non-model species has limited the development of these genomic toolkits. Using HTS and de novo assembly technology, the present study aimed to establish, for the first time for Sardinops sagax (Pacific sardine), Scomber japonicas (Pacific chub mackerel) and Pleuronichthys verticalis (hornyhead turbot), a de novo global transcriptome database of the liver, the primary organ involved in detoxification. The assembled transcriptomes provide a foundation for further downstream validation, comparative genomic analysis and biomarker development for future applications in ecotoxicogenomic studies, as well as environmental evaluation (e.g., climate change) and public health safety (e.g., dietary screening).
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Affiliation(s)
- Dylan J Richards
- Bioengineering Department, Clemson University, Charleston, SC 29425, USA.
| | - Ludivine Renaud
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Nisha Agarwal
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
| | - E Starr Hazard
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
- Academic Affairs Faculty & Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - John Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA 92037, USA.
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA.
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
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11
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Shamchuk AL, Blunt BJ, Lyons DD, Wang MQ, Gasheva A, Lewis CR, Tomlin K, Hazard ES, Hardiman G, Tierney KB. Nucleobase-containing compounds evoke behavioural, olfactory, and transcriptional responses in model fishes. Facets (Ott) 2018. [DOI: 10.1139/facets-2017-0101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The sensory system of animals detects a massive and unknown array of chemical cues that evoke a diversity of physiological and behavioural responses. One group of nitrogen-containing carbon ring chemicals—nucleobases—are thought to be involved in numerous behaviours yet have received little attention. We took a top-down approach to examine responses evoked by nucleobases at behavioural, tissue, and gene expression levels. Fish generally avoided nucleobases, and this behaviour, when observed, was driven by purines but not pyrimidines. At the tissue level, olfactory neuron generator potential responses tended to be concentration specific and robust at concentrations lower than amino acid detection ranges. In terms of gene expression, more than 2000 genes were significantly upregulated following nucleobase exposure, some of which were expected (e.g., genes involved in purine binding) and some of which were not (e.g., tubulin-related genes). Humanized RNA pathway analysis showed that we had exposed the animal to a nucleobase. Our data indicate that responses to nucleobase-containing compounds may be highly structure based and are evident from changes in behaviour to mRNA expression. Many of these responses were surprising, and all provide numerous routes for further research endeavour.
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Affiliation(s)
- Angela L. Shamchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brian J. Blunt
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Danielle D. Lyons
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mo Qi Wang
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Anastasia Gasheva
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Carlie R. Lewis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Kirsten Tomlin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - E. Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Library Science and Informatics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gary Hardiman
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Medicine and Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - Keith B. Tierney
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- School of Public Health, University of Alberta, Edmonton, AB T6G 1C9, Canada
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12
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Shamchuk AL, Blunt BJ, Lyons DD, Wang MQ, Gasheva A, Lewis CR, Tomlin K, Hazard ES, Hardiman G, Tierney KB. Correction: Nucleobase-containing compounds evoke behavioural, olfactory, and transcriptional responses in model fishes. Facets (Ott) 2018. [DOI: 10.1139/facets-2018-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Angela L. Shamchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brian J. Blunt
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Danielle D. Lyons
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mo Qi Wang
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Anastasia Gasheva
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Carlie R. Lewis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Kirsten Tomlin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - E. Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Library Science and Informatics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gary Hardiman
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Medicine and Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - Keith B. Tierney
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- School of Public Health, University of Alberta, Edmonton, AB T6G 1C9, Canada
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13
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de Leeuw R, McNair C, Schiewer MJ, Neupane NP, Brand LJ, Augello MA, Li Z, Cheng LC, Yoshida A, Courtney SM, Hazard ES, Hardiman G, Hussain MH, Diehl JA, Drake JM, Kelly WK, Knudsen KE. MAPK Reliance via Acquired CDK4/6 Inhibitor Resistance in Cancer. Clin Cancer Res 2018; 24:4201-4214. [PMID: 29739788 PMCID: PMC6125187 DOI: 10.1158/1078-0432.ccr-18-0410] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/07/2018] [Accepted: 05/03/2018] [Indexed: 12/18/2022]
Abstract
Purpose: Loss of cell-cycle control is a hallmark of cancer, which can be targeted with agents, including cyclin-dependent kinase-4/6 (CDK4/6) kinase inhibitors that impinge upon the G1-S cell-cycle checkpoint via maintaining activity of the retinoblastoma tumor suppressor (RB). This class of drugs is under clinical investigation for various solid tumor types and has recently been FDA-approved for treatment of breast cancer. However, development of therapeutic resistance is not uncommon.Experimental Design: In this study, palbociclib (a CDK4/6 inhibitor) resistance was established in models of early stage, RB-positive cancer.Results: This study demonstrates that acquired palbociclib resistance renders cancer cells broadly resistant to CDK4/6 inhibitors. Acquired resistance was associated with aggressive in vitro and in vivo phenotypes, including proliferation, migration, and invasion. Integration of RNA sequencing analysis and phosphoproteomics profiling revealed rewiring of the kinome, with a strong enrichment for enhanced MAPK signaling across all resistance models, which resulted in aggressive in vitro and in vivo phenotypes and prometastatic signaling. However, CDK4/6 inhibitor-resistant models were sensitized to MEK inhibitors, revealing reliance on active MAPK signaling to promote tumor cell growth and invasion.Conclusions: In sum, these studies identify MAPK reliance in acquired CDK4/6 inhibitor resistance that promotes aggressive disease, while nominating MEK inhibition as putative novel therapeutic strategy to treat or prevent CDK4/6 inhibitor resistance in cancer. Clin Cancer Res; 24(17); 4201-14. ©2018 AACR.
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Affiliation(s)
- Renée de Leeuw
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christopher McNair
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Matthew J Schiewer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Lucas J Brand
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Michael A Augello
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Zhen Li
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Larry C Cheng
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
- Graduate Program in Cellular and Molecular Pharmacology, School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Akihiro Yoshida
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
| | - Sean M Courtney
- Center for Genomic Medicine Bioinformatics, Medical University of South Carolina (MUSC), Charleston, South Carolina
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - E Starr Hazard
- Center for Genomic Medicine Bioinformatics, Medical University of South Carolina (MUSC), Charleston, South Carolina
- Library Science and Informatics, Medical University of South Carolina, Charleston, South Carolina
| | - Gary Hardiman
- Center for Genomic Medicine Bioinformatics, Medical University of South Carolina (MUSC), Charleston, South Carolina
- Departments of Medicine and Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Maha H Hussain
- Division of Hematology and Oncology, Department of Medicine, Feinberg School of Medicine, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
| | - Justin M Drake
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
- Graduate Program in Cellular and Molecular Pharmacology, School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Division of Medical Oncology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Wm Kevin Kelly
- Department of Medical Oncology, Urology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.
- Department of Medical Oncology, Urology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferon University, Philadelphia, Pennsylvania
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14
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Leeuw RD, McNair CM, Schiewer MJ, Neupane NP, Augello MA, Li Z, Cheng L, Yoshida A, Diehl JA, Hazard ES, McCourtney SM, Hardiman G, Hussain MH, Drake JM, Kelly WK, Knudsen KE. Abstract A043: Bypass kinase pathways lead to acquired CDK4/6 inhibitor resistance in prostate cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-a043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cyclin dependent kinase-4/6 (CDK4/6) kinase inhibitors have shown clinical benefit in treatment of solid tumor types, including breast cancer. However, resistance is common, and the underpinning mechanisms of action are not well understood. Given the dependence of CDK4/6 inhibitors on retinoblastoma tumor suppressor (RB) function for activity, this class of agents may be particularly effective in tumor types for which RB loss is infrequent or occurs late in tumor progression. Here, models of acquired palbociclib resistance were generated in early-stage, RB-positive cancers, wherein it was shown that acquired palbociclib resistance resulted in cross-resistance to other CDK4/6 inhibitors under clinical testing. Furthermore, cells showing acquired resistance exhibited aggressive in vitro and in vivo phenotypes without genetic loss of RB or RB pathway members, including enhanced proliferative capacity, migratory potential, and characteristics of epithelial-to-mesenchymal transition. Further analyses through integration of RNA sequencing and phospho-proteomics identified activation of the MAPK signaling pathway as a mediator of CDK4/6 inhibitor resistance, capable of bypassing CDK4/6 activity. However, this altered kinase dependence resulted in sensitization to MEK inhibitors, suggestive of new clinical opportunities in CDK4/6-resistant tumors. In sum, the studies herein not only identify activation of the MAPK pathway as capable of bypassing the CDK4/6 requirement and promoting aggressive tumor characteristics, but also nominate MEK inhibitors as potential mechanisms to treat or prevent CDK4/6 inhibitor resistance.
Citation Format: Renee de Leeuw, Christopher M. McNair, Matthew J. Schiewer, Neermala P. Neupane, Michael A. Augello, Zhen Li, Larry Cheng, Akihiro Yoshida, J. Alan Diehl, E Starr Hazard, Sean M. McCourtney, Gary Hardiman, Maha H. Hussain, Justin M. Drake, Wm. Kevin Kelly, Karen E. Knudsen. Bypass kinase pathways lead to acquired CDK4/6 inhibitor resistance in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A043.
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Affiliation(s)
| | | | | | | | | | - Zhen Li
- 2Rutgers Cancer Institute, New Brunswick, NJ,
| | - Larry Cheng
- 2Rutgers Cancer Institute, New Brunswick, NJ,
| | | | - J. Alan Diehl
- 3Medical University of South Carolina, Charleston, SC,
| | | | | | - Gary Hardiman
- 3Medical University of South Carolina, Charleston, SC,
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15
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Renaud L, Silveira WAD, Hazard ES, Simpson J, Falcinelli S, Chung D, Carnevali O, Hardiman G. The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome. Genes (Basel) 2017; 8:genes8100269. [PMID: 29027980 PMCID: PMC5664119 DOI: 10.3390/genes8100269] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/18/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023] Open
Abstract
Ubiquitous exposure to bisphenol A (BPA), an endocrine disruptor (ED), has raised concerns for both human and ecosystem health. Epigenetic factors, including microRNAs (miRNAs), are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops a disease that resembles human cancer. Using zebrafish as a systems toxicology model, we hypothesized that chronic BPA-exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. After a 3 week exposure to 100 nM BPA, RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression (DE) analyses comparing BPA-exposed to control specimens were performed using established bioinformatics pipelines. In the BPA-exposed liver, 6188 mRNAs and 15 miRNAs were differently expressed (q ≤ 0.1). By analyzing human orthologs of the DE zebrafish genes, signatures associated with non-alcoholic fatty liver disease (NAFLD), oxidative phosphorylation, mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome and transcriptome in adult zebrafish with the potential to cause adverse health outcomes including cancer.
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Affiliation(s)
- Ludivine Renaud
- Division of Nephrology, Department of Medicine, Medical University of South Carolina (MUSC),Charleston, SC 29425, USA.
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA.
| | - Willian A da Silveira
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
| | - E Starr Hazard
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
- Library Science and Informatics, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
| | - Jonathan Simpson
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
| | - Silvia Falcinelli
- Dipartimento Scienze della Vita e dell'Ambiente, Universita Politecnica delle Marche, 60131 Ancona, Italy.
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
| | - Oliana Carnevali
- Dipartimento Scienze della Vita e dell'Ambiente, Universita Politecnica delle Marche, 60131 Ancona, Italy.
| | - Gary Hardiman
- Division of Nephrology, Department of Medicine, Medical University of South Carolina (MUSC),Charleston, SC 29425, USA.
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
- Department of Medicine, University of California, La Jolla, CA 92093, USA.
- Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.
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Xu EG, Khursigara AJ, Magnuson J, Hazard ES, Hardiman G, Esbaugh AJ, Roberts AP, Schlenk D. Larval Red Drum (Sciaenops ocellatus) Sublethal Exposure to Weathered Deepwater Horizon Crude Oil: Developmental and Transcriptomic Consequences. Environ Sci Technol 2017; 51:10162-10172. [PMID: 28768411 DOI: 10.1021/acs.est.7b02037] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The Deepwater Horizon (DWH) incident resulted in extensive oiling of the pelagic zone and shoreline habitats of many commercially important fish species. Exposure to the water-accommodated fraction (WAF) of oil from the spill causes developmental toxicity through cardiac defects in pelagic fish species. However, few studies have evaluated the effects of the oil on near-shore estuarine fish species such as red drum (Sciaenops ocellatus). Following exposure to a certified weathered slick oil (4.74 μg/L ∑PAH50) from the DWH event, significant sublethal impacts were observed ranging from impaired nervous system development [average 17 and 22% reductions in brain and eye area at 48 h postfertilization (hpf), respectively] to abnormal cardiac morphology (100% incidence at 24, 48, and 72 hpf) in red drum larvae. Consistent with the phenotypic responses, significantly differentially expressed transcripts, enriched gene ontology, and altered functions and canonical pathways predicted adverse outcomes in nervous and cardiovascular systems, with more pronounced changes at later larval stages. Our study demonstrated that the WAF of weathered slick oil of DWH caused morphological abnormalities predicted by a suite of advanced bioinformatic tools in early developing red drum and also provided the basis for a better understanding of molecular mechanisms of crude oil toxicity in fish.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences, University of California , Riverside, California 92521, United States
| | - Alex J Khursigara
- Marine Science Institute, University of Texas at Austin , Port Aransas, Texas 78373, United States
| | - Jason Magnuson
- Department of Biological Sciences & Advanced Environmental Research Institute, University of North Texas , Denton, Texas 76203, United States
| | - E Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina , Charleston, South Carolina 29403, United States
- Computational Biology Resource Center, Medical University of South Carolina , Charleston, South Carolina 29403, United States
| | - Gary Hardiman
- Computational Biology Resource Center, Medical University of South Carolina , Charleston, South Carolina 29403, United States
- Departments of Medicine and Public Health Sciences, Medical University of South Carolina , Charleston, South Carolina 29403, United States
| | - Andrew J Esbaugh
- Marine Science Institute, University of Texas at Austin , Port Aransas, Texas 78373, United States
| | - Aaron P Roberts
- Department of Biological Sciences & Advanced Environmental Research Institute, University of North Texas , Denton, Texas 76203, United States
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California , Riverside, California 92521, United States
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17
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Xu EG, Mager EM, Grosell M, Stieglitz JD, Hazard ES, Hardiman G, Schlenk D. Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus). PLoS One 2017; 12:e0180454. [PMID: 28692652 PMCID: PMC5503239 DOI: 10.1371/journal.pone.0180454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/15/2017] [Indexed: 12/03/2022] Open
Abstract
Mahi-mahi (Coryphaena hippurus) is a commercially and ecologically important species of fish occurring in tropical and temperate waters worldwide. Understanding early life events is crucial for predicting effects of environmental stress, which is largely restricted by a lack of genetic resources regarding expression of early developmental genes and regulation of pathways. The need for anchoring developmental stages to transcriptional activities is highlighted by increasing evidence on the impacts of recurrent worldwide oil spills in this sensitive species during early development. By means of high throughput sequencing, we characterized the developmental transcriptome of mahi-mahi at three critical developmental stages, from pharyngula embryonic stage (24 hpf) to 48 hpf yolk-sac larva (transition 1), and to 96 hpf free-swimming larva (transition 2). With comparative analysis by multiple bioinformatic tools, a larger number of significantly altered genes and more diverse gene ontology terms were observed during transition 2 than transition 1. Cellular and tissue development terms were more significantly enriched in transition 1, while metabolism related terms were more enriched in transition 2, indicating a switch progressing from general embryonic development to metabolism during the two transitions. Special focus was given on the most significant common canonical pathways (e.g. calcium signaling, glutamate receptor signaling, cAMP response element-binding protein signaling, cardiac β-adrenergic signaling, etc.) and expression of developmental genes (e.g. collagens, myosin, notch, glutamate metabotropic receptor etc.), which were associated with morphological changes of nervous, muscular, and cardiovascular system. These data will provide an important basis for understanding embryonic development and identifying molecular mechanisms of abnormal development in fish species.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences, University of California, Riverside, California, United States of America
- * E-mail: (DS); (EGX)
| | - Edward M. Mager
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Martin Grosell
- Department of Marine Biology and Ecology, University of Miami, Miami, Florida, United Sates of America
| | - John D. Stieglitz
- Department of Marine Biology and Ecology, University of Miami, Miami, Florida, United Sates of America
| | - E. Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, South Carolina, United Sates of America
- Computational Biology Resource Center, Medical University of South Carolina, Charleston, South Carolina, United Sates of America
| | - Gary Hardiman
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, South Carolina, United Sates of America
- Departments of Medicine & Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, United Sates of America
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, South Carolina, United Sates of America
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, California, United States of America
- * E-mail: (DS); (EGX)
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18
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Xu EG, Mager EM, Grosell M, Hazard ES, Hardiman G, Schlenk D. Novel transcriptome assembly and comparative toxicity pathway analysis in mahi-mahi (Coryphaena hippurus) embryos and larvae exposed to Deepwater Horizon oil. Sci Rep 2017; 7:44546. [PMID: 28295044 PMCID: PMC5353654 DOI: 10.1038/srep44546] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
The impacts of Deepwater Horizon (DWH) oil on morphology and function during embryonic development have been documented for a number of fish species, including the economically and ecologically important pelagic species, mahi-mahi (Coryphaena hippurus). However, further investigations on molecular events and pathways responsible for developmental toxicity have been largely restricted due to the limited molecular data available for this species. We sought to establish the de novo transcriptomic database from the embryos and larvae of mahi-mahi exposed to water accommodated fractions (HEWAFs) of two DWH oil types (weathered and source oil), in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses. By high throughput sequencing (HTS), we obtained the first de novo transcriptome of mahi-mahi, with 60,842 assembled transcripts and 30,518 BLAST hits. Among them, 2,345 genes were significantly regulated in 96hpf larvae after exposure to weathered oil. With comparative analysis to a reference-transcriptome-guided approach on gene ontology and tox-pathways, we confirmed the novel approach effective for exploring tox-pathways in non-model species, and also identified a list of co-expressed genes as potential biomarkers which will provide information for the construction of an Adverse Outcome Pathway which could be useful in Ecological Risk Assessments.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Edward M Mager
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Martin Grosell
- Department of Marine Biology and Ecology, University of Miami, Miami, FL 33149, USA
| | - E Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29403, USA.,Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29403, USA
| | - Gary Hardiman
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29403, USA.,Departments of Medicine &Public Health Sciences, Medical University of South Carolina, Charleston, SC 29403, USA.,Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
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19
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Davis-Turak J, Courtney SM, Hazard ES, Glen WB, da Silveira WA, Wesselman T, Harbin LP, Wolf BJ, Chung D, Hardiman G. Genomics pipelines and data integration: challenges and opportunities in the research setting. Expert Rev Mol Diagn 2017; 17:225-237. [PMID: 28092471 DOI: 10.1080/14737159.2017.1282822] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine. Areas covered: The very success of this industry also translates into daunting big data challenges for researchers and institutions that extend beyond the traditional academic focus of algorithms and tools. The main obstacles revolve around analysis provenance, data management of massive datasets, ease of use of software, interpretability and reproducibility of results. Expert commentary: The authors review the challenges associated with implementing bioinformatics best practices in a large-scale setting, and highlight the opportunity for establishing bioinformatics pipelines that incorporate data tracking and auditing, enabling greater consistency and reproducibility for basic research, translational or clinical settings.
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Affiliation(s)
| | - Sean M Courtney
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,c Department of Pathology and Laboratory Medicine , MUSC , Charleston , USA
| | - E Starr Hazard
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,d Library Science and Informatics , MUSC , Charleston , USA
| | - W Bailey Glen
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,c Department of Pathology and Laboratory Medicine , MUSC , Charleston , USA
| | - Willian A da Silveira
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,c Department of Pathology and Laboratory Medicine , MUSC , Charleston , USA
| | | | - Larry P Harbin
- e Department of Public Health Sciences , MUSC , Charleston , USA
| | - Bethany J Wolf
- e Department of Public Health Sciences , MUSC , Charleston , USA
| | - Dongjun Chung
- e Department of Public Health Sciences , MUSC , Charleston , USA
| | - Gary Hardiman
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,e Department of Public Health Sciences , MUSC , Charleston , USA.,f Department of Medicine , MUSC , Charleston , USA
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20
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Janakiraman H, House RP, Talwar S, Courtney SM, Hazard ES, Hardiman G, Mehrotra S, Howe PH, Gangaraju V, Palanisamy V. Repression of caspase-3 and RNA-binding protein HuR cleavage by cyclooxygenase-2 promotes drug resistance in oral squamous cell carcinoma. Oncogene 2016; 36:3137-3148. [PMID: 27941877 PMCID: PMC5453834 DOI: 10.1038/onc.2016.451] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022]
Abstract
A well-studied RNA-binding protein Hu Antigen-R (HuR), controls post-transcriptional gene regulation and undergoes stress-activated caspase-3 dependent cleavage in cancer cells. The cleavage products of HuR are known to promote cell death however, the underlying molecular mechanisms facilitating caspase-3 activation and HuR cleavage remains unknown. Here, we show that HuR cleavage associated with active caspase-3 in oral cancer cells treated with ionizing radiation and chemotherapeutic drug, paclitaxel. We determined that oral cancer cells overexpressing cyclooxygenase-2 (COX-2) limited the cleavage of caspase-3 and HuR, which reduced the rate of cell death in paclitaxel resistant oral cancer cells. Specific inhibition of COX-2 by celecoxib, promoted apoptosis through activation of caspase-3 and cleavage of HuR in paclitaxel-resistant oral cancer cells, both in vitro and in vivo. In addition, oral cancer cells overexpressing cellular HuR increased the half-life of COX-2 mRNA, promoted COX-2 protein expression and exhibited enhanced tumor growth in vivo in comparison with cells expressing a cleavable form of HuR. Finally, our ribonucleoprotein immunoprecipitation and sequencing (RIP-seq) analyses of HuR in oral cancer cells treated with ionizing radiation (IR), determined that HuR cleavage product-1 (HuR-CP1) bound and promoted the expression of mRNAs encoding proteins involved in apoptosis. Our results indicated that, cellular non-cleavable HuR controls COX-2 mRNA expression and enzymatic activity. In addition, overexpressed COX-2 protein repressed the cleavage of caspase-3 and HuR to promote drug resistance and tumor growth. Altogether, our observations support the use of the COX-2 inhibitor celecoxib, in combination with paclitaxel, for the management of paclitaxel resistant oral cancer cells.
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Affiliation(s)
- H Janakiraman
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - R P House
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - S Talwar
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - S M Courtney
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, Charleston, SC, USA
| | - E S Hazard
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Library Science and Informatics, Medical University of South Carolina, Charleston, SC, USA
| | - G Hardiman
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Departments of Medicine and Public Health, Medical University of South Carolina, Charleston, SC, USA
| | - S Mehrotra
- Department of Surgery, Medical University of South Carolina, Charleston, SC, USA
| | - P H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - V Gangaraju
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - V Palanisamy
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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21
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House RP, Talwar S, Hazard ES, Hill EG, Palanisamy V. RNA-binding protein CELF1 promotes tumor growth and alters gene expression in oral squamous cell carcinoma. Oncotarget 2016; 6:43620-34. [PMID: 26498364 PMCID: PMC4791255 DOI: 10.18632/oncotarget.6204] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/09/2015] [Indexed: 12/15/2022] Open
Abstract
The RNA binding protein CELF1 (also known as CUGBP1) is emerging as a critical regulator of cancer cell proliferation and apoptosis. Here, to provide a global prospective of CELF1 regulation of oral squamous cell carcinoma, we performed RNA-sequencing in oral cancer cells and CELF1 overexpression analysis in non-malignant human oral keratinocytes. Our approaches identified 1283 mRNAs differentially regulated as a function of CELF1 expression and more importantly CELF1 promoted alternative splicing of several target pre-mRNAs, which are known to be involved in various cancer biological processes. Overexpression of CELF1 in non-malignant human oral keratinocytes protected cells against oxidative damage and altered gene expression patterns. Finally, we provide evidence that reduction of CELF1 protein using a xenograft tumorigenesis mouse model decreased tumor growth. Altogether, these data provided a comprehensive view of the CELF1 mRNA regulatory network in oral cancer and suggests that CELF1 and/or its target mRNAs are viable candidates for therapeutic intervention.
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Affiliation(s)
- Reniqua P House
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sudha Talwar
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - E Starr Hazard
- Division of Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Elizabeth G Hill
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Viswanathan Palanisamy
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
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22
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Xu EG, Mager EM, Grosell M, Pasparakis C, Schlenker LS, Stieglitz JD, Benetti D, Hazard ES, Courtney SM, Diamante G, Freitas J, Hardiman G, Schlenk D. Time- and Oil-Dependent Transcriptomic and Physiological Responses to Deepwater Horizon Oil in Mahi-Mahi (Coryphaena hippurus) Embryos and Larvae. Environ Sci Technol 2016; 50:7842-7851. [PMID: 27348429 DOI: 10.1021/acs.est.6b02205] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Deepwater Horizon (DWH) oil spill contaminated the spawning habitats for numerous commercially and ecologically important fishes. Exposure to the water accommodated fraction (WAF) of oil from the spill has been shown to cause cardiac toxicity during early developmental stages across fishes. To better understand the molecular events and explore new pathways responsible for toxicity, RNA sequencing was performed in conjunction with physiological and morphological assessments to analyze the time-course (24, 48, and 96 h post fertilization (hpf)) of transcriptional and developmental responses in embryos/larvae of mahi-mahi exposed to WAF of weathered (slick) and source DWH oils. Slick oil exposure induced more pronounced changes in gene expression over time than source oil exposure. Predominant transcriptomic responses included alteration of EIF2 signaling, steroid biosynthesis, ribosome biogenesis and activation of the cytochrome P450 pathway. At 96 hpf, slick oil exposure resulted in significant perturbations in eye development and peripheral nervous system, suggesting novel targets in addition to the heart may be involved in the developmental toxicity of DHW oil. Comparisons of changes of cardiac genes with phenotypic responses were consistent with reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences, University of California , Riverside, California 92521, United States
| | - Edward M Mager
- Department of Marine Biology and Ecology, University of Miami , Miami, Florida 33149, United States
| | - Martin Grosell
- Department of Marine Biology and Ecology, University of Miami , Miami, Florida 33149, United States
| | - Christina Pasparakis
- Department of Marine Biology and Ecology, University of Miami , Miami, Florida 33149, United States
| | - Lela S Schlenker
- Department of Marine Biology and Ecology, University of Miami , Miami, Florida 33149, United States
| | - John D Stieglitz
- Department of Marine Biology and Ecology, University of Miami , Miami, Florida 33149, United States
| | - Daniel Benetti
- Department of Marine Biology and Ecology, University of Miami , Miami, Florida 33149, United States
| | - E Starr Hazard
- Center for Genomics Medicine, Medical University of South Carolina , Charleston, South Carolina 29403, United States
- Computational Biology Resource Center, Medical University of South Carolina , Charleston, South Carolina 29403, United States
| | - Sean M Courtney
- Center for Genomics Medicine, Medical University of South Carolina , Charleston, South Carolina 29403, United States
| | - Graciel Diamante
- Department of Environmental Sciences, University of California , Riverside, California 92521, United States
| | - Juliane Freitas
- Department of Environmental Sciences, University of California , Riverside, California 92521, United States
| | - Gary Hardiman
- Center for Genomics Medicine, Medical University of South Carolina , Charleston, South Carolina 29403, United States
- Departments of Medicine & Public Health Sciences, Medical University of South Carolina , Charleston, South Carolina 29403, United States
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California , Riverside, California 92521, United States
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23
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Hardiman G, Savage SJ, Hazard ES, Wilson RC, Courtney SM, Smith MT, Hollis BW, Halbert CH, Gattoni-Celli S. Systems analysis of the prostate transcriptome in African-American men compared with European-American men. Pharmacogenomics 2016; 17:1129-1143. [PMID: 27359067 DOI: 10.2217/pgs-2016-0025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIM African-Americans (AA) have increased prostate cancer risk and a greater mortality rate than European-Americans (EA). AA exhibit a high prevalence of vitamin D deficiency. We examined the global prostate transcriptome in AA and EA, and the effect of vitamin D3 supplementation. PATIENTS & METHODS Twenty-seven male subjects (ten AA and 17 EA), slated to undergo prostatectomy were enrolled in the study. Fourteen subjects received vitamin D3 (4000 IU daily) and 13 subjects received placebo for 2 months prior to surgery. RESULTS AA show higher expression of genes associated with immune response and inflammation. CONCLUSION Systems level analyses support the concept that Inflammatory processes may contribute to disease progression in AA. These transcripts can be modulated by a short course of vitamin D3 supplementation.
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Affiliation(s)
- Gary Hardiman
- Department of Medicine & Public Health, Medical University of South Carolina, Charleston, SC, USA.,Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Stephen J Savage
- Department of Urology.,Ralph H Johnson VA Medical Center, Charleston, SC, USA
| | - E Starr Hazard
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Library Science and Informatics, Medical University of South Carolina, Charleston, SC, USA
| | - Robert C Wilson
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Pathology & Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sean M Courtney
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Michael T Smith
- Department of Pathology & Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Bruce W Hollis
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Chanita Hughes Halbert
- Ralph H Johnson VA Medical Center, Charleston, SC, USA.,Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Sebastiano Gattoni-Celli
- Ralph H Johnson VA Medical Center, Charleston, SC, USA.,Department of Radiation Oncology, Medical University of South Carolina, Charleston, SC, USA
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24
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Rose KML, Wang Z, Magrath GN, Hazard ES, Hildebrandt JD, Schey KL. Aquaporin 0-calmodulin interaction and the effect of aquaporin 0 phosphorylation. Biochemistry 2007; 47:339-47. [PMID: 18081321 DOI: 10.1021/bi701980t] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aquaporin 0 (AQP0), also known as major intrinsic protein of lens, is the most abundant membrane protein in the lens and it undergoes a host of C-terminally directed posttranslational modifications. The C-terminal region containing the major phosphorylation sites is a putative calmodulin-binding site, and calmodulin has been shown to regulate AQP0 water permeability. The purpose of the present study was to elucidate the role of AQP0 phosphorylation on calmodulin binding. AQP0 C-terminal peptides were synthesized with and without serine phosphorylation on S231 and S235, and the ability of these peptides to bind dansyl-labeled calmodulin and the calcium dependence of the interaction was assessed using a fluorescence binding assay. The AQP0 C-terminal phosphorylated peptides were found to have 20-50-fold lower affinities for calmodulin than the unphosphorylated peptide. Chemical cross-linking studies revealed specific sites of AQP0-calmodulin interaction that are significantly reduced by AQP0 phosphorylation. These data suggest that AQP0 C-terminal phosphorylation affects calmodulin binding in vivo and has a role in regulation of AQP0 function.
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Affiliation(s)
- K M Lindsey Rose
- Department of Cell and Molecular Pharmacology, 173 Ashley Avenue, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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25
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Wu BX, Darden AG, Laser M, Li Y, Crosson CE, Hazard ES, Ma JX. The rat Apg3p/Aut1p homolog is upregulated by ischemic preconditioning in the retina. Mol Vis 2006; 12:1292-302. [PMID: 17110912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
PURPOSE Retinas can be protected from subsequent severe ischemic injury by ischemic preconditioning. Ischemic preconditioning is dependent on gene expression and protein synthesis; however, it is not clear which genes are important in this process. In this study, we have identified and characterized the rat homolog of yeast Apg3p/Aut1p, an important autophagy protein encoded by the autophagy 3-like (APG3L) gene. We have also further characterized the homologous human APG3L gene. METHODS A fragment of the rat Apg3 cDNA was identified by mRNA differential display from hypoxia-treated E1A-NR3, an immortalized cell line derived from rat retinal cells that manifests phenotypes of retinal neurons. The full length of rat Apg3 (rApg3) cDNA sequence (about 1.4 kb) encoding 341 amino acids was cloned from a rat retinal cDNA library and characterized using Southern and northern blot analysis, and a global GenBank search. Protein expression was determined by western blotting, and immunohistochemistry. Ischemic preconditioning was achieved by ligation of the retinal arteries of the right eye for 5 min followed by 5 h reperfusion. The prolonged retinal ischemia was induced by ligation of the retinal arteries for 45 min followed by 5 h reperfusion. The full-length homologous human APG3L gene was cloned and sequenced from a human genomic DNA library. RESULTS The combination of genomic Southern blot analysis and a global GenBank search indicated that rat APG3L is a single copy gene. Rat Apg3 mRNA is expressed in the retina at a high level but is also detected in other tissues. In the process of comparing the rat and human APG3L genes we showed that the organization of the human APG3L gene includes a unique transcriptional start site, a coding region with 12 translated exons and 11 introns and is located on human chromosome 3q13.1. Subcellular localization studies showed that recombinant rat autophagocytosis protein (Apg3p) is a cytosolic protein. Rat Apg3 mRNA level was upregulated by ischemic preconditioning but downregulated by prolonged ischemia. CONCLUSIONS Our results suggest that the upregulation of rApg3 is a specific response to ischemic preconditioning rather than to retina ischemia, and autophagy may contribute to the neuroprotective effect of ischemic preconditioning in the retina.
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Affiliation(s)
- Bill X Wu
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, USA
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26
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Darden AG, Wu BX, Znoiko SL, Hazard ES, Kono M, Crouch RK, Ma JX. A novel Xenopus SWS2, P434 visual pigment: structure, cellular location, and spectral analyses. Mol Vis 2003; 9:191-9. [PMID: 12764253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
PURPOSE The purpose of this study was to clone and characterize the green rod pigment in Xenopus laevis. METHODS The cDNA for the Xenopus "green rod" pigment was cloned and sequenced from Xenopus retina mRNA by reverse transcription polymerase chain reaction and the 5' end cloned by rapid amplification of the cDNA ends. The cellular localization of the Xenopus opsin was determined by immunolabeling of flat-mounted retinas using a specific antibody against this opsin. Spectral properties of the expressed protein were determined by absorption spectroscopy using recombinant pigment. RESULTS A novel Xenopus opsin cDNA containing a full-length coding region has been cloned and sequenced. The deduced amino acid sequence predicts a protein of 362 amino acids, forming 7 hydrophobic helices. Sequence analysis indicates that it belongs firmly to the SWS2 class of visual pigments and has 89%, 80%, and 75% amino acid sequence identity with bullfrog, tiger salamander, and newt SWS2 pigments, respectively. Staining of Xenopus retina with a Xenopus SWS2 opsin-specific polyclonal antibody demonstrated that the SWS2 pigment is expressed in green rods. After expression in COS cells, reconstitution with 11-cis retinal, and purification, the SWS2 pigment exhibits an absolute absorption maximum of 434 nm Thus, the name "SWS2, P434" was assigned for this opsin. The pigment decays rapidly in hydroxylamine in the dark, unlike the red rod pigment, rhodopsin. CONCLUSIONS A novel green rod opsin cDNA has been cloned and sequenced from the retina of adult Xenopus laevis, which encodes a protein belonging to the SWS2 group of opsins. The expressed opsin possesses cone-opsin-like properties although it was identified only in the Xenopus green rod cells.
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Affiliation(s)
- Alix G Darden
- Storm Eye Institute, Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, USA.
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Abstract
The visual pigment from the ultraviolet (UV) cone photoreceptor of the tiger salamander has been cloned, expressed, and characterized. The cDNA contains a full-length open reading frame encoding 347 amino acids. The phylogenetic analysis indicates that the highest sequence homology is to the visual pigments in the S group. The UV opsin was tagged at the carboxy-terminus with the sequence for the 1D4 epitope. This fusion opsin was expressed in COS-1 cells, regenerated with 11-cis retinal (A1) and immuno-purified, yielding a pigment with an absorbance maximum (lambdamax) of 356 nm which is blue shifted from the absorption of retinal itself. The transducin activation assay demonstrated that this pigment is able to activate rod transducin in a light-dependent manner. Regeneration with 11-cis 3,4-dehydroretinal (A2) yielded a pigment with a lambdamax of 360 nm, only 4 nm red shifted from that of the A1 pigment, while bovine rhodopsin generated with A2 showed a 16-nm red shift from the corresponding A1 pigment. These results demonstrate that the trend for a shorter wavelength pigment to have a smaller shift of lambdamax between the A1 and A2 pigments also fits UV pigments. We hypothesize that the small red shift with A2 could be due to a twist in the chromophore that essentially isolates the ring double bond(s) from conjugation with the rest of the polyene chain.
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Affiliation(s)
- J X Ma
- Department of Ophthalmology, Medical University of South Carolina, Charleston 29403, USA.
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Datta-Gupta N, Crouch RK, Hazard ES. Categorizing reactivity of bacteriorhodopsin cysteine mutants crosslinking to 4-bromoretinal. Biochem Mol Biol Int 1999; 47:773-80. [PMID: 10365248 DOI: 10.1080/15216549900201863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The structure of bacteriorhodopsin (bR) has been probed by a large number of experimental methods. In earlier work distance constraints measured from the 1BRD Brookhaven structure (1, 2) were used to guide site-directed mutagenesis/affinity labeling experiments (3-5). In the present study we report on the use of limited molecular dynamics (MD) investigations of the same bR/affinity label system. We show here that the chiral center introduced when 4-bromo-all-trans retinal is synthesized produces variable impact on potential crosslinking. Our MD analysis suggests the following ranking of binding site mutants in order of reactivity: R118C > S118C >> S121C > R141C >> S141C >>> R121C, R138C, S138C. Chirality appears to have limited effect for the M118C mutants but shows more dramatic impact for the T121C and S141C mutants. These results are in excellent agreement with the experimental observations and offer encouragement that MD can be a useful component of experimental design with considerable predictive power.
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Affiliation(s)
- N Datta-Gupta
- Department of Physical Sciences, South Carolina State University, Orangeburg 29117, USA
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DeHaven JE, Schwartz DA, Dahm MW, Hazard ES, Trifiletti R, Lacy ER, Norris JS. Novel retroviral sequences are expressed in the epididymis and uterus of Syrian hamsters. J Gen Virol 1998; 79 ( Pt 11):2687-94. [PMID: 9820144 DOI: 10.1099/0022-1317-79-11-2687] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combined androgen and oestrogen treatment of male or female Syrian hamsters results via an unknown mechanism in the formation of leiomyosarcomas in the reproductive tract. We have examined the possibility that retroviral gene expression may play a role in tumorigenesis. Evidence of virus-like particles in epididymis and seminal fluid is shown in electron micrographs. We identified expressed retroviral sequences by using RT-PCR to amplify a conserved retroviral reverse transcriptase coding region in RNA isolated from epididymis, testis, clarified seminal fluid and uterus. Phylogenetic analysis allowed us to classify the sequences into two distinct groups: (1) mammalian type-C viruses, having similarity to Moloney murine leukaemia virus, feline leukaemia virus and gibbon ape leukaemia virus amongst others; (2) a mixed ABCD group containing, for example, Chinese hamster and murine intracisternal A-particle virus sequences, mouse mammary tumour virus and human and simian retroviral sequences. The presence of putative full-length retrovirus related to mammalian type-C viruses in the epididymis and uterus was confirmed by Northern blot analysis. However, steroid treatment did not alter retroviral RNA levels in the epididymis or in a uterine tumour relative to untreated uterus. In summary, Syrian hamster reproductive tissues were found to express unique retroviral sequences; however, their role, if any, in hormonal carcinogenesis remains unresolved.
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Affiliation(s)
- J E DeHaven
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston 29425, USA
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30
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Xu L, Hazard ES, Lockman DK, Crouch RK, Ma J. Molecular cloning of the salamander red and blue cone visual pigments. Mol Vis 1998; 4:10. [PMID: 9675215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
PURPOSE Salamander retinas are known to contain at least three cone pigments and two rod pigments. The purpose of this study was to clone and characterize the visual pigments from salamander cones. METHODS cDNA fragments of cone pigments were amplified from a salamander retina cDNA library by PCR using a pair of primers with consensus for visual pigments. These fragments were cloned and used as probes for library-screening. The full-length cDNAs were isolated from the retinal library using the cloned PCR products as probes. DNA sequences were determined by the dideoxynucleotide chain termination method. RESULTS Two pigment cDNAs were cloned and sequenced from the salamander library. The global GenBank search showed that they do not match any existing sequences but have significant sequence similarity to visual pigments. One of the pigment cDNAs showed a high sequence homology with red cone pigments from other species and thus, was designated as a red cone opsin. The other pigment was designated as a blue cone opsin as it is most homologous to the chicken and goldfish blue cone pigments. Both cDNAs contain a full-length coding region encoding 365 amino acids in the red and 363 amino acids in the blue cone pigment. Hydropathy analysis predicted that both pigments could form seven hydrophobic transmembrane helices. Both pigments retain the key amino acid residues critical for maintaining the structure and function of opsins and have similar G-protein interaction sequences which differ from that of rod opsin. Phylogenetic analysis indicates that the red opsin belongs to the L group and the blue opsin belongs to the M1 group of visual pigments. CONCLUSIONS The salamander red and blue cone pigments share high sequence homology with the cone pigments of other species.
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Affiliation(s)
- L Xu
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
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Chen N, Ma JX, Corson DW, Hazard ES, Crouch RK. Molecular cloning of a rhodopsin gene from salamander rods. Invest Ophthalmol Vis Sci 1996; 37:1907-13. [PMID: 8759361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
PURPOSE Salamander photoreceptor cells have been used widely as models in vision research. However, the salamander opsin genes had not been cloned. The purpose of this study was to clone a salamander rhodopsin and to determine its primary structure and cell type-specific expression. METHODS Using salamander retina RNA as a template and Xenopus rhodopsin-specific oligonucleotides as primers, reverse transcription and polymerase chain reaction (RT-PCR) were used to amplify and clone a rhodopsin cDNA fragment. This fragment was used as a probe to isolate a full-length cDNA of the rhodopsin from a cDNA library of salamander retina. The dideoxynucleotide chain termination method was used to determine the nucleotide sequence. Single rod and cone cells were isolated by micromanipulation, and the absorbance spectra of the rod outer segments were measured with a photon-counting microspectrophotometer. Individual rod and cone cells were lysed for RT-PCR and Southern blot analysis to detect cell-specific expression of this gene. RESULTS A 1.2 kb rhodopsin cDNA containing the full-length coding region of rhodopsin has been cloned and sequenced from the larval tiger salamander, Ambystoma tigrinum. This cDNA encodes 354 amino acids that, by hydropathy profile, could form seven transmembrane domains characteristic of other rhodopsins. Sequence identity was found with other amphibian rhodopsins at the nucleic acid (82% to 83%) and the amino acid (88% to 89%) levels. Key amino acids critical for structure and function of rhodopsin have been retained. The mRNA of this rhodopsin was identified in red rod cells (lambda max 506 nm). No expression of the gene was detected in cone cells. CONCLUSIONS The cloned rhodopsin is a newly isolated member of the G protein-coupled receptor superfamily. This protein is expressed in rods but not in cones.
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Affiliation(s)
- N Chen
- Department of Ophthalmology, Storm Eye Institute, Medical University of South Carolina, Charleston 29425, USA
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Feng Y, Menick DR, Katz BM, Beischel CJ, Hazard ES, Misra S, Ebrey TG, Crouch RK. Probing of the retinal binding site of bacteriorhodopsin by affinity labeling. Biochemistry 1994; 33:11624-30. [PMID: 7918376 DOI: 10.1021/bi00204a025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The position of the chromophore within bacteriorhodopsin has been identified by cross-linking a cysteine group, introduced by site-specific mutagenesis, with a chromophore suitably derivatized with an active leaving group. Since bacteriorhodopsin has no cysteines, a site-specific cysteine mutant will contain only one free sulfhydryl group capable of reacting with the retinal analog. Met118, Thr121, and Ser141 were selected to be mutated to cysteine. No pigment absorbing in the visible region was obtained for the Ser141Cys mutant. The Met118Cys and Thr121Cys mutants have similar absorption maxima, proton pumping efficiencies and photocycles to those of the wild-type pigment. 4-Bromoretinal, in which the reactive allylic halide readily undergoes nucleophilic displacement, was used as the reactive chromophore. Pigments were obtained on reaction of all-trans-4-bromoretinal with the apoproteins of Met118Cys, Thr121Cys, and wild-type bacteriorhodopsin (lambda max = 464-470 nm). Analysis of the denatured pigments on SDS-polyacrylamide gels showed incorporation of tritiated chromophore into the Met118Cys mutant but not into the wild-type or Th4121Cys pigments. Met118Cys apoprotein which was preincubated with the cysteine-specific reagent N-ethylmaleimide formed a pigment with 4-bromoretinal but no cross-linking was observed, providing evidence that the cross-linking of the chromophore is to the cysteine at 118. We conclude that Met118 is positioned in the chromophore binding pocket, proximal to the C-4 position of cyclohexyl ring of retinal.
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Affiliation(s)
- Y Feng
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston 29425
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33
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Beischel CJ, Gray K, Hazard ES, Knapp DR, Crouch RK. Evaluation of photoaffinity labeled sites of bacteriorhodopsin using molecular modeling. Biochem Mol Biol Int 1994; 32:933-9. [PMID: 8069243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Three successful photoaffinity labeling experiments of bacteriorhodopsin (bR) have been reported that used photoactivatible analogs of retinal to label the retinal binding site of the protein. Using molecular modeling techniques, the information about the retinal binding site derived from these studies is compared to the retinal binding site as defined by Henderson et al. (1990) using electron diffraction data. This comparison suggests some limitations to the use of photoaffinity labeling experiments for the determination of high resolution structural information.
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Affiliation(s)
- C J Beischel
- Department of Pharmacology, Medical University of South Carolina, Charleston 29425
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34
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Kumar GN, Oatis JE, Thornburg KR, Heldrich FJ, Hazard ES, Walle T. 6 alpha-Hydroxytaxol: isolation and identification of the major metabolite of taxol in human liver microsomes. Drug Metab Dispos 1994; 22:177-9. [PMID: 7908626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- G N Kumar
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston 29425
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Abstract
Halobacterium halobium, grown in a defined medium where tyrosine had been largely replaced with m-fluorotyrosine, biosynthetically produced purple membrane. Analysis of this membrane by high pressure liquid chromatography of phenylthiocarbamyl derivatized amino acids of membrane acid hydrolysates revealed that up to 50% of the tyrosine was present as the m-fluorotyrosine form. Yields of the purple membrane decreased as the level of incorporation increased. The experimental purple membrane showed a single 19F NMR resonance at -61.983 ppm (relative to trifluoroacetic acid). The bacteriorhodopsin (bR) in the purple membrane was normal as assayed by gel electrophoresis, isoelectric focusing, circular dichroic spectra, and UV-visible spectra. However, the fluorinated tyrosine bacteriorhodopsins at near neutral pH exhibited slightly slower rates of proton uptake and a slower M-state decay with biphasic kinetics reminiscent of alkaline solutions of bR (pH > 9). These results imply that the tyrosines in bacteriorhodopsin may play a role in the photoactivated proton translocation process of this pigment.
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Affiliation(s)
- E S Hazard
- Department of Ophthalmology, Medical University of South Carolina, Charleston 29425-2501
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Crouch RK, Hazard ES, Lind T, Wiggert B, Chader G, Corson DW. Interphotoreceptor retinoid-binding protein and alpha-tocopherol preserve the isomeric and oxidation state of retinol. Photochem Photobiol 1992; 56:251-5. [PMID: 1502268 DOI: 10.1111/j.1751-1097.1992.tb02154.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Retinol decomposes rapidly into a number of products, including its aldehyde form, retinal, when introduced into buffer in phospholipid vesicles or ethanol. Interphotoreceptor retinoid-binding protein at low concentrations is found to protect retinol from isomerization and oxidation. The addition of alpha-tocopherol to either liposomes or an ethanolic-buffer solution also prevents decomposition. Neither of these agents interferes with the successful regeneration of pigment with 9-cis retinal in rod outer segment preparations or the restoration of sensitivity by retinoids in isolated rod photoreceptors.
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Affiliation(s)
- R K Crouch
- Department of Ophthalmology, Medical University of South Carolina, Charleston 29425
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Mayeux PR, Morinelli TA, Williams TC, Hazard ES, Mais DE, Oatis JE, Baron DA, Halushka PV. Differential effect of pH on thromboxane A2/prostaglandin H2 receptor agonist and antagonist binding in human platelets. J Biol Chem 1991; 266:13752-8. [PMID: 1830308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The effects of changes in pH on the binding of agonists and antagonists to the human platelet thromboxane A2/prostaglandin H2 (TXA2/PGH2) receptor were determined. Competition binding studies were performed with the TXA2/PGH2 mimetic [1S-1 alpha,2 beta (5Z), 3 alpha(1E,3R*),4 alpha)]-7-[3-(3-hydroxy-4'-iodophenoxy)-1-buteny) 7-oxabicyclo-[2.2.1]-heptan-2-yl]-5-heptenoic acid ([125I]BOP). The pH optimum for binding of [125I] BOP to washed human platelets was broad with a range of pH 4-6 in contrast to that of the TXA2/PGH2 receptor antagonist 9,11-dimethyl-methano-11,12-methano-16-(3-iodo-4-hydroxyl)-13-aza-15 alpha,beta-omega-tetranorthromboxane A2 ([125I]PTA-OH) which was 7.4. Scatchard analysis of [125I]BOP binding in washed platelets at pH 7.4, 6.0, and 5.0 revealed an increase in affinity (Kd = 1.16 +/- 0.06, 0.64 +/- 0.09, and 0.48 +/- 0.05 nM, respectively) and an increase in the number of receptors (Bmax = 2807 +/- 415, 5397 +/- 636, and 7265 +/- 753 sites/platelet, respectively). The potency of I-BOP to induce shape change in washed platelets at pH 6.0 was also significantly increased from an EC50 value of 0.34 +/- 0.016 nM at pH 7.4 to 0.174 +/- 0.014 nM at pH 6.0 (n = 6, p less than 0.05). In contrast, the EC50 value for thrombin was unaffected by the change in pH. In competition binding studies with [125I]BOP, the affinity of the agonists U46619 and ONO11113 were increased at pH 6.0 compared to 7.4. In contrast, the affinity of the TXA2/PGH2 receptor antagonists I-PTA-OH, SQ29548, and L657925 were either decreased or unchanged at pH 6.0 compared to 7.4. Diethyl pyrocarbonate and N-bromosuccinimide, reagents used to modify histidine residues, reversed the increase in affinity of [125I]BOP at pH 6.0 to values equivalent to those at pH 7.4. In solubilized platelet membranes, the effects of NBS were blocked by coincubation with the TXA2/PGH2 mimetic U46619. The results suggest that agonist and antagonist binding characteristics are different for the TXA2/PGH2 receptor and that histidine residue(s) may play an important role in the binding of TXA2/PGH2 ligands to the receptor.
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Affiliation(s)
- P R Mayeux
- Department of Cell and Molecular Pharmacology, and Experimental Therapeutics, Medical University of South Carolina, Charleston 29425
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Abstract
Protoheme-CO in aqueous solution does not exhibit a geminate ligand recombination reaction. Addition of a protein, either globin or serum albumin, to which heme binds strongly, leads to an observable geminate reaction in aqueous solution. The bimolecular kinetic data for the albumin-heme-CO complex show two stable components, one heme-like in rate and difference spectrum, and one hemoglobin-like. The geminate reaction correlates spectrally with the hemoglobin-like component.
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Affiliation(s)
- M C Marden
- INSERM U299, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
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Abstract
Flash photolysis kinetics of carbon monoxide hemoglobin show a decrease in the fraction of ligand recombination occurring as geminate when the hemoglobin has fewer ligands bound. Fully saturated samples, normally referred to as R state, show approximately 50% geminate phase, while samples at low saturation (T state) show less than 3%. The latter result was obtained by photolysis of samples with a short delay after stopped flow of solutions of deoxy hemoglobin (Hb) and ligand. The decrease in the fraction of geminate phase was also observed using a double flash technique. The transient mixture of R and T states generated by flash photolysis of Hb-CO was probed with a weaker time-delayed photolysis pulse. The kinetics of both the geminate and bimolecular phases following the second pulse were measured. The fraction geminate signal was least at delays where the maximum proportion of liganded T state tetramer is expected. The biphasic bimolecular process is also an indicator of the allosteric state of Hb. The populations of R and T may be determined from the overall ligand recombination kinetics; however, the analysis is model-dependent. The fraction geminate reaction may provide a rapid measure of the amount of liganded hemes in the R and T states.
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Affiliation(s)
- M C Marden
- Section of Biochemistry and Molecular Biology, Cornell University, Ithaca, New York
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40
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Abstract
Three allosteric states are required to describe the relaxation of (carbon monoxy) hemoglobin following flash photolysis. Combined absorbance and fluorescence probes were used. The absorbance signals consist of a component corresponding to ligand recombination and a component for the R-T transition. The fluorescence of 8-hydroxy-1,3,6-pyrenetrisulfonate (HPT), an analogue of 2,3-diphosphoglycerate, shows rates and amplitudes correlated with the absorbance transients. Measurements were made at pII 6, 6.5, and 7.0 at CO partial pressures of 0.1 and 1 atm. The fractional photolysis was varied in each case to change the initial distribution of the R states. Data show an immediate absorbance change due to ligand dissociation, while the changes in the ligand isosbestic and the fluorescence signals occur with time constants of 80 microseconds (at pH 6.5). The signals then show a biphasic return to equilibrium, characteristic of the allosteric system. The measurements provide three independent probes of the kinetics of the substates of hemoglobin. Although the ligand binding data can be generally represented by a two-state model, the fluorescence data require T states with different affinities for HPT.
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Abstract
Recombination kinetics of CO to protoheme after laser photolysis have been measured vs. temperature and viscosity. A 25-ns laser pulse was focused on the sample to produce an excitation rate of 10(9)/s per heme. This temporarily populates the heme-CO state of dissociated pairs which either separate or recombine on a picosecond time scale in viscous glycerol-water solutions. From the equilibrium amplitude of the fraction dissociated during the laser pulse, the geminate recombination rate constant is calculated to be 3 X 10(9)/s. This rate coefficient is only weakly dependent on temperature or viscosity. As previously observed the fraction that escapes depends on the solvent viscosity [Marden, M. C. (1983) Ph.D. Thesis, University of Illinois-Urbana]. A model consisting of a single barrier plus diffusive escape is used to simulate the kinetics during and just after the flash.
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Hazard ES, Gibson QH. Binding characteristics of a fluorescent analogue of diphosphoglyceric acid to human, amphibian and fish hemoglobins. ACTA ACUST UNITED AC 1984; 79:195-201. [PMID: 6548941 DOI: 10.1016/0305-0491(84)90013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An attempt was made to establish the binding of N-(2,4-diphosphobenzyl)-1-amino-5-naphthalenesulfonic acid, DIPANS, as an estimator of conformation in the carbonmonoxy (CO)-hemoglobins (Hbs) of several vertebrates. DIPANS failed to bind menhaden I, trout I or tuna Hbs which are ligand insensitive. Below a pH of 7.0, DIPANS bound menhaden II, Bufo, Xenopus, and human Hbs with a binding stoichiometry greater than one. The charge of the DIPANS molecule does not control its binding to these Hbs. The binding to human CO-Hb can not be due to Hb conformation. For Xenopus Hbs and menhaden II, conformation predominates DIPANS binding. The binding to CO-Hb of DIPANS, can not be unambiguously attributed to the Hb's quaternary conformation.
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Hutchison VH, Hazard ES. Erythrocytic organic phosphates: diel and seasonal cycles in the frog, Rana berlandieri. Comp Biochem Physiol A Comp Physiol 1984; 79:533-8. [PMID: 6150789 DOI: 10.1016/0300-9629(84)90443-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Hemoglobin (Hb) concentration, hematocrit (Hct), total organic phosphates (Ptot), nucleoside triphosphates (NTP), 2,3-diphosphoglycerate (DPG), and "inositol polyphosphates" (IPP) were measured in the erythrocytes of adult frogs at different times of day in winter and summer after acclimatization to 15 degrees C and an LD 12:12 photoperiod. The same measurements were also made on animals acclimated to LD 16:8 in summer. All of the measured parameters varied significantly at different times of the day and between seasons in animals acclimated to an LD 12:12 photoperiod. Summer animals acclimated to LD 16:8 showed significant diel cycles only in Hct and Hb.
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