1
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Huang H, Wang W. Molecular mechanisms of glucocorticoid resistance. Eur J Clin Invest 2023; 53:e13901. [PMID: 36346177 DOI: 10.1111/eci.13901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND As a powerful anti-inflammatory, immunosuppressive, and antiproliferative drug, glucocorticoid (GC) plays an important role in the treatment of various diseases. However, some patients may experience glucocorticoid resistance (GCR) in clinical, and its molecular mechanism have not been determined. METHODS The authors performed a review of the literature on GCR focusing on mutations in the NR3C1 gene and impaired glucocorticoid receptor (GR) signalling, using METSTR (2000 through May 2022) to identify original articles and reviews on this topic. The search terms included 'glucocorticoid resistance/insensitive', 'steroid resistance/insensitive', 'NR3C1', and 'glucocorticoid receptor'. RESULTS Primary GCR is mainly caused by NR3C1 gene mutation, and 31 NR3C1 gene mutations have been reported so far. Secondary GCR is caused by impaired GC signalling pathways, including decreased expression of GR, impaired nuclear translocation of GR, and impaired binding of GR to GC and GR to target genes. However, the current research is more on the expression level of GR, and there are relatively few studies on other mechanisms. In addition, methods for improving GC sensitivity are rarely reported. CONCLUSION The molecular mechanisms of GCR are complex and may differ in different diseases or different patients. In future studies, when exploring the mechanism of GCR, methods to improve GC sensitivity should also be investigated.
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Affiliation(s)
- Huanming Huang
- The Fourth Hospital of Hebei Medical University, Hebei Medical University, Shijiazhuang, China
| | - Wenqing Wang
- The Fourth Hospital of Hebei Medical University, Hebei Medical University, Shijiazhuang, China
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2
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Role of glucocorticoid receptor mutations in hypertension and adrenal gland hyperplasia. Pflugers Arch 2022; 474:829-840. [PMID: 35732960 PMCID: PMC9217122 DOI: 10.1007/s00424-022-02715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/06/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
Hypertension is one of the leading causes of premature death in humans and exhibits a complex aetiology including environmental and genetic factors. Mutations within the glucocorticoid receptor (GR) can cause glucocorticoid resistance, which is characterized by several clinical features like hypercortisolism, hypokalaemia, adrenal hyperplasia and hypertension. Altered glucocorticoid receptor signalling further affects sodium and potassium homeostasis as well as blood pressure regulation and cell proliferation and differentiation that influence organ development and function. In salt-sensitive hypertension, excessive renal salt transport and sympathetic nervous system stimulation may occur simultaneously, and, thus, both the mineralocorticoid receptor (MR) and the GR-signalling may be implicated or even act interdependently. This review focuses on identified GR mutations in human primary generalized glucocorticoid resistance (PGGR) patients and their related clinical phenotype with specific emphasis on adrenal gland hyperplasia and hypertension. We compare these findings to mouse and rat mutants harbouring genetically engineered mutations to further dissect the cause and/or the consequence of clinical features which are common or different.
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3
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Krämer J, Kang R, Grimm LM, De Cola L, Picchetti P, Biedermann F. Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chem Rev 2022; 122:3459-3636. [PMID: 34995461 PMCID: PMC8832467 DOI: 10.1021/acs.chemrev.1c00746] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.
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Affiliation(s)
- Joana Krämer
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rui Kang
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Laura M. Grimm
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Luisa De Cola
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Dipartimento
DISFARM, University of Milano, via Camillo Golgi 19, 20133 Milano, Italy
- Department
of Molecular Biochemistry and Pharmacology, Instituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156 Milano, Italy
| | - Pierre Picchetti
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- P.P.: email,
| | - Frank Biedermann
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- F.B.: email,
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4
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Nicolaides NC, Charmandari E. Primary Generalized Glucocorticoid Resistance and Hypersensitivity Syndromes: A 2021 Update. Int J Mol Sci 2021; 22:ijms221910839. [PMID: 34639183 PMCID: PMC8509180 DOI: 10.3390/ijms221910839] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Glucocorticoids are the final products of the neuroendocrine hypothalamic-pituitary-adrenal axis, and play an important role in the stress response to re-establish homeostasis when it is threatened, or perceived as threatened. These steroid hormones have pleiotropic actions through binding to their cognate receptor, the human glucocorticoid receptor, which functions as a ligand-bound transcription factor inducing or repressing the expression of a large number of target genes. To achieve homeostasis, glucocorticoid signaling should have an optimal effect on all tissues. Indeed, any inappropriate glucocorticoid effect in terms of quantity or quality has been associated with pathologic conditions, which are characterized by short-term or long-lasting detrimental effects. Two such conditions, the primary generalized glucocorticoid resistance and hypersensitivity syndromes, are discussed in this review article. Undoubtedly, the tremendous progress of structural, molecular, and cellular biology, in association with the continued progress of biotechnology, has led to a better and more in-depth understanding of these rare endocrinologic conditions, as well as more effective therapeutic management.
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Affiliation(s)
- Nicolas C. Nicolaides
- First Department of Pediatrics, Division of Endocrinology, Metabolism and Diabetes, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece;
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, University of Athens, 11527 Athens, Greece
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
- Correspondence:
| | - Evangelia Charmandari
- First Department of Pediatrics, Division of Endocrinology, Metabolism and Diabetes, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece;
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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5
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Martins CS, de Castro M. Generalized and tissue specific glucocorticoid resistance. Mol Cell Endocrinol 2021; 530:111277. [PMID: 33864884 DOI: 10.1016/j.mce.2021.111277] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022]
Abstract
Glucocorticoids (GCs) are steroid hormones that influence several physiologic functions and are among the most frequently prescribed drugs worldwide. Resistance to GCs has been observed in the context of the familial generalized GC resistance (Chrousos' syndrome) or tissue specific GC resistance in chronic inflammatory states. In this review, we have summarized the major factors that influence individual glucocorticoid sensitivity/resistance. The fine-tuning of GC action is determined in a tissue-specific fashion that includes the combination of different GC receptor promoters, translation initiation sites, splice isoforms, interacting proteins, post-translational modifications, and alternative mechanisms of signal transduction.
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Affiliation(s)
- Clarissa Silva Martins
- Department of Internal Medicine - Ribeirao Preto Medical School - University of Sao Paulo, Ribeirao Preto, SP, Brazil; School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Margaret de Castro
- Department of Internal Medicine - Ribeirao Preto Medical School - University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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6
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A Novel Pathogenic Variant in the N-Terminal Domain of the Glucocorticoid Receptor, Causing Glucocorticoid Resistance. Mol Diagn Ther 2020; 24:473-485. [DOI: 10.1007/s40291-020-00480-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Othman MAK, Đurišić M, Samardzija G, Vujić D, Lakic N, Zecevic Z, Al-Shaheri F, Aroutiounian R, Melo JB, Carreira IM, Meyer B, Liehr T. Complex karyotype with cryptic FUS gene rearrangement and deletion of NR3C1 and VPREB1 genes in childhood B-cell acute lymphoblastic leukemia: A case report. Oncol Lett 2020; 19:2957-2962. [PMID: 32218851 DOI: 10.3892/ol.2020.11387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/02/2019] [Indexed: 12/18/2022] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is a hematopoietic malignancy characterized by overproduction of immature B-lymphoblasts. B-ALL is the most common pediatric tumor and remains the leading cause of mortality in children and adolescents. Molecular and cytogenetic analyses of B-ALL revealed recurrent genetic and structural genomic alterations which are routinely applied for diagnosis, prognosis and choice of treatment regimen. The present case report describes a 4-year-old female diagnosed with B-ALL. GTG-banding at low resolution revealed an abnormal clone with 46,XX,?t(X;19)(q13;q13.3),der(9) besides normal cells. Molecular cytogenetics demonstrated a balanced translocation between chromosomes 16 and 19, and an unbalanced translocation involving chromosomes 5 and 9. A locus-specific probe additionally identified that the FUS gene in 16p11.2 was split and its 5' region was translocated to subband 19q13.33, whereas the 3' region of the FUS gene remained on the derivative chromosome 16. Overall, this complex karyotype included four different chromosomes and five break events. Further analyses, including array-comparative genomic hybridization, additionally revealed biallelic deletion of the tumor suppressor genes CDKN2A/B, and deletion of the NR3C1 and VPREB1 genes. The patient passed away under treatment due to sepsis.
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Affiliation(s)
- Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D-07747 Jena, Germany
| | - Marina Đurišić
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Gordana Samardzija
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Dragana Vujić
- Medical School, University of Belgrade, 11000 Belgrade, Serbia
| | - Nina Lakic
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Zeljko Zecevic
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Fawaz Al-Shaheri
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D-07747 Jena, Germany
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, 0025 Yerevan, Armenia
| | - Joana B Melo
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO, Center for Research in The Environment, Genetics and Oncobiology, 3000-548 Coimbra, Portugal
| | - Isabel M Carreira
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO, Center for Research in The Environment, Genetics and Oncobiology, 3000-548 Coimbra, Portugal
| | | | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D-07747 Jena, Germany
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8
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Lu YT, Fan P, Zhang D, Zhang Y, Meng X, Zhang QY, Zhao L, Yang KQ, Zhou XL. Overview of Monogenic Forms of Hypertension Combined With Hypokalemia. Front Pediatr 2020; 8:543309. [PMID: 33569358 PMCID: PMC7868374 DOI: 10.3389/fped.2020.543309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
Hypertension is an important risk factor in many conditions and creates a heavy burden of disease and mortality globally. Polygenic hypertension is the most common form; however, it is increasingly recognized that monogenic hypertension is not rare, especially in patients with electrolyte disorders. Single genetic alterations are associated with plasma volume expansion and catecholamines/sympathetic excess with simultaneously increased potassium excretion in the urine and potassium intracellular shift. Early-onset refractory hypertension and profound hypokalemia are characteristics of monogenic hypertension. However, accumulated evidence shows the existence of phenotypic heterogeneity in monogenic hypertension meaning that, even for mild symptoms, clinicians cannot easily exclude the possibility of monogenic hypertension. Genetic, epigenetic and non-genetic factors are all possible mechanisms influencing phenotypic diversity. Genetic sequencing is a precise and efficient method that can broaden the mutant gene spectrum of the disease and is very helpful for understanding the pathophysiology of monogenic hypertension. Genetic sequencing, along with biochemical tests and imaging modalities, is essential for the early diagnosis and targeted management of monogenic hypertension to avoid long-term catastrophic complications.
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Affiliation(s)
- Yi-Ting Lu
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Fan
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Di Zhang
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Zhang
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xu Meng
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiong-Yu Zhang
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Zhao
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kun-Qi Yang
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xian-Liang Zhou
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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9
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Vitellius G, Delemer B, Caron P, Chabre O, Bouligand J, Pussard E, Trabado S, Lombes M. Impaired 11β-Hydroxysteroid Dehydrogenase Type 2 in Glucocorticoid-Resistant Patients. J Clin Endocrinol Metab 2019; 104:5205-5216. [PMID: 31225872 DOI: 10.1210/jc.2019-00800] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/17/2019] [Indexed: 02/13/2023]
Abstract
CONTEXT Six patients carrying heterozygous loss-of-function mutations of glucocorticoid (GC) receptor (GR) presented with hypercortisolism, associated with low kalemia, low plasma renin, and aldosterone levels, with or without hypertension, suggesting a pseudohypermineralocorticism whose mechanisms remain unclear. We hypothesize that an impaired activity of the 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2; encoded by the HSD11B2 gene), catalyzing cortisol (F) inactivation, may account for an inappropriate activation of a renal mineralocorticoid signaling pathway in these GC-resistant patients. OBJECTIVE We aim at studying the GR-mediated regulation of HSD11B2. DESIGN The HSD11B2 promoter was subcloned and luciferase reporter assays evaluated GR-dependent HSD11B2 regulation, and 11β-HSD2 expression/activity was studied in human breast cancer MCF7 cells, endogenously expressing this enzyme. RESULTS Transfection assays revealed that GR transactivated the long (2.1-kbp) HSD11B2 promoter construct, whereas a defective 501H GR mutant was unable to stimulate luciferase activity. GR-mediated transactivation of the HSD11B2 gene was inhibited by the GR antagonist RU486. A threefold increase in HSD11B2 mRNA levels was observed after dexamethasone (DXM) treatment of MCF7 cells, inhibited by RU486 or by actinomycin, supporting a GR-dependent transcription. Chromatin immunoprecipitation further demonstrated a DXM-dependent GR recruitment onto the HSD11B2 promoter. 11β-HSD2 activity, evaluated by the cortisone/F ratio, quantified by liquid chromatography/tandem mass spectrometry, was 10-fold higher in the supernatant of DXM-treated cells than controls, consistent with a GR-dependent stimulation of 11β-HSD2 catalytic activity. CONCLUSION Collectively, we demonstrate that 11β-HSD2 expression and activity are transcriptionally regulated by GR. In the context of GR haploinsufficiency, these findings provide evidence that defective GR signaling may account for apparent mineralocorticoid excess in GC-resistant patients.
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Affiliation(s)
- Géraldine Vitellius
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche_S U1185, Faculty of Medicine at Université Paris-Sud, University Paris-Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - Brigitte Delemer
- Service d'Endocrinologie-Diabète-Nutrition, Hôpital Robert Debré, Centre Hospitalier Universitaire de Reims, Reims, France
| | - Philippe Caron
- Service d'Endocrinologie, Pôle Cardio-Vasculaire et Métabolique, Centre Hospitalier Universitaire de Larrey, Toulouse, France
| | - Olivier Chabre
- Endocrinologie, Pavillon des Écrins, Centre Hospitalier Universitaire de Grenoble, La Tronche, Grenoble, France
| | - Jérôme Bouligand
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche_S U1185, Faculty of Medicine at Université Paris-Sud, University Paris-Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris-Sud, Assistance Publique-Hôpitaux de Paris, Centre Hospitalier Universitaire de Bicêtre, France
| | - Eric Pussard
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche_S U1185, Faculty of Medicine at Université Paris-Sud, University Paris-Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris-Sud, Assistance Publique-Hôpitaux de Paris, Centre Hospitalier Universitaire de Bicêtre, France
| | - Séverine Trabado
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche_S U1185, Faculty of Medicine at Université Paris-Sud, University Paris-Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris-Sud, Assistance Publique-Hôpitaux de Paris, Centre Hospitalier Universitaire de Bicêtre, France
| | - Marc Lombes
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche_S U1185, Faculty of Medicine at Université Paris-Sud, University Paris-Sud, Université Paris-Saclay, Le Kremlin Bicêtre, France
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10
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Jalili V, Matteucci M, Masseroli M, Ceri S. Explorative visual analytics on interval-based genomic data and their metadata. BMC Bioinformatics 2017; 18:536. [PMID: 29202689 PMCID: PMC5715631 DOI: 10.1186/s12859-017-1945-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 11/19/2017] [Indexed: 02/07/2023] Open
Abstract
Background With the wide-spreading of public repositories of NGS processed data, the availability of user-friendly and effective tools for data exploration, analysis and visualization is becoming very relevant. These tools enable interactive analytics, an exploratory approach for the seamless “sense-making” of data through on-the-fly integration of analysis and visualization phases, suggested not only for evaluating processing results, but also for designing and adapting NGS data analysis pipelines. Results This paper presents abstractions for supporting the early analysis of NGS processed data and their implementation in an associated tool, named GenoMetric Space Explorer (GeMSE). This tool serves the needs of the GenoMetric Query Language, an innovative cloud-based system for computing complex queries over heterogeneous processed data. It can also be used starting from any text files in standard BED, BroadPeak, NarrowPeak, GTF, or general tab-delimited format, containing numerical features of genomic regions; metadata can be provided as text files in tab-delimited attribute-value format. GeMSE allows interactive analytics, consisting of on-the-fly cycling among steps of data exploration, analysis and visualization that help biologists and bioinformaticians in making sense of heterogeneous genomic datasets. By means of an explorative interaction support, users can trace past activities and quickly recover their results, seamlessly going backward and forward in the analysis steps and comparative visualizations of heatmaps. Conclusions GeMSE effective application and practical usefulness is demonstrated through significant use cases of biological interest. GeMSE is available at http://www.bioinformatics.deib.polimi.it/GeMSE/, and its source code is available at https://github.com/Genometric/GeMSE under GPLv3 open-source license.
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Affiliation(s)
- Vahid Jalili
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy.
| | - Matteo Matteucci
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy
| | - Marco Masseroli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy
| | - Stefano Ceri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy
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11
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Irving JAE, Enshaei A, Parker CA, Sutton R, Kuiper RP, Erhorn A, Minto L, Venn NC, Law T, Yu J, Schwab C, Davies R, Matheson E, Davies A, Sonneveld E, den Boer ML, Love SB, Harrison CJ, Hoogerbrugge PM, Revesz T, Saha V, Moorman AV. Integration of genetic and clinical risk factors improves prognostication in relapsed childhood B-cell precursor acute lymphoblastic leukemia. Blood 2016; 128:911-22. [PMID: 27229005 PMCID: PMC5026463 DOI: 10.1182/blood-2016-03-704973] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 12/13/2022] Open
Abstract
Somatic genetic abnormalities are initiators and drivers of disease and have proven clinical utility at initial diagnosis. However, the genetic landscape and its clinical utility at relapse are less well understood and have not been studied comprehensively. We analyzed cytogenetic data from 427 children with relapsed B-cell precursor ALL treated on the international trial, ALLR3. Also we screened 238 patients with a marrow relapse for selected copy number alterations (CNAs) and mutations. Cytogenetic risk groups were predictive of outcome postrelapse and survival rates at 5 years for patients with good, intermediate-, and high-risk cytogenetics were 68%, 47%, and 26%, respectively (P < .001). TP53 alterations and NR3C1/BTG1 deletions were associated with a higher risk of progression: hazard ratio 2.36 (95% confidence interval, 1.51-3.70, P < .001) and 2.15 (1.32-3.48, P = .002). NRAS mutations were associated with an increased risk of progression among standard-risk patients with high hyperdiploidy: 3.17 (1.15-8.71, P = .026). Patients classified clinically as standard and high risk had distinct genetic profiles. The outcome of clinical standard-risk patients with high-risk cytogenetics was equivalent to clinical high-risk patients. Screening patients at relapse for key genetic abnormalities will enable the integration of genetic and clinical risk factors to improve patient stratification and outcome. This study is registered at www.clinicaltrials.org as #ISCRTN45724312.
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Affiliation(s)
- Julie A E Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amir Enshaei
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catriona A Parker
- Children's Cancer Group, Institute of Cancer, Faculty of Medical & Human Sciences, The University of Manchester, Manchester, United Kingdom; Royal Manchester Children's Hospital, Central Manchester University Hospitals Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Rosemary Sutton
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amy Erhorn
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lynne Minto
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicola C Venn
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Tamara Law
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Jiangyan Yu
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire Schwab
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rosanna Davies
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Matheson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alysia Davies
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Monique L den Boer
- Dutch Childhood Oncology Group, The Hague, The Netherlands; Department of Paediatric Oncology and Haematology, Erasmus MC-Sophia Children's Hospital, University Medical Centre, Rotterdam, The Netherlands
| | - Sharon B Love
- Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
| | - Christine J Harrison
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter M Hoogerbrugge
- Dutch Childhood Oncology Group, The Hague, The Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Tamas Revesz
- Department of Haematology-Oncology, SA Pathology at Women's and Children's Hospital and University of Adelaide, Adelaide, Australia; and
| | - Vaskar Saha
- Children's Cancer Group, Institute of Cancer, Faculty of Medical & Human Sciences, The University of Manchester, Manchester, United Kingdom; Royal Manchester Children's Hospital, Central Manchester University Hospitals Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Tata Translational Cancer Research Centre, Tata Medical Center, New Town, Kolkata, India
| | - Anthony V Moorman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
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Targeted sequencing of refractory myeloma reveals a high incidence of mutations in CRBN and Ras pathway genes. Blood 2016; 128:1226-33. [PMID: 27458004 DOI: 10.1182/blood-2016-02-698092] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
In this study, targeted sequencing to screen 50 multidrug refractory multiple myeloma (rMM) patients was performed by using the Multiple Myeloma Mutation Panel. Patients were pretreated with both immunomodulatory drugs (IMiDs) and proteasome inhibitors (PIs), and 88%, 78%, and 68% were refractory to an IMiD, a PI, or both, respectively. The majority of patients had progressive (82%) or refractory (78%) disease immediately before sampling, with 43% being IMiD refractory and 46% being PI refractory in the most recent line of therapy. Compared with newly diagnosed MM, an increased prevalence of mutations in the Ras pathway genes KRAS, NRAS, and/or BRAF (72%), as well as TP53 (26%), CRBN (12%), and CRBN pathway genes (10%) was observed. Longitudinal analyses performed in 3 patients with CRBN mutations at time of IMiD resistance confirmed that these mutations were undetectable at earlier, IMiD-sensitive time points. Furthermore, the functional introduction of these mutations in MM cells conferred lenalidomide resistance in vitro. These data indicate a differential genetic landscape in rMM associated with drug response.
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Sautron V, Terenina E, Gress L, Lippi Y, Billon Y, Larzul C, Liaubet L, Villa-Vialaneix N, Mormède P. Time course of the response to ACTH in pig: biological and transcriptomic study. BMC Genomics 2015; 16:961. [PMID: 26578410 PMCID: PMC4650497 DOI: 10.1186/s12864-015-2118-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/20/2015] [Indexed: 11/10/2022] Open
Abstract
Background HPA axis plays a major role in physiological homeostasis. It is also involved in stress and adaptive response to the environment. In farm animals in general and specifically in pigs, breeding strategies have highly favored production traits such as lean growth rate, feed efficiency and prolificacy at the cost of robustness. On the hypothesis that the HPA axis could contribute to the trade-off between robustness and production traits, we have designed this experiment to explore individual variation in the biological response to the main stress hormone, cortisol, in pigs. We used ACTH injections to trigger production of cortisol in 120 juvenile Large White (LW) pigs from 28 litters and the kinetics of the response was measured with biological variables and whole blood gene expression at 4 time points. A multilevel statistical analysis was used to take into account the longitudinal aspect of the data. Results Cortisol level reached its peak 1 h after ACTH injection. White blood cell composition was modified with a decrease of lymphocytes and monocytes and an increase of granulocytes (FDR<0.05). Basal level of cortisol was correlated with birth and weaning weights. Microarray analysis identified 65 unique genes of which expression responded to the injection of ACTH (adjusted P<0.05). These genes were classified into 4 clusters with distinctive kinetics in response to ACTH injection. The first cluster identified genes strongly correlated to cortisol and previously reported as being regulated by glucocorticoids. In particular, DDIT4, DUSP1, FKBP5, IL7R, NFKBIA, PER1, RGS2 and RHOB were shown to be connected to each other by the glucocorticoid receptor NR3C1. Most of the differentially expressed genes that encode transcription factors have not been described yet as being important in transcription networks involved in stress response. Their co-expression may mean co-regulation and they could thus provide new patterns of biomarkers of the individual sensitivity to cortisol. Conclusions We identified 65 genes as biological markers of HPA axis activation at the gene expression level. These genes might be candidates for a better understanding of the molecular mechanisms of the stress response. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2118-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valérie Sautron
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Elena Terenina
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Laure Gress
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | | | - Yvon Billon
- INRA, UE 1372 GenESI, Surgeres, F-17700, France.
| | - Catherine Larzul
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Laurence Liaubet
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Nathalie Villa-Vialaneix
- INRA, UR 0875 MIAT Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, F-31326, France.
| | - Pierre Mormède
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
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Romanov RA, Alpár A, Zhang MD, Zeisel A, Calas A, Landry M, Fuszard M, Shirran SL, Schnell R, Dobolyi Á, Oláh M, Spence L, Mulder J, Martens H, Palkovits M, Uhlen M, Sitte HH, Botting CH, Wagner L, Linnarsson S, Hökfelt T, Harkany T. A secretagogin locus of the mammalian hypothalamus controls stress hormone release. EMBO J 2014; 34:36-54. [PMID: 25430741 DOI: 10.15252/embj.201488977] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A hierarchical hormonal cascade along the hypothalamic-pituitary-adrenal axis orchestrates bodily responses to stress. Although corticotropin-releasing hormone (CRH), produced by parvocellular neurons of the hypothalamic paraventricular nucleus (PVN) and released into the portal circulation at the median eminence, is known to prime downstream hormone release, the molecular mechanism regulating phasic CRH release remains poorly understood. Here, we find a cohort of parvocellular cells interspersed with magnocellular PVN neurons expressing secretagogin. Single-cell transcriptome analysis combined with protein interactome profiling identifies secretagogin neurons as a distinct CRH-releasing neuron population reliant on secretagogin's Ca(2+) sensor properties and protein interactions with the vesicular traffic and exocytosis release machineries to liberate this key hypothalamic releasing hormone. Pharmacological tools combined with RNA interference demonstrate that secretagogin's loss of function occludes adrenocorticotropic hormone release from the pituitary and lowers peripheral corticosterone levels in response to acute stress. Cumulatively, these data define a novel secretagogin neuronal locus and molecular axis underpinning stress responsiveness.
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Affiliation(s)
- Roman A Romanov
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alán Alpár
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ming-Dong Zhang
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Amit Zeisel
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - André Calas
- Laboratory for Central Mechanisms of Pain Sensitization, Interdisciplinary Institute for Neuroscience, CNRS UMR 5297 Université Bordeaux 2, Bordeaux, France
| | - Marc Landry
- Laboratory for Central Mechanisms of Pain Sensitization, Interdisciplinary Institute for Neuroscience, CNRS UMR 5297 Université Bordeaux 2, Bordeaux, France
| | - Matthew Fuszard
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Sally L Shirran
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Robert Schnell
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Árpád Dobolyi
- Department of Anatomy, Semmelweis University, Budapest, Hungary
| | - Márk Oláh
- Department of Human Morphology and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Lauren Spence
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Miklós Palkovits
- Human Brain Tissue Bank and Laboratory, Semmelweis University, Budapest, Hungary
| | - Mathias Uhlen
- Science for Life Laboratory, Albanova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Harald H Sitte
- Center for Physiology and Pharmacology, Institute of Pharmacology Medical University of Vienna, Vienna, Austria
| | | | - Ludwig Wagner
- University Clinic for Internal Medicine III General Hospital Vienna, Vienna, Austria
| | - Sten Linnarsson
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Hökfelt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tibor Harkany
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
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Quax RA, Manenschijn L, Koper JW, Hazes JM, Lamberts SWJ, van Rossum EFC, Feelders RA. Glucocorticoid sensitivity in health and disease. Nat Rev Endocrinol 2013; 9:670-86. [PMID: 24080732 DOI: 10.1038/nrendo.2013.183] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glucocorticoids regulate many physiological processes and have an essential role in the systemic response to stress. For example, gene transcription is modulated by the glucocorticoid-glucocorticoid receptor complex via several mechanisms. The ultimate biologic responses to glucocorticoids are determined by not only the concentration of glucocorticoids but also the differences between individuals in glucocorticoid sensitivity, which is influenced by multiple factors. Differences in sensitivity to glucocorticoids in healthy individuals are partly genetically determined by functional polymorphisms of the gene that encodes the glucocorticoid receptor. Hereditary syndromes have also been identified that are associated with increased and decreased sensitivity to glucocorticoids. As a result of their anti-inflammatory properties, glucocorticoids are widely used in the treatment of allergic, inflammatory and haematological disorders. The variety in clinical responses to treatment with glucocorticoids reflects the considerable variation in glucocorticoid sensitivity between individuals. In immune-mediated disorders, proinflammatory cytokines can induce localized resistance to glucocorticoids via several mechanisms. Individual differences in how tissues respond to glucocorticoids might also be involved in the predisposition for and pathogenesis of the metabolic syndrome and mood disorders. In this Review, we summarize the mechanisms that influence glucocorticoid sensitivity in health and disease and discuss possible strategies to modulate glucocorticoid responsiveness.
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Affiliation(s)
- Rogier A Quax
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, Netherlands
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Rog-Zielinska EA, Thomson A, Kenyon CJ, Brownstein DG, Moran CM, Szumska D, Michailidou Z, Richardson J, Owen E, Watt A, Morrison H, Forrester LM, Bhattacharya S, Holmes MC, Chapman KE. Glucocorticoid receptor is required for foetal heart maturation. Hum Mol Genet 2013; 22:3269-82. [PMID: 23595884 DOI: 10.1093/hmg/ddt182] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoids are vital for the structural and functional maturation of foetal organs, yet excessive foetal exposure is detrimental to adult cardiovascular health. To elucidate the role of glucocorticoid signalling in late-gestation cardiovascular maturation, we have generated mice with conditional disruption of glucocorticoid receptor (GR) in cardiomyocytes and vascular smooth muscle cells using smooth muscle protein 22-driven Cre recombinase (SMGRKO mice) and compared them with mice with global deficiency in GR (GR(-/-)). Echocardiography shows impaired heart function in both SMGRKO and GR(-/-) mice at embryonic day (E)17.5, associated with generalized oedema. Cardiac ultrastructure is markedly disrupted in both SMGRKO and GR(-/-) mice at E17.5, with short, disorganized myofibrils and cardiomyocytes that fail to align in the compact myocardium. Failure to induce critical genes involved in contractile function, calcium handling and energy metabolism underpins this common phenotype. However, although hearts of GR(-/-) mice are smaller, with 22% reduced ventricular volume at E17.5, SMGRKO hearts are normally sized. Moreover, while levels of mRNA encoding atrial natriuretic peptide are reduced in E17.5 GR(-/-) hearts, they are normal in foetal SMGRKO hearts. These data demonstrate that structural, functional and biochemical maturation of the foetal heart is dependent on glucocorticoid signalling within cardiomyocytes and vascular smooth muscle, though some aspects of heart maturation (size, ANP expression) are independent of GR at these key sites.
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Affiliation(s)
- Eva A Rog-Zielinska
- Centre for Cardiovascular Science, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
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