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Text Mining Gene Selection to Understand Pathological Phenotype Using Biological Big Data. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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Quinkler M, Murray RD. In Response to: Prednisolone Replacement Therapy Mimics the Circadian Rhythm More Closely than Other Glucocorticoids. J Appl Lab Med 2017; 1:753-755. [DOI: 10.1373/jalm.2016.022616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/16/2016] [Indexed: 11/06/2022]
Affiliation(s)
| | - Robert D Murray
- Department of Endocrinology, Leeds Teaching Hospitals NHS Trust, St James's University Hospital, Leeds, UK
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Quinkler M, Ekman B, Marelli C, Uddin S, Zelissen P, Murray RD. Prednisolone is associated with a worse lipid profile than hydrocortisone in patients with adrenal insufficiency. Endocr Connect 2017; 6:1-8. [PMID: 27864317 PMCID: PMC5148794 DOI: 10.1530/ec-16-0081] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/18/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Prednisolone is used as glucocorticoid replacement therapy for adrenal insufficiency (AI). Recent data indicate that its use in AI is associated with low bone mineral density. Data on risk factors for cardiovascular disease in patients with AI treated with prednisolone are scarce, despite this condition being the predominant cause of excess mortality. We aimed to address this question using real-world data from the European Adrenal Insufficiency Registry (EU-AIR). DESIGN/METHODS EU-AIR, comprising of 19 centres across Germany, the Netherlands, Sweden and the UK, commenced enrolling patients with AI in August 2012. Patients receiving prednisolone (3-6 mg/day, n = 50) or hydrocortisone (15-30 mg/day, n = 909) were identified and grouped at a ratio of 1:3 (prednisolone:hydrocortisone) by matching for gender, age, duration and type of disease. Data from baseline and follow-up visits were analysed. Data from patients with congenital adrenal hyperplasia were excluded. RESULTS Significantly higher mean ± s.d. total (6.3 ± 1.6 vs 5.4 ± 1.1 mmol/L; P = 0.003) and low-density lipoprotein (LDL) cholesterol levels (3.9 ± 1.4 vs 3.2 ± 1.0 mmol/L; P = 0.013) were identified in 47 patients on prednisolone vs 141 receiving hydrocortisone at baseline and at follow-up (P = 0.005 and P = 0.006, respectively). HbA1c, high-density lipoprotein and triglyceride levels, body mass index, systolic and diastolic blood pressure and waist circumference were not significantly different. CONCLUSIONS This is the first matched analysis of its kind. Significantly higher LDL levels in patients receiving prednisolone relative to hydrocortisone could predict a higher relative risk of cardiovascular disease in the former group.
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Affiliation(s)
| | - Bertil Ekman
- Departments of Endocrinology and Medical and Health SciencesLinköping University, Linköping, Sweden
| | | | | | - Pierre Zelissen
- Department of Internal Medicine and EndocrinologyUniversity Medical Center Utrecht, Utrecht, the Netherlands
| | - Robert D Murray
- Department of EndocrinologyLeeds Teaching Hospitals NHS Trust, St James's University Hospital, Leeds, UK
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Gene Expression Profiles from Disease Discordant Twins Suggest Shared Antiviral Pathways and Viral Exposures among Multiple Systemic Autoimmune Diseases. PLoS One 2015; 10:e0142486. [PMID: 26556803 PMCID: PMC4640563 DOI: 10.1371/journal.pone.0142486] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/22/2015] [Indexed: 12/27/2022] Open
Abstract
Viral agents are of interest as possible autoimmune triggers due to prior reported associations and widely studied molecular mechanisms of antiviral immune responses in autoimmunity. Here we examined new viral candidates for the initiation and/or promotion of systemic autoimmune diseases (SAID), as well as possible related signaling pathways shared in the pathogenesis of those disorders. RNA isolated from peripheral blood samples from 33 twins discordant for SAID and 33 matched, unrelated healthy controls was analyzed using a custom viral-human gene microarray. Paired comparisons were made among three study groups—probands with SAID, their unaffected twins, and matched, unrelated healthy controls—using statistical and molecular pathway analyses. Probands and unaffected twins differed significantly in the expression of 537 human genes, and 107 of those were associated with viral infections. These 537 differentially expressed human genes participate in overlapping networks of several canonical, biologic pathways relating to antiviral responses and inflammation. Moreover, certain viral genes were expressed at higher levels in probands compared to either unaffected twins or unrelated, healthy controls. Interestingly, viral gene expression levels in unaffected twins appeared intermediate between those of probands and the matched, unrelated healthy controls. Of the viruses with overexpressed viral genes, herpes simplex virus-2 (HSV-2) was the only human viral pathogen identified using four distinct oligonucleotide probes corresponding to three HSV-2 genes associated with different stages of viral infection. Although the effects from immunosuppressive therapy on viral gene expression remain unclear, this exploratory study suggests a new approach to evaluate shared viral agents and antiviral immune responses that may be involved in the development of SAID.
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Application of text mining in the biomedical domain. Methods 2015; 74:97-106. [PMID: 25641519 DOI: 10.1016/j.ymeth.2015.01.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 12/12/2022] Open
Abstract
In recent years the amount of experimental data that is produced in biomedical research and the number of papers that are being published in this field have grown rapidly. In order to keep up to date with developments in their field of interest and to interpret the outcome of experiments in light of all available literature, researchers turn more and more to the use of automated literature mining. As a consequence, text mining tools have evolved considerably in number and quality and nowadays can be used to address a variety of research questions ranging from de novo drug target discovery to enhanced biological interpretation of the results from high throughput experiments. In this paper we introduce the most important techniques that are used for a text mining and give an overview of the text mining tools that are currently being used and the type of problems they are typically applied for.
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Ellero-Simatos S, Fleuren WWM, Bauerschmidt S, Dokter WHA, Toonen EJM. Identification of gene signatures for prednisolone-induced metabolic dysfunction in collagen-induced arthritic mice. Pharmacogenomics 2014; 15:629-41. [PMID: 24798720 DOI: 10.2217/pgs.14.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Prednisolone is a potent anti-inflammatory glucocorticoid (GC) but chronic use is hampered by metabolic side effects. Little is known about the long-term effects of GCs on gene-expression in vivo during inflammation. AIM Identify gene signatures underlying prednisolone-induced metabolic side effects in a complex in vivo inflammatory setting after long-term treatment. MATERIALS & METHODS We performed whole-genome expression profiling in liver and muscle from arthritic and nonarthritic mice treated with several doses of prednisolone for 3 weeks and used text-mining to link gene signatures to metabolic pathways. RESULTS Prednisolone-induced gene signatures were highly tissue specific. We identified a short-list of genes significantly affected by both prednisolone and inflammation in liver and involved in glucose and fatty acid metabolism. For several of these genes the association with GCs is novel. CONCLUSION The identified gene signatures may provide useful starting points for the development of GCs with a better safety profile.
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Affiliation(s)
- Sandrine Ellero-Simatos
- Division Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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Heskamp S, van Laarhoven HWM, van der Graaf WTA, Oyen WJG, Boerman OC. Radionuclide imaging of drug delivery for patient selection in targeted therapy. Expert Opin Drug Deliv 2014; 11:175-85. [DOI: 10.1517/17425247.2014.870552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Improved outcome of biliary atresia with postoperative high-dose steroid. Gastroenterol Res Pract 2013; 2013:902431. [PMID: 24348545 PMCID: PMC3857902 DOI: 10.1155/2013/902431] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 12/14/2022] Open
Abstract
Objective. The dosage, duration, and the benefits of high-dose steroid treatment and outcome in biliary atresia (BA) remain controversial. In this study, we evaluated the impact of high-dose steroid therapy on the outcome of BA after the Kasai procedure. Methods. Intravenous prednisolone administration was started 1 week after surgery, followed by 8 to 12 weeks of oral prednisolone. Total bilirubin (TB) levels (3, 6, and 12 months after surgery), early onset of cholangitis, and two-year native liver survival were evaluated. Results. 53.4%, 56.9%, and 58.1% of the patients in the high-dose steroid group were jaundice-free 3, 6, and 12 months after surgery, respectively; these values were significantly higher than the 38.7%, 39.4%, and 43.3% of the low-dose steroid group. One year after surgery, the incidence of cholangitis in the high-dose group (32.0%) was lower than that in the low-dose group (48.0%). Infants with native liver in the high-dose group had a better two-year survival compared to those in the low-dose steroid group (53.7% versus 42.6%). Conclusions. The high-dose steroid protocol can reduce the incidence of cholangitis, increase the jaundice-free rate, and improve two-year survival with native liver after the Kasai operation.
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Fleuren WWM, Linssen MML, Toonen EJM, van der Zon GCM, Guigas B, de Vlieg J, Dokter WHA, Ouwens DM, Alkema W. Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes. Arch Physiol Biochem 2013; 119:52-64. [PMID: 23506355 PMCID: PMC3665230 DOI: 10.3109/13813455.2013.774022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic glucocorticoids are potent anti-inflammatory drugs but show dose-dependent metabolic side effects such as the development of insulin resistance and obesity. The precise mechanisms involved in these glucocorticoid-induced side effects, and especially the participation of adipose tissue in this are not completely understood. We used a combination of transcriptomics, antibody arrays and bioinformatics approaches to characterize prednisolone-induced alterations in gene expression and adipokine secretion, which could underlie metabolic dysfunction in 3T3-L1 adipocytes. Several pathways, including cytokine signalling, Akt signalling, and Wnt signalling were found to be regulated at multiple levels, showing that these processes are targeted by prednisolone. These results suggest that mechanisms by which prednisolone induce insulin resistance include dysregulation of wnt signalling and immune response processes. These pathways may provide interesting targets for the development of improved glucocorticoids.
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Affiliation(s)
- Wilco W. M. Fleuren
- CDD, CMBI, NCMLS, Radboud University Medical CentreNijmegenThe Netherlands
- Netherlands Bioinformatics Centre (NBIC)NijmegenThe Netherlands
| | - Margot M. L. Linssen
- Department of Molecular Cell Biology, Leiden University Medical CenterLeidenThe Netherlands
| | - Erik J. M. Toonen
- Department of Medicine, Radboud University Medical CentreNijmegenThe Netherlands
| | | | - Bruno Guigas
- Department of Molecular Cell Biology, Leiden University Medical CenterLeidenThe Netherlands
- Department of Parasitology, Leiden University Medical CenterLeidenThe Netherlands
| | - Jacob de Vlieg
- CDD, CMBI, NCMLS, Radboud University Medical CentreNijmegenThe Netherlands
- Netherlands eScience CenterAmsterdamThe Netherlands
| | | | - D. Margriet Ouwens
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes CenterDüsseldorfGermany
- Department of Endocrinology, Ghent University HospitalGhentBelgium
| | - Wynand Alkema
- CDD, CMBI, NCMLS, Radboud University Medical CentreNijmegenThe Netherlands
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Saugstad OD, Kwinta P, Wollen EJ, Bik - Multanowski M, Madetko - Talowska A, Jagła M, Tomasik T, Pietrzyk JJ. Impact of antenatal glucocorticosteroids on whole-genome expression in preterm babies. Acta Paediatr 2013; 102:349-55. [PMID: 23347050 DOI: 10.1111/apa.12166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 11/20/2012] [Accepted: 01/11/2013] [Indexed: 12/19/2022]
Abstract
AIM To study the impact that using antenatal steroid to treat threatened preterm delivery has on whole-genome expression. METHODS A prospective whole-genome expression study was carried out on 50 newborn infants, delivered before 32 weeks gestation, who had been exposed to antenatal steroids, including 40 who had received a full antenatal steroid course. Seventy infants not exposed to antenatal steroids formed the control group. Microarray analyses were performed five and 28 days after delivery, and the results were validated by real-time PCR. The study was conducted between September 2008 and November 2010. RESULTS Twenty thousand six hundred and ninety-three genes were studied in the infants' leucocytes. Thirteen were differentially expressed 5 days after delivery, but there were no differences at day 28. Four genes related to cancer or inflammation were up-regulated. Nine genes were down-regulated: six were Y-linked and associated with malignancies, graft-versus-host disease, male infertility and cell differentiation and three were associated with pre-eclampsia, oxidative stress and chloride/bicarbonate exchange. Seven gene pathways were up-regulated at day five and only one at day 28. These were associated with cell growth, cell cycle regulation, metabolism and apoptosis. CONCLUSION Antenatal steroid therapy affects a limited number of genes and gene pathways in leucocytes in preterm babies at day five of life. The effect is short-lived, but long-term effects cannot be ruled out.
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Affiliation(s)
- Ola Didrik Saugstad
- Department of Pediatric Research; Clinic of Women and Child Health; Oslo University Hospital; University of Oslo; Norway
| | - Przemko Kwinta
- Department of Pediatrics; Jagiellonian University; Medical College; Krakow Poland
| | - Embjørg Julianne Wollen
- Department of Pediatric Research; Clinic of Women and Child Health; Oslo University Hospital; University of Oslo; Norway
| | | | | | - Mateusz Jagła
- Department of Pediatrics; Jagiellonian University; Medical College; Krakow Poland
| | - Tomasz Tomasik
- Department of Pediatrics; Jagiellonian University; Medical College; Krakow Poland
| | - Jacek Józef Pietrzyk
- Department of Pediatrics; Jagiellonian University; Medical College; Krakow Poland
- Department of Clinical Genetics; Jagiellonian University; Medical College; Krakow Poland
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van Lierop MJC, Alkema W, Laskewitz AJ, Dijkema R, van der Maaden HM, Smit MJ, Plate R, Conti PGM, Jans CGJM, Timmers CM, van Boeckel CAA, Lusher SJ, McGuire R, van Schaik RC, de Vlieg J, Smeets RL, Hofstra CL, Boots AMH, van Duin M, Ingelse BA, Schoonen WGEJ, Grefhorst A, van Dijk TH, Kuipers F, Dokter WHA. Org 214007-0: a novel non-steroidal selective glucocorticoid receptor modulator with full anti-inflammatory properties and improved therapeutic index. PLoS One 2012; 7:e48385. [PMID: 23152771 PMCID: PMC3495945 DOI: 10.1371/journal.pone.0048385] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 09/24/2012] [Indexed: 11/18/2022] Open
Abstract
Glucocorticoids (GCs) such as prednisolone are potent immunosuppressive drugs but suffer from severe adverse effects, including the induction of insulin resistance. Therefore, development of so-called Selective Glucocorticoid Receptor Modulators (SGRM) is highly desirable. Here we describe a non-steroidal Glucocorticoid Receptor (GR)-selective compound (Org 214007-0) with a binding affinity to GR similar to that of prednisolone. Structural modelling of the GR-Org 214007-0 binding site shows disturbance of the loop between helix 11 and helix 12 of GR, confirmed by partial recruitment of the TIF2-3 peptide. Using various cell lines and primary human cells, we show here that Org 214007-0 acts as a partial GC agonist, since it repressed inflammatory genes and was less effective in induction of metabolic genes. More importantly, in vivo studies in mice indicated that Org 214007-0 retained full efficacy in acute inflammation models as well as in a chronic collagen-induced arthritis (CIA) model. Gene expression profiling of muscle tissue derived from arthritic mice showed a partial activity of Org 214007-0 at an equi-efficacious dosage of prednisolone, with an increased ratio in repression versus induction of genes. Finally, in mice Org 214007-0 did not induce elevated fasting glucose nor the shift in glucose/glycogen balance in the liver seen with an equi-efficacious dose of prednisolone. All together, our data demonstrate that Org 214007-0 is a novel SGRMs with an improved therapeutic index compared to prednisolone. This class of SGRMs can contribute to effective anti-inflammatory therapy with a lower risk for metabolic side effects.
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