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Cortes S, Farhat E, Talarico G, Mennigen JA. The dynamic transcriptomic response of the goldfish brain under chronic hypoxia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101233. [PMID: 38608489 DOI: 10.1016/j.cbd.2024.101233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Oxygen is essential to fuel aerobic metabolism. Some species evolved mechanisms to tolerate periods of severe hypoxia and even anoxia in their environment. Among them, goldfish (Carassius auratus) are unique, in that they do not enter a comatose state under severely hypoxic conditions. There is thus significant interest in the field of comparative physiology to uncover the mechanistic basis underlying hypoxia tolerance in goldfish, with a particular focus on the brain. Taking advantage of the recently published and annotated goldfish genome, we profile the transcriptomic response of the goldfish brain under normoxic (21 kPa oxygen saturation) and, following gradual reduction, constant hypoxic conditions after 1 and 4 weeks (2.1 kPa oxygen saturation). In addition to analyzing differentially expressed protein-coding genes and enriched pathways, we also profile differentially expressed microRNAs (miRs). Using in silico approaches, we identify possible miR-mRNA relationships. Differentially expressed transcripts compared to normoxia were either common to both timepoints of hypoxia exposure (n = 174 mRNAs; n = 6 miRs), or exclusive to 1-week (n = 441 mRNAs; n = 23 miRs) or 4-week hypoxia exposure (n = 491 mRNAs; n = 34 miRs). Under chronic hypoxia, an increasing number of transcripts, including those of paralogous genes, was downregulated over time, suggesting a decrease in transcription. GO-terms related to the vascular system, oxidative stress, stress signalling, oxidoreductase activity, nucleotide- and intermediary metabolism, and mRNA posttranscriptional regulation were found to be enriched under chronic hypoxia. Known 'hypoxamiRs', such as miR-210-3p/5p, and miRs such as miR-29b-3p likely contribute to posttranscriptional regulation of these pathways under chronic hypoxia in the goldfish brain.
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Affiliation(s)
- S Cortes
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada; Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - E Farhat
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway
| | - Ggm Talarico
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada
| | - J A Mennigen
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada.
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2
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Bergmans S, Noel NCL, Masin L, Harding EG, Krzywańska AM, De Schutter JD, Ayana R, Hu CK, Arckens L, Ruzycki PA, MacDonald RB, Clark BS, Moons L. Age-related dysregulation of the retinal transcriptome in African turquoise killifish. Aging Cell 2024:e14192. [PMID: 38742929 DOI: 10.1111/acel.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNAseq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in the ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterized, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNAseq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasizes the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.
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Affiliation(s)
- Steven Bergmans
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research Group, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Nicole C L Noel
- University College London, Institute of Ophthalmology, London, UK
| | - Luca Masin
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research Group, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Ellen G Harding
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, Missouri, USA
| | | | - Julie D De Schutter
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research Group, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Rajagopal Ayana
- Department of Biology, Animal Physiology and Neurobiology Section, Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Chi-Kuo Hu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, USA
| | - Lut Arckens
- Department of Biology, Animal Physiology and Neurobiology Section, Laboratory of Neuroplasticity and Neuroproteomics, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Philip A Ruzycki
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Ryan B MacDonald
- University College London, Institute of Ophthalmology, London, UK
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center of Regenerative Medicine, Center of Regenerative Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Lieve Moons
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research Group, KU Leuven, Leuven Brain Institute, Leuven, Belgium
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3
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Chhunchha B, Kumar R, Kubo E, Thakur P, Singh DP. Prdx6 Regulates Nlrp3 Inflammasome Activation-Driven Inflammatory Response in Lens Epithelial Cells. Int J Mol Sci 2023; 24:16276. [PMID: 38003466 PMCID: PMC10671722 DOI: 10.3390/ijms242216276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The continuum of antioxidant response dysregulation in aging/oxidative stress-driven Nlrp3 inflammasome activation-mediated inflammatory response is associated with age-related diseases. Peroxiredoxin (Prdx) 6 is a key antioxidant that provides cytoprotection by regulating redox homeostasis. Herein, using lens epithelial cells (LECs) derived from the targeted inactivation of Prdx6 gene and aging lenses, we present molecular evidence that Prdx6-deficiency causes oxidative-driven Nlrp3 inflammasome activation, resulting in pyroptosis in aging/redox active cells wherein Prdx6 availability offsets the inflammatory process. We observed that Prdx6-/- and aging LECs harboring accumulated reactive oxygen species (ROS) showed augmented activation of Nlrp3 and bioactive inflammatory components, like Caspase-1, IL-1β, ASC and Gasdermin-D. Similar to lipopolysaccharide treatment, oxidative exposure led to further ROS amplification with increased activation of the Nlrp3 inflammasome pathway. Mechanistically, we found that oxidative stress enhanced Kruppel-like factor 9 (Klf9) expression in aging/Prdx6-/- mLECs, leading to a Klf9-dependent increase in Nlrp3 transcription, while the elimination of ROS by the delivery of Prdx6 or by silencing Klf9 prevented the inflammatory response. Altogether, our data identify the biological significance of Prdx6 as an intrinsic checkpoint for regulating the cellular health of aging or redox active LECs and provide opportunities to develop antioxidant-based therapeutic(s) to prevent oxidative/aging-related diseases linked to aberrant Nlrp3 inflammasome activation.
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Affiliation(s)
- Bhavana Chhunchha
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (R.K.); (P.T.)
| | - Rakesh Kumar
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (R.K.); (P.T.)
| | - Eri Kubo
- Department of Ophthalmology, Kanazawa Medical University, Kahoku 9200293, Ishikawa, Japan;
| | - Priyanka Thakur
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (R.K.); (P.T.)
| | - Dhirendra P. Singh
- Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (R.K.); (P.T.)
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Thakkar C, Alikunju S, Niranjan N, Rizvi W, Abbas A, Abdellatif M, Sayed D. Klf9 plays a critical role in GR -dependent metabolic adaptations in cardiomyocytes. Cell Signal 2023; 111:110886. [PMID: 37690661 PMCID: PMC10591860 DOI: 10.1016/j.cellsig.2023.110886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Glucocorticoids through activation of the Glucocorticoid receptor (GR) play an essential role in cellular homeostasis during physiological variations and in response to stress. Our genomic GR binding and transcriptome data from Dexamethasone (Dex) treated cardiomyocytes showed an early differential regulation of mostly transcription factors, followed by sequential change in genes involved in downstream functional pathways. We examined the role of Krüppel-like factor 9 (Klf9), an early direct target of GR in cardiomyocytes. Klf9-ChIPseq identified 2150 genes that showed an increase in Klf9 binding in response to Dex. Transcriptome analysis of Dex treated cardiomyocytes with or without knockdown of Klf9 revealed differential regulation of 1777 genes, of which a reversal in expression is seen in 1640 genes with knockdown of Klf9 compared to Dex. Conversely, only 137 (∼8%) genes show further dysregulation in expression with siKLf9, as seen with Dex treated cardiomyocytes. Functional annotation identified genes of metabolic pathways on the top of differentially expressed genes, including those involved in glycolysis and oxidative phosphorylation. Knockdown of Klf9 in cardiomyocytes inhibited Dex induced increase in glycolytic function and mitochondrial spare respiratory capacity, as measured by glycolysis and mito stress tests, respectively. Thus, we conclude that cyclic, diurnal GR activation, through Klf9 -dependent feedforward signaling plays a central role in maintaining cellular homeostasis through metabolic adaptations in cardiomyocytes.
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Affiliation(s)
- Chandni Thakkar
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Saleena Alikunju
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Nandita Niranjan
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Wajiha Rizvi
- High School Research Intern, Wayne Hills High School, Wayne, NJ 07470, United States of America
| | - Ali Abbas
- From the Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07103, United States of America
| | - Maha Abdellatif
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Danish Sayed
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America.
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5
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Eachus H, Oberski L, Paveley J, Bacila I, Ashton JP, Esposito U, Seifuddin F, Pirooznia M, Elhaik E, Placzek M, Krone NP, Cunliffe VT. Glucocorticoid receptor regulates protein chaperone, circadian clock and affective disorder genes in the zebrafish brain. Dis Model Mech 2023; 16:dmm050141. [PMID: 37525888 PMCID: PMC10565112 DOI: 10.1242/dmm.050141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023] Open
Abstract
Glucocorticoid resistance is commonly observed in depression, and has been linked to reduced expression and/or function of the glucocorticoid receptor (NR3C1 in human, hereafter referred to as GR). Previous studies have shown that GR-mutant zebrafish exhibit behavioural abnormalities that are indicative of an affective disorder, suggesting that GR plays a role in brain function. We compared the brain methylomes and brain transcriptomes of adult wild-type and GR-mutant zebrafish, and identified 249 differentially methylated regions (DMRs) that are regulated by GR. These include a cluster of CpG sites within the first intron of fkbp5, the gene encoding the glucocorticoid-inducible heat shock protein co-chaperone Fkbp5. RNA-sequencing analysis revealed that genes associated with chaperone-mediated protein folding, the regulation of circadian rhythm and the regulation of metabolism are particularly sensitive to loss of GR function. In addition, we identified subsets of genes exhibiting GR-regulated transcription that are known to regulate behaviour, and are linked to unipolar depression and anxiety. Taken together, our results identify key biological processes and novel molecular mechanisms through which the GR is likely to mediate responses to stress in the adult zebrafish brain, and they provide further support for the zebrafish GR mutant as a model for the study of affective disorders.
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Affiliation(s)
- Helen Eachus
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Lara Oberski
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Jack Paveley
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Irina Bacila
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - John-Paul Ashton
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Umberto Esposito
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Building 12, 12 South Drive, Bethesda, MD 20892, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Building 12, 12 South Drive, Bethesda, MD 20892, USA
| | - Eran Elhaik
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Marysia Placzek
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Nils P. Krone
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Vincent T. Cunliffe
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Drepanos L, Gans IM, Grendler J, Guitar S, Fuqua JH, Maki NJ, Tilden AR, Graber JH, Coffman JA. Loss of Krüppel-like factor 9 deregulates both physiological gene expression and development. Sci Rep 2023; 13:12239. [PMID: 37507475 PMCID: PMC10382561 DOI: 10.1038/s41598-023-39453-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Krüppel-like factor 9 (Klf9) is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress-responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 days post-fertilization (dpf). However, klf9 expression oscillates diurnally, and the sampled time point corresponded to its expression nadir. To determine if the transcriptomic effects of the klf9-/- mutation vary with time of day, we performed bulk RNA-seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9-/- mutation that we reported previously are robust to time of day, the mutation has additional effects that manifest only at the predawn time point. We used a published single-cell atlas of zebrafish development to associate the effects of the klf9-/- mutation with different cell types and found that the mutation increased mRNA associated with digestive organs (liver, pancreas, and intestine) and decreased mRNA associated with differentiating neurons and blood. Measurements from confocally-imaged larvae suggest that overrepresentation of liver mRNA in klf9-/- mutants is due to development of enlarged livers.
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Affiliation(s)
| | - Ian M Gans
- MDI Biological Laboratory, Salisbury Cove, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | | | | | | | | | | | | | - James A Coffman
- MDI Biological Laboratory, Salisbury Cove, ME, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
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7
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Yerra VG, Drosatos K. Specificity Proteins (SP) and Krüppel-like Factors (KLF) in Liver Physiology and Pathology. Int J Mol Sci 2023; 24:4682. [PMID: 36902112 PMCID: PMC10003758 DOI: 10.3390/ijms24054682] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
The liver acts as a central hub that controls several essential physiological processes ranging from metabolism to detoxification of xenobiotics. At the cellular level, these pleiotropic functions are facilitated through transcriptional regulation in hepatocytes. Defects in hepatocyte function and its transcriptional regulatory mechanisms have a detrimental influence on liver function leading to the development of hepatic diseases. In recent years, increased intake of alcohol and western diet also resulted in a significantly increasing number of people predisposed to the incidence of hepatic diseases. Liver diseases constitute one of the serious contributors to global deaths, constituting the cause of approximately two million deaths worldwide. Understanding hepatocyte transcriptional mechanisms and gene regulation is essential to delineate pathophysiology during disease progression. The current review summarizes the contribution of a family of zinc finger family transcription factors, named specificity protein (SP) and Krüppel-like factors (KLF), in physiological hepatocyte functions, as well as how they are involved in the onset and development of hepatic diseases.
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Affiliation(s)
| | - Konstantinos Drosatos
- Metabolic Biology Laboratory, Cardiovascular Center, Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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8
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Gans IM, Coffman JA. Glucocorticoid-Mediated Developmental Programming of Vertebrate Stress Responsivity. Front Physiol 2021; 12:812195. [PMID: 34992551 PMCID: PMC8724051 DOI: 10.3389/fphys.2021.812195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023] Open
Abstract
Glucocorticoids, vertebrate steroid hormones produced by cells of the adrenal cortex or interrenal tissue, function dynamically to maintain homeostasis under constantly changing and occasionally stressful environmental conditions. They do so by binding and thereby activating nuclear receptor transcription factors, the Glucocorticoid and Mineralocorticoid Receptors (MR and GR, respectively). The GR, by virtue of its lower affinity for endogenous glucocorticoids (cortisol or corticosterone), is primarily responsible for transducing the dynamic signals conveyed by circadian and ultradian glucocorticoid oscillations as well as transient pulses produced in response to acute stress. These dynamics are important determinants of stress responsivity, and at the systemic level are produced by feedforward and feedback signaling along the hypothalamus-pituitary-adrenal/interrenal axis. Within receiving cells, GR signaling dynamics are controlled by the GR target gene and negative feedback regulator fkpb5. Chronic stress can alter signaling dynamics via imperfect physiological adaptation that changes systemic and/or cellular set points, resulting in chronically elevated cortisol levels and increased allostatic load, which undermines health and promotes development of disease. When this occurs during early development it can "program" the responsivity of the stress system, with persistent effects on allostatic load and disease susceptibility. An important question concerns the glucocorticoid-responsive gene regulatory network that contributes to such programming. Recent studies show that klf9, a ubiquitously expressed GR target gene that encodes a Krüppel-like transcription factor important for metabolic plasticity and neuronal differentiation, is a feedforward regulator of GR signaling impacting cellular glucocorticoid responsivity, suggesting that it may be a critical node in that regulatory network.
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Affiliation(s)
- Ian M. Gans
- MDI Biological Laboratory, Salisbury Cove, ME, United States
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
| | - James A. Coffman
- MDI Biological Laboratory, Salisbury Cove, ME, United States
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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