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Larsen TV, Maansson CT, Daugaard TF, Andresen BS, Sorensen BS, Nielsen AL. Trans-Regulation of Alternative PD-L1 mRNA Processing by CDK12 in Non-Small-Cell Lung Cancer Cells. Cells 2023; 12:2844. [PMID: 38132164 PMCID: PMC10741404 DOI: 10.3390/cells12242844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Immunotherapy using checkpoint inhibitors targeting the interaction between PD-1 on T cells and PD-L1 on cancer cells has shown significant results in non-small-cell lung cancer (NSCLC). Not all patients respond to the therapy, and PD-L1 expression heterogeneity is proposed to be one determinant for this. The alternative processing of PD-L1 RNA, which depends on an alternative poly-A site in intron 4, generates a shorter mRNA variant (PD-L1v4) encoding soluble PD-L1 (sPD-L1), relative to the canonical PD-L1v1 mRNA encoding membrane-associated PD-L1 (mPD-L1). This study aimed to identify factors influencing the ratio between these two PD-L1 mRNAs in NSCLC cells. First, we verified the existence of the alternative PD-L1 RNA processing in NSCLC cells, and from in silico analyses, we identified a candidate list of regulatory factors. Examining selected candidates showed that CRISPR/Cas9-generated loss-of-function mutations in CDK12 increased the PD-L1v4/PD-L1v1 mRNA ratio and, accordingly, the sPD-L1/mPD-L1 balance. The CDK12/13 inhibitor THZ531 could also increase the PD-L1v4/PD-L1v1 mRNA ratio and impact the PD-L1 transcriptional response to IFN-γ stimulation. The fact that CDK12 regulates PD-L1 transcript variant formation in NSCLC cells is consistent with CDK12's role in promoting transcriptional elongation over intron-located poly-A sites. This study lays the groundwork for clinical investigations to delineate the implications of the CDK12-mediated balancing of sPD-L1 relative to mPD-L1 for immunotherapeutic responses in NSCLC.
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Affiliation(s)
- Trine V. Larsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
| | - Christoffer T. Maansson
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark;
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Tina F. Daugaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
| | - Brage S. Andresen
- Department of Biology and Molecular Biology, Southern University of Denmark, 5230 Odense, Denmark;
| | - Boe S. Sorensen
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark;
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Anders L. Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
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2
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Larsen TV, Dybdal N, Daugaard TF, Lade-Keller J, Lin L, Sorensen BS, Nielsen AL. Examination of the Functional Relationship between PD-L1 DNA Methylation and mRNA Expression in Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:cancers15061909. [PMID: 36980795 PMCID: PMC10047551 DOI: 10.3390/cancers15061909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/04/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Immunotherapy targeting the interaction between programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) is a treatment option for patients with non-small-cell lung cancer (NSCLC). The expression of PD-L1 by the NSCLC cells determines treatment effectiveness, but the relationship between PD-L1 DNA methylation and expression has not been clearly described. We investigated PD-L1 DNA methylation, mRNA expression, and protein expression in NSCLC cell lines and tumor biopsies. We used clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas9) to modify PD-L1 genetic contexts and endonuclease deficient Cas9 (dCas9) fusions with ten-eleven translocation methylcytosine dioxygenase 1 (TET1) and DNA (cytosine-5)-methyltransferase 3A (DNMT3A) to manipulate PD-L1 DNA methylation. In NSCLC cell lines, we identified specific PD-L1 CpG sites with methylation levels inversely correlated with PD-L1 mRNA expression. However, inducing PD-L1 mRNA expression with interferon-γ did not decrease the methylation level for these CpG sites, and using CRISPR-Cas9, we found that the CpG sites did not directly confer a negative regulation. dCas9-TET1 and dCas9-DNMT3A could induce PD-L1 hypo- and hyper-methylation, respectively, with the latter conferring a decrease in expression showing the functional impact of methylation. In NSCLC biopsies, the inverse correlation between the methylation and expression of PD-L1 was weak. We conclude that there is a regulatory link between PD-L1 DNA methylation and expression. However, since these measures are weakly associated, this study highlights the need for further research before PD-L1 DNA methylation can be implemented as a biomarker and drug target for measures to improve the effectiveness of PD-1/PD-L1 immunotherapy in NSCLC.
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Affiliation(s)
- Trine V Larsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Nina Dybdal
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Tina F Daugaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Boe S Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
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3
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Akotsen-Mensah C, Blaauw B, Short B, Leskey TC, Bergh JC, Polk D, Nielsen AL. Using IPM-CPR as a Management Program for Apple Orchards. J Econ Entomol 2020; 113:1894-1902. [PMID: 32447399 DOI: 10.1093/jee/toaa087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Indexed: 06/11/2023]
Abstract
We have demonstrated how management of key orchard pests including the insect invasive species Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) can be accomplished using a systems-level approach termed IPM-CPR (Integrated Pest Management-Crop Perimeter Restructuring) in apple. We conducted on-farm comparisons of IPM-CPR to standard management program for managing H. halys, Cydia pomonella (L.) (Lepidoptera: Tortricidae), Grapholita molesta (Busck) (Lepidoptera: Tortricidae), and Lygus lineolaris Palisot de Beauvois (Hemiptera: Miridae) in commercial apple orchards in 2014, 2016, and 2017 in New Jersey, Maryland, and Virginia. The presence and abundance of key pests and fruit injury at harvest were used as a measure of success of the program. We compared the amount of insecticide applied for each management program. In majority of instances, there were no differences in the IPM-CPR and the standard management program in terms of H. halys numbers in baited pyramid traps and stink bug injury at harvest. Damage from C. pomonella and G. molesta in the IPM-CPR treatment was significantly lower than the standard management program in 2014 and 2017. Amount of active ingredient used was on average 62.1% lower in the IPM-CPR treatment compared with standard management program. Despite a reduction in insecticide use, there were minimal impacts on beneficial insects. Overall, IPM-CPR in apples successfully managed key orchard pests, including H. halys, and used significantly less insecticide than a standard insecticide-based management program and could be adopted as a systems-level approach for pest population reduction.
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Affiliation(s)
- C Akotsen-Mensah
- Department of Entomology, Rutgers University, Bridgeton, NJ
- Cooperative Extension and Research, Lincoln University, Jefferson City, MO
| | - B Blaauw
- Department of Entomology, University of Georgia, Athens, GA
| | - B Short
- AFRS, USDA-ARS, Kearneysville, WV
| | | | - J C Bergh
- Virginia Tech, AHS AREC, Winchester, VA
| | - D Polk
- Department of Agriculture and Natural Resources, Rutgers University, Bridgeton, NJ
| | - A L Nielsen
- Department of Entomology, Rutgers University, Bridgeton, NJ
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4
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Fa S, Larsen TV, Bilde K, Daugaard TF, Ernst EH, Lykke-Hartmann K, Olesen RH, Mamsen LS, Ernst E, Larsen A, Nielsen AL. Changes in first trimester fetal CYP1A1 and AHRR DNA methylation and mRNA expression in response to exposure to maternal cigarette smoking. Environ Toxicol Pharmacol 2018; 57:19-27. [PMID: 29169084 DOI: 10.1016/j.etap.2017.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
Prenatal exposure to maternal cigarette smoking increases the risk of intrauterine growth retardation, adverse pregnancy outcomes, and diseases later in life. Exposure can result in postnatal global and gene-specific DNA methylation changes, with the latter well documented for the CYP1A1 and AHRR genes involved in the detoxification of xenobiotic substances. This study assessed the impact of exposure to maternal smoking on first trimester fetal CYP1A1 and AHRR mRNA expression and DNA methylation for CpG-sites displaying maternal smoking during pregnancy-mediated methylation changes at birth. The analyses included first trimester (6-12 weeks) placentas (N=39) and livers (N=43). For AHRR, exposure to maternal smoking was associated with increased DNA methylation in the placentas of female fetuses; mRNA expression, however, was unchanged. While exposure to maternal smoking was not associated with AHRR DNA methylation changes in fetal livers; mRNA expression was increased. For CYP1A1, exposure to maternal smoking was not associated with fetal DNA methylation changes whereas mRNA expression increased in placentas and male fetal livers. These results show that first trimester exposure to maternal smoking is associated with CYP1A1 and AHRR DNA methylation and mRNA expression changes. However, the results also indicate that maternal smoking during pregnancy-mediated postnatal CYP1A1 and AHRR DNA methylation changes are not imprinted during the first trimester.
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Affiliation(s)
- Svetlana Fa
- Department of Biomedicine, Aarhus University, Denmark; Faculty of Sciences, University of Novi Sad, Serbia
| | | | - Katrine Bilde
- Department of Biomedicine, Aarhus University, Denmark
| | | | - Emil H Ernst
- Department of Biomedicine, Aarhus University, Denmark
| | - Karin Lykke-Hartmann
- Department of Biomedicine, Aarhus University, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | | | - Linn S Mamsen
- Laboratory of Reproductive Biology, The Juliane Marie Centre for Women, Children and Reproduction, University Hospital of Copenhagen, Rigshospitalet, Denmark
| | - Erik Ernst
- Department of Biomedicine, Aarhus University, Denmark; Department of Obstetrics and Gynecology, University Hospital of Aarhus, Skejby Sygehus, Denmark
| | - Agnete Larsen
- Department of Biomedicine, Aarhus University, Denmark
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5
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Dudele A, Hougaard KS, Kjølby M, Hokland M, Winther G, Elfving B, Wegener G, Nielsen AL, Larsen A, Nøhr MK, Pedersen SB, Wang T, Lund S. Chronic maternal inflammation or high-fat-feeding programs offspring obesity in a sex-dependent manner. Int J Obes (Lond) 2017; 41:1420-1426. [PMID: 28588305 DOI: 10.1038/ijo.2017.136] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/24/2017] [Accepted: 05/25/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND/OBJECTIVES The current world-wide obesity epidemic partially results from a vicious circle whereby maternal obesity during pregnancy predisposes the offspring for accelerated weight gain and development of metabolic syndrome. Here we investigate whether low-grade inflammation, characteristic of the obese state, provides a causal role for this disastrous fetal programming in mice. METHODS We exposed pregnant and lactating C57BL/6JBom female mice to either high-fat diet (HFD), or continuous infusion of lipopolysaccharide (LPS), a potent trigger of innate immunity, and studied offspring phenotypes. RESULTS Both maternal LPS or HFD treatments rendered the offspring hyperphagic and inept of coping with a HFD challenge during adulthood, increasing their adiposity and weight gain. The metabolic effects were more pronounced in female offspring, while exposed male offspring mounted a larger inflammatory response to HFD at adulthood. CONCLUSIONS This supports our hypothesis and highlights the programming potential of inflammation in obese pregnancies.
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Affiliation(s)
- A Dudele
- Department of Bioscience, Section for Zoophysiology, Aarhus University, Aarhus, Denmark
| | - K S Hougaard
- Department of Public Health, Section for Occupational and Environmental Health, University of Copenhagen, Copenhagen, Denmark
| | - M Kjølby
- Department of Biomedicine, The Danish Research Institute of Translational Neuroscience, Nordic EMBL Partnership for Molecular Medicine and Danish Diabetes Academy, Aarhus University, Aarhus, Denmark
| | - M Hokland
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - G Winther
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Risskov, Denmark
| | - B Elfving
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Risskov, Denmark
| | - G Wegener
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Risskov, Denmark
| | - A L Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - A Larsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - M K Nøhr
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Endocrinology and Metabolism C, Aarhus University Hospital, Aarhus, Denmark
| | - S B Pedersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Endocrinology and Metabolism C, Aarhus University Hospital, Aarhus, Denmark
| | - T Wang
- Department of Bioscience, Section for Zoophysiology, Aarhus University, Aarhus, Denmark
| | - S Lund
- Department of Endocrinology and Internal Medicine Medical Research Laboratory, Aarhus University Hospital, Aarhus, Denmark
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6
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Bak ST, Staunstrup NH, Starnawska A, Daugaard TF, Nyengaard JR, Nyegaard M, Børglum A, Mors O, Dorph-Petersen KA, Nielsen AL. Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples. Mol Neurobiol 2016; 55:668-681. [PMID: 27995571 DOI: 10.1007/s12035-016-0345-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/05/2016] [Indexed: 01/14/2023]
Abstract
We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.
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Affiliation(s)
- Stine T Bak
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark
| | - Nicklas H Staunstrup
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Tina F Daugaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark
| | - Jens R Nyengaard
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
| | - Anders Børglum
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karl-Anton Dorph-Petersen
- Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark.,Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
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7
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Sølvsten CAE, de Paoli F, Christensen JH, Nielsen AL. Voluntary Physical Exercise Induces Expression and Epigenetic Remodeling of VegfA in the Rat Hippocampus. Mol Neurobiol 2016; 55:567-582. [DOI: 10.1007/s12035-016-0344-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 12/22/2022]
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8
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Fa S, Larsen TV, Bilde K, Daugaard TF, Ernst EH, Olesen RH, Mamsen LS, Ernst E, Larsen A, Nielsen AL. Assessment of global DNA methylation in the first trimester fetal tissues exposed to maternal cigarette smoking. Clin Epigenetics 2016; 8:128. [PMID: 27924165 PMCID: PMC5123323 DOI: 10.1186/s13148-016-0296-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/18/2016] [Indexed: 01/10/2023] Open
Abstract
AIMS Maternal cigarette smoking during pregnancy increases the risk of negative health consequences for the exposed child. Epigenetic mechanisms constitute a likely link between the prenatal exposure to maternal cigarette smoking and the increased risk in later life for diverse pathologies. Maternal smoking induces gene-specific DNA methylation alterations as well as global DNA hypermethylation in the term placentas and hypomethylation in the cord blood. Early pregnancy represents a developmental time where the fetal epigenome is remodeled and accordingly can be expected to be highly prone to exposures with an epigenetic impact. We have assessed the influence of maternal cigarette smoking during the first trimester for fetal global DNA methylation. METHODS AND RESULTS We analyzed the human fetal intestines and livers as well as the placentas from the first trimester pregnancies. Global DNA methylation levels were quantified with ELISA using a methylcytosine antibody as well as with the bisulfite pyrosequencing of surrogate markers for global methylation status, LINE-1, and AluYb8. We identified gender-specific differences in global DNA methylation levels, but no significant DNA methylation changes in exposure responses to the first trimester maternal cigarette smoking. CONCLUSIONS Acknowledging that only examining subsets of global DNA methylation markers and fetal sample availability represents possible limitations for the analyses, our presented results indicate that the first trimester maternal cigarette smoking is not manifested in immediate aberrations of fetal global DNA methylation.
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Affiliation(s)
- Svetlana Fa
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark.,Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Trine Vilsbøll Larsen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
| | - Katrine Bilde
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
| | - Tina F Daugaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
| | - Emil H Ernst
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
| | - Rasmus H Olesen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
| | - Linn S Mamsen
- Laboratory of Reproductive Biology, The Juliane Marie Centre for Women, Children and Reproduction, University Hospital of Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Erik Ernst
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark.,Department of Obstetrics and Gynecology, University Hospital of Aarhus, Skejby Sygehus, Aarhus, Denmark
| | - Agnete Larsen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000 Aarhus C, Denmark
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9
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Staunstrup NH, Starnawska A, Nyegaard M, Christiansen L, Nielsen AL, Børglum A, Mors O. Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots. Clin Epigenetics 2016; 8:81. [PMID: 27462375 PMCID: PMC4960904 DOI: 10.1186/s13148-016-0242-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed. RESULTS Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample. CONCLUSIONS In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.
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Affiliation(s)
- Nicklas H Staunstrup
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
| | - Anna Starnawska
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Lene Christiansen
- Department of Public Health, University of Southern Denmark, Odense C, 5000 Denmark
| | - Anders L Nielsen
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
| | - Anders Børglum
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Ole Mors
- Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
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10
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Starnawska A, Demontis D, Pen A, Hedemand A, Nielsen AL, Staunstrup NH, Grove J, Als TD, Jarram A, O'Brien NL, Mors O, McQuillin A, Børglum AD, Nyegaard M. CACNA1C hypermethylation is associated with bipolar disorder. Transl Psychiatry 2016; 6:e831. [PMID: 27271857 PMCID: PMC4931616 DOI: 10.1038/tp.2016.99] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/05/2016] [Accepted: 04/15/2016] [Indexed: 12/19/2022] Open
Abstract
The CACNA1C gene, encoding a subunit of the L-type voltage-gated calcium channel is one of the best-supported susceptibility genes for bipolar disorder (BD). Genome-wide association studies have identified a cluster of non-coding single-nucleotide polymorphisms (SNPs) in intron 3 to be highly associated with BD and schizophrenia. The mechanism by which these SNPs confer risk of BD appears to be through an altered regulation of CACNA1C expression. The role of CACNA1C DNA methylation in BD has not yet been addressed. The aim of this study was to investigate if CACNA1C DNA methylation is altered in BD. First, the methylation status of five CpG islands (CGIs) across CACNA1C in blood from BD subjects (n=40) and healthy controls (n=38) was determined. Four islands were almost completely methylated or completely unmethylated, while one island (CGI 3) in intron 3 displayed intermediate methylation levels. In the main analysis, the methylation status of CGI 3 was analyzed in a larger sample of BD subjects (n=582) and control individuals (n=319). Out of six CpG sites that were investigated, five sites showed significant hypermethylation in cases (lowest P=1.16 × 10(-7) for CpG35). Nearby SNPs were found to influence the methylation level, and we identified rs2238056 in intron 3 as the strongest methylation quantitative trait locus (P=2.6 × 10(-7)) for CpG35. In addition, we found an increased methylation in females, and no difference between bipolar I and II. In conclusion, we find that CACNA1C methylation is associated with BD and suggest that the regulatory effect of the non-coding risk variants involves a shift in DNA methylation.
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Affiliation(s)
- A Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - D Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - A Pen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - A Hedemand
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - A L Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - N H Staunstrup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - J Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - T D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - A Jarram
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - N L O'Brien
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - O Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Research Department P, Aarhus University Hospital, Risskov, Denmark
| | - A McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - A D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - M Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
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Starnawska A, Demontis D, McQuillin A, O’Brien NL, Staunstrup NH, Mors O, Nielsen AL, Børglum AD, Nyegaard M. Hypomethylation of FAM63B in bipolar disorder patients. Clin Epigenetics 2016; 8:52. [PMID: 27175219 PMCID: PMC4865008 DOI: 10.1186/s13148-016-0221-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/04/2016] [Indexed: 01/07/2023] Open
Abstract
Bipolar disorder (BD) and schizophrenia (SZ) are known to share common genetic and psychosocial risk factors. A recent epigenome-wide association study performed on blood samples from SZ patients found significant hypomethylation of FAM63B in exon 9. Here, we used iPLEX-based methylation analysis to investigate two CpG sites in FAM63B in blood samples from 459 BD cases and 268 controls. Both sites were significantly hypomethylated in BD cases (lowest p value = 3.94 × 10(-8)). The methylation levels at the two sites were correlated, and no strong correlation was found with nearby single nucleotide polymorphisms (SNPs), suggesting that methylation differences at these sites are not readably picked up by genome-wide association studies. Overall, FAM63B hypomethylation was found in BD patients, thus replicating the initial finding in SZ patients. This study suggests that FAM63B is a shared epigenetic risk gene for the two disorders.
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Affiliation(s)
- Anna Starnawska
- />Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK- 8000 Aarhus C, Denmark
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- />Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK- 8000 Aarhus C, Denmark
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Andrew McQuillin
- />Molecular Psychiatry Laboratory, Division of Psychiatry, Rockefeller Building, University College London, London, UK
| | - Niamh L. O’Brien
- />Molecular Psychiatry Laboratory, Division of Psychiatry, Rockefeller Building, University College London, London, UK
| | - Nicklas H. Staunstrup
- />Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK- 8000 Aarhus C, Denmark
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- />Translational Neuropsychiatry Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ole Mors
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Anders L. Nielsen
- />Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK- 8000 Aarhus C, Denmark
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Anders D. Børglum
- />Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK- 8000 Aarhus C, Denmark
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Mette Nyegaard
- />Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK- 8000 Aarhus C, Denmark
- />The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- />Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
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12
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Fryland T, Christensen JH, Pallesen J, Mattheisen M, Palmfeldt J, Bak M, Grove J, Demontis D, Blechingberg J, Ooi HS, Nyegaard M, Hauberg ME, Tommerup N, Gregersen N, Mors O, Corydon TJ, Nielsen AL, Børglum AD. Identification of the BRD1 interaction network and its impact on mental disorder risk. Genome Med 2016; 8:53. [PMID: 27142060 PMCID: PMC4855718 DOI: 10.1186/s13073-016-0308-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/15/2016] [Indexed: 01/23/2023] Open
Abstract
Background The bromodomain containing 1 (BRD1) gene has been implicated with transcriptional regulation, brain development, and susceptibility to schizophrenia and bipolar disorder. To advance the understanding of BRD1 and its role in mental disorders, we characterized the protein and chromatin interactions of the BRD1 isoforms, BRD1-S and BRD1-L. Methods Stable human cell lines expressing epitope tagged BRD1-S and BRD1-L were generated and used as discovery systems for identifying protein and chromatin interactions. Protein-protein interactions were identified using co-immunoprecipitation followed by mass spectrometry and chromatin interactions were identified using chromatin immunoprecipitation followed by next generation sequencing. Gene expression profiles and differentially expressed genes were identified after upregulating and downregulating BRD1 expression using microarrays. The presented functional molecular data were integrated with human genomic and transcriptomic data using available GWAS, exome-sequencing datasets as well as spatiotemporal transcriptomic datasets from the human brain. Results We present several novel protein interactions of BRD1, including isoform-specific interactions as well as proteins previously implicated with mental disorders. By BRD1-S and BRD1-L chromatin immunoprecipitation followed by next generation sequencing we identified binding to promoter regions of 1540 and 823 genes, respectively, and showed correlation between BRD1-S and BRD1-L binding and regulation of gene expression. The identified BRD1 interaction network was found to be predominantly co-expressed with BRD1 mRNA in the human brain and enriched for pathways involved in gene expression and brain function. By interrogation of large datasets from genome-wide association studies, we further demonstrate that the BRD1 interaction network is enriched for schizophrenia risk. Conclusion Our results show that BRD1 interacts with chromatin remodeling proteins, e.g. PBRM1, as well as histone modifiers, e.g. MYST2 and SUV420H1. We find that BRD1 primarily binds in close proximity to transcription start sites and regulates expression of numerous genes, many of which are involved with brain development and susceptibility to mental disorders. Our findings indicate that BRD1 acts as a regulatory hub in a comprehensive schizophrenia risk network which plays a role in many brain regions throughout life, implicating e.g. striatum, hippocampus, and amygdala at mid-fetal stages. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0308-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tue Fryland
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Jane H Christensen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Jonatan Pallesen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University Hospital, 8200, Skejby, Denmark
| | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark.,Bioinformatics Research Centre (BiRC, Aarhus University, 8000, Aarhus C, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Jenny Blechingberg
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark
| | - Hong Sain Ooi
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Mads E Hauberg
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Aarhus University Hospital, 8200, Skejby, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark.,Research Department P, Aarhus University Hospital, 8240, Risskov, Denmark
| | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark. .,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark. .,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark. .,Research Department P, Aarhus University Hospital, 8240, Risskov, Denmark.
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Dudele A, Hougaard KS, Kjølby MF, Hokland M, Winther G, Elfving B, Wegener G, Nielsen AL, Larsen A, Nøhr MK, Pedersen SB, Wang T, Lund S. Maternal inflammation or high fat feeding during pregnancy and lactation programs offspring obesity in mice. Reprod Toxicol 2015. [DOI: 10.1016/j.reprotox.2015.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Wolf G, Yang P, Füchtbauer AC, Füchtbauer EM, Silva AM, Park C, Wu W, Nielsen AL, Pedersen FS, Macfarlan TS. The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev 2015; 29:538-54. [PMID: 25737282 PMCID: PMC4358406 DOI: 10.1101/gad.252767.114] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Endogenous retroviruses (ERVs) are epigenetically silenced during development, yet the cellular factors recognizing ERVs in a sequence-specific manner remain elusive. Wolf et al. find that ZFP809 initiates the silencing of ERVs in a sequence-specific manner via recruitment of heterochromatin-inducing complexes. ERV reactivation is accompanied by an epigenetic shift from repressive to active histone modifications. ZFP809 is required to initiate ERV silencing during embryonic development but becomes largely dispensable in somatic tissues. Retroviruses have been invading mammalian germlines for millions of years, accumulating in the form of endogenous retroviruses (ERVs) that account for nearly one-tenth of the mouse and human genomes. ERVs are epigenetically silenced during development, yet the cellular factors recognizing ERVs in a sequence-specific manner remain elusive. Here we demonstrate that ZFP809, a member of the Krüppel-associated box zinc finger protein (KRAB-ZFP) family, initiates the silencing of ERVs in a sequence-specific manner via recruitment of heterochromatin-inducing complexes. ZFP809 knockout mice display highly elevated levels of ZFP809-targeted ERVs in somatic tissues. ERV reactivation is accompanied by an epigenetic shift from repressive to active histone modifications but only slight destabilization of DNA methylation. Importantly, using conditional alleles and rescue experiments, we demonstrate that ZFP809 is required to initiate ERV silencing during embryonic development but becomes largely dispensable in somatic tissues. Finally, we show that the DNA-binding specificity of ZFP809 is evolutionarily conserved in the Muroidea superfamily of rodents and predates the endogenization of retroviruses presently targeted by ZFP809 in Mus musculus. In sum, these data provide compelling evidence that ZFP809 evolved to recognize foreign DNA and establish histone modification-based epigenetic silencing of ERVs.
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Affiliation(s)
- Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Peng Yang
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Annette C Füchtbauer
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Andreia M Silva
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Chungoo Park
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Warren Wu
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Finn S Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA;
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Kumar A, Browne C, Scotland S, Krishnamurthy K, Nielsen AL. Selected enteropathogens and clinical course in children hospitalized with severe acute gastroenteritis in Barbados. Int J Health Sci (Qassim) 2014; 8:409-417. [PMID: 25780359 PMCID: PMC4350894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
OBJECTIVES The primary aim of this study was to determine the prevalence of selected bacterial and viral enteropathogens in children hospitalized with acute gastroenteritis and the secondary aim was to characterize the clinical course and the outcome. METHODOLOGY A retrospective audit of children (<15 years) admitted with acute gastroenteritis during January 2008 to October 2010. Stool samples were analyzed for bacterial pathogens and for the Rotavirus. Demographics, clinical presentations, hospital course and outcome were extracted from the admission records. RESULTS There were 571 children hospitalized with acute gastroenteritis, which accounted for 11% of all medical hospitalization in children. Overall, 42.9% of these children were ≤12 months in age. Stool test result was documented in 46.6% of children hospitalized with gastroenteritis and an enteropathogen was isolated in 36.8% of cases with documented stool test result. Non-typhoidal Salmonella species was the most commonly isolated enteropathogen accounting for 21.1% of all the documented cases. Rotavirus was identified as an etiological agent in 9.0%. Of the 56 children who had non-typhoidal salmonella gastroenteritis, 54(96.4%) were younger than 5 years. The median duration of hospitalization was 2 days (Range 1 day to 9 days). There were no deaths. CONCLUSION Non-typhoidal salmonella was the most common enteropathogen isolated and this was followed by the Rotavirus.
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Affiliation(s)
- Alok Kumar
- Faculty of Medical Sciences, University of the West Indies, Barbados
| | | | | | | | - Anders L Nielsen
- Faculty of Medical Sciences, University of the West Indies, Barbados
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Thomsen R, Pallesen J, Daugaard TF, Børglum AD, Nielsen AL. Genome wide assessment of mRNA in astrocyte protrusions by direct RNA sequencing reveals mRNA localization for the intermediate filament protein nestin. Glia 2013; 61:1922-37. [DOI: 10.1002/glia.22569] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 07/31/2013] [Accepted: 08/05/2013] [Indexed: 12/26/2022]
Affiliation(s)
- Rune Thomsen
- Department of Biomedicine; Aarhus University; Aarhus Denmark
| | - Jonatan Pallesen
- Department of Biomedicine; Aarhus University; Aarhus Denmark
- Center for Integrative Sequencing, iSEQ, Department of Biomedicine; Aarhus University; Aarhus Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Department of Biomedicine; Aarhus University; Aarhus Denmark
| | | | - Anders D. Børglum
- Department of Biomedicine; Aarhus University; Aarhus Denmark
- Center for Integrative Sequencing, iSEQ, Department of Biomedicine; Aarhus University; Aarhus Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Department of Biomedicine; Aarhus University; Aarhus Denmark
- Center for Psychiatric Research; Aarhus University Hospital; Aarhus Denmark
| | - Anders L. Nielsen
- Department of Biomedicine; Aarhus University; Aarhus Denmark
- Center for Integrative Sequencing, iSEQ, Department of Biomedicine; Aarhus University; Aarhus Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Department of Biomedicine; Aarhus University; Aarhus Denmark
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Kristensen LH, Nielsen AL, Helgstrand C, Lees M, Cloos P, Kastrup JS, Helin K, Olsen L, Gajhede M. Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4-pyridine-dicarboxylic acid as an in vitro and in cell inhibitor. FEBS J 2012; 279:1905-14. [PMID: 22420752 DOI: 10.1111/j.1742-4658.2012.08567.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dynamic methylations and demethylations of histone lysine residues are important for gene regulation and are facilitated by histone methyltransferases and histone demethylases (HDMs). KDM5B/Jarid1B/PLU1 is an H3K4me3/me2-specific lysine demethylase belonging to the JmjC domain-containing family of histone demethylases (JHDMs). Several studies have linked KDM5B to breast, prostate and skin cancer, highlighting its potential as a drug target. However, most inhibitor studies have focused on other JHDMs, and inhibitors for KDM5B remain to be explored. Here, we report the expression, purification and characterization of the catalytic core of recombinant KDM5B (ccKDM5B, residues 1-769). We show that ccKDM5B, recombinantly expressed in insect cells, demethylates H3K4me3 and H3K4me2 in vitro. The kinetic characterization showed that ccKDM5B has an apparent Michaelis constant (K(m) (app) ) value of 0.5 μm for its trimethylated substrate H3(1-15)K4me3, a considerably increased apparent substrate affinity than reported for related HDMs. Despite the presence of a PHD domain, the catalytic activity was not affected by additional methylation at the H3K9 position, suggesting that in vitro chromatin cross-talk between H3K4 and H3K9 does not occur for ccKDM5B. Inhibition studies of ccKDM5B showed both in vitro and in cell inhibition of ccKDM5B by 2,4-pyridinedicarboxylic acid (2,4-PDCA) with a potency similar to that reported for the HDM KDM4C. Structure-guided sequence alignment indicated that the binding mode of 2,4-PDCA is conserved between KDM4A/C and KDM5B.
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Affiliation(s)
- Line H Kristensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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18
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Nielsen AL, Kristensen LH, Stephansen KB, Kristensen JBL, Helgstrand C, Lees M, Cloos P, Helin K, Gajhede M, Olsen L. Identification of catechols as histone-lysine demethylase inhibitors. FEBS Lett 2012; 586:1190-4. [PMID: 22575654 DOI: 10.1016/j.febslet.2012.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/28/2012] [Accepted: 03/01/2012] [Indexed: 12/21/2022]
Abstract
Identification of inhibitors of histone-lysine demethylase (HDM) enzymes is important because of their involvement in the development of cancer. An ELISA-based assay was developed for identification of inhibitors of the HDM KDM4C in a natural products library. Based on one of the hits with affinity in the low μM range (1, a catechol), a subset of structurally related compounds was selected and tested against a panel of HDMs. In this subset, two inhibitors (2 and 10) had comparable affinities towards KDM4C and KDM6A but no effect on PHF8. One inhibitor restored H3K9me3 levels in KDM4C transfected U2-OS cells.
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Affiliation(s)
- Anders L Nielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Kristensen JB, Nielsen AL, Jørgensen L, Kristensen LH, Helgstrand C, Juknaite L, Kristensen JL, Kastrup JS, Clausen RP, Olsen L, Gajhede M. Erratum to “Enzyme kinetic studies of histone demethylases KDM4C and KDM6A: Towards understanding selectivity of inhibitors targeting oncogenic histone demethylases” [FEBS Lett. 585 (2011) 1951-1956]. FEBS Lett 2011. [DOI: 10.1016/j.febslet.2011.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Lohse B, Nielsen AL, Kristensen JBL, Helgstrand C, Cloos PAC, Olsen L, Gajhede M, Clausen RP, Kristensen JL. Targeting histone lysine demethylases by truncating the histone 3 tail to obtain selective substrate-based inhibitors. Angew Chem Int Ed Engl 2011; 50:9100-3. [PMID: 21919140 DOI: 10.1002/anie.201101849] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Brian Lohse
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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Lohse B, Nielsen AL, Kristensen JBL, Helgstrand C, Cloos PAC, Olsen L, Gajhede M, Clausen RP, Kristensen JL. Targeting Histone Lysine Demethylases by Truncating the Histone 3 Tail to Obtain Selective Substrate-Based Inhibitors. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101849] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Kristensen JB, Nielsen AL, Jørgensen L, Kristensen LH, Helgstrand C, Juknaite L, Kristensen JL, Kastrup JS, Clausen RP, Olsen L, Gajhede M. Enzyme kinetic studies of histone demethylases KDM4C and KDM6A: Towards understanding selectivity of inhibitors targeting oncogenic histone demethylases. FEBS Lett 2011; 585:1951-6. [DOI: 10.1016/j.febslet.2011.05.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 05/04/2011] [Indexed: 10/18/2022]
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Thomsen R, Christensen DB, Rosborg S, Linnet TE, Blechingberg J, Nielsen AL. Analysis of HP1α regulation in human breast cancer cells. Mol Carcinog 2011; 50:601-13. [PMID: 21374739 DOI: 10.1002/mc.20755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 01/10/2011] [Accepted: 01/27/2011] [Indexed: 12/20/2022]
Abstract
The three mammalian HP1 proteins, HP1α/CBX5, HP1β/CBX1, and HPγ/CBX3, are involved in chromatin packing and gene regulation. The HP1α protein is down-regulated in invasive compared to non-invasive breast cancer cells and HP1α is a suppressor of cell migration and invasion. In this report, we examined the background for HP1α protein down-regulation in invasive breast cancer cells. We identified a strict correlation between HP1α down-regulation at the protein level and the mRNA level. The HP1α mRNA down-regulation in invasive cancer cells was not caused by mRNA destabilization. Chromatin immunoprecipitation analysis of the HP1α gene showed a decrease in the histone mark for transcriptional activity H3-K36 tri-methylation and RNA polymerase II in invasive breast cancer cells which correlated with a decreased abundance of basal transcription factors at the HP1α promoter. E2F transcription factors regulate HP1α transcription and we identified that E2F5 depletion increased HP1α expression in invasive breast cancer cells. Finally, we have characterized two HP1α mRNA isoforms and both HP1α mRNA isoforms were down-regulated to a similar extend at the transcriptional level in invasive breast cancer cells. Collectively the presented results show that HP1α down-regulation in invasive breast cancer cells is primary a transcriptional effect and demonstrates a novel set of mechanisms involved in HP1α transcriptional regulation. The finding that HP1α is down-regulated primarily at the transcriptional level provides a new insight for the further elucidation of the detailed molecular mechanisms causing the HP1α down-regulation in invasive breast cancer cells.
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Affiliation(s)
- Rune Thomsen
- Department of Human Genetics, Aarhus University, Denmark
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Nexø BA, Christensen T, Frederiksen J, Møller-Larsen A, Oturai AB, Villesen P, Hansen B, Nissen KK, Laska MJ, Petersen TS, Bonnesen S, Hedemand A, Wu T, Wang X, Zhang X, Brudek T, Maric R, Søndergaard HB, Sellebjerg F, Brusgaard K, Kjeldbjerg AL, Rasmussen HB, Nielsen AL, Nyegaard M, Petersen T, Børglum AD, Pedersen FS. The etiology of multiple sclerosis: genetic evidence for the involvement of the human endogenous retrovirus HERV-Fc1. PLoS One 2011; 6:e16652. [PMID: 21311761 PMCID: PMC3032779 DOI: 10.1371/journal.pone.0016652] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/23/2010] [Indexed: 01/24/2023] Open
Abstract
We have investigated the role of human endogenous retroviruses in multiple sclerosis by analyzing the DNA of patients and controls in 4 cohorts for associations between multiple sclerosis and polymorphisms near viral restriction genes or near endogenous retroviral loci with one or more intact or almost-intact genes. We found that SNPs in the gene TRIM5 were inversely correlated with disease. Conversely, SNPs around one retroviral locus, HERV-Fc1, showed a highly significant association with disease. The latter association was limited to a narrow region that contains no other known genes. We conclude that HERV-Fc1 and TRIM5 play a role in the etiology of multiple sclerosis. If these results are confirmed, they point to new modes of treatment for multiple sclerosis.
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Affiliation(s)
- Bjørn A Nexø
- Department of Human Genetics, University of Aarhus, Aarhus C, Denmark.
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Nielsen KB, Søndergaard A, Johansen MG, Schauser K, Vejlsted M, Nielsen AL, Jørgensen AL, Holm IE. Reelin expression during embryonic development of the pig brain. BMC Neurosci 2010; 11:75. [PMID: 20550682 PMCID: PMC2895594 DOI: 10.1186/1471-2202-11-75] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Accepted: 06/15/2010] [Indexed: 11/24/2022] Open
Abstract
Background Reelin is an extracellular glycoprotein of crucial importance in the developmental organisation of neurons in the mammalian cerebral cortex and other laminated brain regions. The pig possesses a gyrencephalic brain that bears resemblance to the human brain. In order to establish an animal model for neuronal migration disorders in the pig, we have studied the expression pattern and structure of Reelin during pig brain development. Results We determined the sequence of pig Reelin mRNA and protein and identified a high degree of homology to human Reelin. A peak in Reelin mRNA and protein expression is present during the period of major neurogenesis and neuronal migration. This resembles observations for human brain development. Immunohistochemical analysis showed the highest expression of Reelin in the Cajal-Reztius cells of the marginal zone, in resemblance with observations for the developing brain in humans and other mammalian species. Conclusions We conclude that the pig might serve as an alternative animal model to study Reelin functions and that manipulation of the pig Reelin could allow the establishment of an animal model for human neuronal migration disorders.
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Affiliation(s)
- Karsten B Nielsen
- Institute of Human Genetics, University of Aarhus, Bartholin Building 1240, Wilhelm Meyers Allé, 8000 Aarhus C, Denmark.
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Nielsen KB, Kruhøffer M, Holm IE, Jørgensen AL, Nielsen AL. 1Identification of genes differentially expressed in the embryonic pig cerebral cortex before and after appearance of gyration. BMC Res Notes 2010; 3:127. [PMID: 20444278 PMCID: PMC2877059 DOI: 10.1186/1756-0500-3-127] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 05/05/2010] [Indexed: 11/10/2022] Open
Abstract
Background Mammalian evolution is characterized by a progressive expansion of the surface area of the cerebral cortex, an increase that is accompanied by gyration of the cortical surface. The mechanisms controlling this gyration process are not well characterized but mutational analyses indicate that genes involved in neuronal migration play an important function. Due to the lack of gyration of the rodent brain it is important to establish alternative models to examine brain development during the gyration process. The pig brain is gyrated and accordingly is a candidate alternative model. Findings In this study we have identified genes differentially expressed in the pig cerebral cortex before and after appearance of gyration. Pig cortical tissue from two time points in development representing a non-folded, lissencephalic, brain (embryonic day 60) and primary-folded, gyrencephalic, brain (embryonic day 80) were examined by whole genome expression microarray studies. 91 differentially expressed transcripts (fold change >3) were identified. 84 transcripts were annotated and encoding proteins involved in for example neuronal migration, calcium binding, and cytoskeletal structuring. Quantitative real-time PCR was used to confirm the regulation of a subset of the identified genes. Conclusion This study provides identification of genes which are differentially expressed in the pig cerebral cortex before and after appearance of brain gyration. The identified genes include novel candidate genes which could have functional importance for brain development.
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Affiliation(s)
- Karsten B Nielsen
- Department of Human Genetics, University of Aarhus, The Bartholin Building, DK-8000 Aarhus C, Denmark.
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Nielsen AL, Jørgensen FS, Olsen L, Christensen SF, Benie AJ, Bjørnholm T, St. Hilaire PM. A diversity optimized combinatorial library for the identification of Fc-fragment binding ligands. Biopolymers 2010; 94:192-205. [DOI: 10.1002/bip.21338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Losson R, Nielsen AL. The NIZP1 KRAB and C2HR domains cross-talk for transcriptional regulation. Biochim Biophys Acta 2010; 1799:463-8. [PMID: 20176155 DOI: 10.1016/j.bbagrm.2010.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 02/08/2010] [Accepted: 02/16/2010] [Indexed: 01/10/2023]
Abstract
The NSD1 histone methyltransferase is involved in the outgrowth disorders Sotos and Weaver syndromes and childhood acute myeloid leukemia. NSD1 is a bona fida transcriptional co-repressor for Nizp1 which is a protein including SCAN, KRAB, C2HR and zinc-finger domains. In this study the Nizp1 KRAB-domain was identified to possess an intrinsic transcriptional activation capacity suppressed in cis by the presence of the C2HR domain. Oppositely, the KRAB-domain supported C2HR domain mediated transcriptional repression. The presence of the KRAB-domain resulted in increased NSD1 co-repressor association with the C2HR domain. This study shows a new function of the KRAB-domain, C2HR-domain, and the associated factors to confer Nizp1 mediated transcriptional regulation.
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Affiliation(s)
- Regine Losson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics, Illkirch, France
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Reid SD, Nielsen AL, Reddock R. Changes in HIV needs identified by the National AIDS Hotline of Trinidad and Tobago. Rev Panam Salud Publica 2010; 27:93-102. [DOI: 10.1590/s1020-49892010000200002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 09/17/2009] [Indexed: 11/21/2022] Open
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Sparsø T, Andersen G, Nielsen T, Burgdorf KS, Gjesing AP, Nielsen AL, Albrechtsen A, Rasmussen SS, Jørgensen T, Borch-Johnsen K, Sandbaek A, Lauritzen T, Madsbad S, Hansen T, Pedersen O. The GCKR rs780094 polymorphism is associated with elevated fasting serum triacylglycerol, reduced fasting and OGTT-related insulinaemia, and reduced risk of type 2 diabetes. Diabetologia 2008; 51:70-5. [PMID: 18008060 DOI: 10.1007/s00125-007-0865-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 09/28/2007] [Indexed: 10/22/2022]
Abstract
AIMS/HYPOTHESIS Recent genome-wide association studies have suggested that a polymorphism in GCKR, the gene encoding the glucokinase regulatory protein, is involved in triacylglycerol regulation. Our aim was to examine in large-scale studies the common GCKR rs780094 polymorphism in relation to metabolic traits (mainly fasting hypertriacylglycerolaemia) and traits related to pancreatic beta cell function. METHODS The polymorphism was genotyped in 16,853 Danes using Taqman allelic discrimination. Association was analysed in case-control studies and quantitative trait analyses. We also analysed the possible interactive effect between the GCK -30G>A polymorphism and the GCKR rs780094 variant on metabolic traits. RESULTS The minor GCKR A-allele of rs780094 is associated with an increased level of fasting serum triacylglycerol (p = 6 x 10(-14)), impaired fasting (p = 0.001) and OGTT-related insulin release (p = 3 x 10(-6)), reduced homeostasis model assessment of insulin resistance (p = 0.0004), WHO-defined dyslipidaemia (p = 6 x 10(-9)) and a modestly decreased risk of type 2 diabetes (p = 0.01). Significantly increased fasting serum insulin concentrations were demonstrated when analysing the GCK -30A and GCKR rs780094 G-alleles in an additive model. CONCLUSIONS/INTERPRETATION The GCKR rs780094 polymorphism, or another variant with which it is in tight linkage disequilibrium, is likely to increase glucokinase regulatory protein activity to induce improved glycaemic regulation at the expense of hypertriacylglycerolaemia as reflected in the present study of 16,853 Danes. We also suggest an additive effect of GCK and GCKR risk alleles on [corrected] serum insulin release.
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Affiliation(s)
- T Sparsø
- Steno Diabetes Center, Niels Steensens Vej 1, NLC2.13, DK-2820, Gentofte, Denmark.
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Nordentoft I, Jeppesen PB, Nielsen AL, Jorgensen P, Hermansen K. Expression Analysis of cPLA2 Alpha Interacting TIP60 in Diabetic KKAy and Non-Diabetic C57BL Wild-Type Mice: No Impact of Transient and Stable TIP60 Overexpression on Glucose-Stimulated Insulin Secretion in Pancreatic Beta-Cells. Rev Diabet Stud 2007; 4:147-58. [PMID: 18084672 DOI: 10.1900/rds.2007.4.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
UNLABELLED In the present study we investigate the expression levels of cytosolic phospholipase A2 alpha (cPLA2alpha) interacting histone acetyl transferase proteins TIP60alpha and TIP60beta in non-diabetic C57BL wild-type mice and obese type 2 diabetic KKAy model mice. The aim was to test our hypothesis that TIP60 plays a regulatory role in glucose-stimulated insulin secretion from pancreatic beta-cells. MATERIAL AND METHODS Ten obese diabetic KKAy mice and ten non-diabetic C57BL mice were fed a standard chow diet. After nine weeks, islet RNA was purified and used to measure TIP60 expression. We investigated the effect of TIP60alpha and TIP60beta on glucose-stimulated insulin secretion by transient and stable overexpression in the pancreatic mouse beta-cell line MIN6 and the rat beta-cell line INS-1E. RESULTS We found that non-diabetic C57BL mice and diabetic KKAy mice have the same level of both the alpha and beta splice forms of TIP60. Furthermore, we demonstrated that transient and stable expression of TIP60 in INS-1E cells affects neither glucose-stimulated insulin secretion, insulin output nor cell insulin content. Also susceptibility to developing gluco-toxicity was unaffected. CONCLUSION TIP60 over-expression does not affect glucose stimulated insulin secretion, insulin content or abnormal beta-cell function during glucotoxicity.
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Affiliation(s)
- Iver Nordentoft
- Department of Endocrinology and Metabolism C, Aarhus Sygehus THG, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000 Aarhus C, Denmark
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Madsen LB, Thomsen B, Larsen K, Bendixen C, Holm IE, Fredholm M, Jørgensen AL, Nielsen AL. Molecular characterization and temporal expression profiling of presenilins in the developing porcine brain. BMC Neurosci 2007; 8:72. [PMID: 17854491 PMCID: PMC2034586 DOI: 10.1186/1471-2202-8-72] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 09/13/2007] [Indexed: 11/21/2022] Open
Abstract
Background The transmembrane presenilin (PSEN) proteins, PSEN1 and PSEN2, have been proposed to be the catalytic components of the γ-secretase protein complex, which is an intramembranous multimeric protease involved in development, cell regulatory processes, and neurodegeneration in Alzheimer's disease. Here we describe the sequencing, chromosomal mapping, and polymorphism analysis of PSEN1 and PSEN2 in the domestic pig (Sus scrofa domesticus). Conclusion The data provide evidence for structural and functional conservation of PSENs in mammalian lineages, and may suggest that the high sequence similarity and colocalization of PSEN1 and PSEN2 in brain tissue reflect a certain degree of functional redundancy. The data show that pigs may provide a new animal model for detailed analysis of the developmental functions of the PSENs.
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Affiliation(s)
- Lone B Madsen
- Section for Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Tjele, Denmark
| | - Bo Thomsen
- Section for Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Tjele, Denmark
| | - Knud Larsen
- Section for Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Tjele, Denmark
| | - Christian Bendixen
- Section for Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Tjele, Denmark
| | - Ida E Holm
- Department of Pathology, Aalborg Hospital, Aarhus University Hospital, Aalborg, Denmark
| | - Merete Fredholm
- Department of Animal and Veterinary Basic Sciences, Division of Genetics, The Royal Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark
| | - Arne L Jørgensen
- Institute of Human Genetics, The Bartholin Building, University of Aarhus, Denmark
| | - Anders L Nielsen
- Institute of Human Genetics, The Bartholin Building, University of Aarhus, Denmark
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Zhou Z, Hamming OJ, Ank N, Paludan SR, Nielsen AL, Hartmann R. Type III interferon (IFN) induces a type I IFN-like response in a restricted subset of cells through signaling pathways involving both the Jak-STAT pathway and the mitogen-activated protein kinases. J Virol 2007; 81:7749-58. [PMID: 17507495 PMCID: PMC1933366 DOI: 10.1128/jvi.02438-06] [Citation(s) in RCA: 372] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Type III interferon (IFN) is a novel member of the interferon family. Type III IFN utilizes a receptor complex different from that of type I IFN, but both types of IFN induce STAT1, STAT2, and STAT3 activation. Here we describe a detailed comparison of signal transduction initiated by type I and type III IFN. Gene expression array analysis showed that IFN types I and III induced a similar subset of genes. In particular, no genes were induced uniquely by type III IFN. Next, we used chromatin immunoprecipitation (ChIP) analysis to investigate the promoter activation by types I and III IFN. The ChIP assays demonstrated that stimulation of cells with both type I and type III IFN resulted in the recruitment of ISGF3 transcription factor components to the promoter region of responsive genes and in an increase of polymerase II loading and histone acetylation. Whereas IFN type I signaling was observed for a broad spectrum of cell lines, type III IFN signaling was more restricted. The lack of IFN type III signaling was correlated with a low expression of the IL28Ra component of the IFN type III receptor, and IL28Ra overexpression was sufficient to restore IFN type III signaling. We also tested the activation of mitogen-activated protein (MAP) kinases by type III IFN and found that type III IFN relies strongly upon both p38 and JNK MAP kinases for gene induction.
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Affiliation(s)
- Zhangle Zhou
- Department of Human Genetics, University of Aarhus, Denmark
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Severinsen JE, Bjarkam CR, Kiaer-Larsen S, Olsen IM, Nielsen MM, Blechingberg J, Nielsen AL, Holm IE, Foldager L, Young BD, Muir WJ, Blackwood DHR, Corydon TJ, Mors O, Børglum AD. Evidence implicating BRD1 with brain development and susceptibility to both schizophrenia and bipolar affective disorder. Mol Psychiatry 2006; 11:1126-38. [PMID: 16924267 DOI: 10.1038/sj.mp.4001885] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Linkage studies suggest that chromosome 22q12-13 may contain one or more shared susceptibility genes for schizophrenia (SZ) and bipolar affective disorder (BPD). In a Faeroese sample, we previously reported association between microsatellite markers located at 22q13.31-qtel and both disorders. The present study reports an association analysis across five genes (including 14 single nucleotide and two microsatellite polymorphisms) in this interval using a case-control sample of 162 BPD, 103 SZ patients and 200 controls. The bromodomain-containing 1 gene (BRD1), which encodes a putative regulator of transcription showed association with both disorders with minimal P-values of 0.0046 and 0.00001 for single marker and overall haplotype analysis, respectively. A specific BRD1 2-marker 'risk' haplotype showed a frequency of approximately 10% in the combined case group versus approximately 1% in controls (P-value 2.8 x 10(-7)). Expression analysis of BRD1 mRNA revealed widespread expression in mammalian brain tissue, which was substantiated by immunohistochemical detection of BRD1 protein in the nucleus, perikaryal cytosol and proximal dendrites of the neurons in the adult rat, rabbit and human CNS. Quantitative mRNA analysis in developing fetal pig brain revealed spatiotemporal differences with high expression at early embryonic stages, with intense nuclear and cytosolar immunohistochemical staining of the neuroepithelial layer and early neuroblasts, whilst more mature neurons at later embryonic stages had less nuclear staining. The results implicate BRD1 with SZ and BPD susceptibility and provide evidence that suggests a role for BRD1 in neurodevelopment.
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Affiliation(s)
- J E Severinsen
- Institute of Human Genetics, University of Aarhus, Aarhus, Denmark
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Singh R, Nielsen AL, Johansen MG, Jørgensen AL. Genetic polymorphism and sequence evolution of an alternatively spliced exon of the glial fibrillary acidic protein gene, GFAP. Genomics 2003; 82:185-93. [PMID: 12837269 DOI: 10.1016/s0888-7543(03)00106-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Isoform GFAPepsilon of the human cytoskeletal protein GFAP carries, as the result of alternative splicing of exon 7a of GFAP, a novel 42-amino-acid-long C-terminal region with binding capacity for the presenilin proteins. Here we show that exon 7a is present in a variety of mammals but absent from GFAP of chicken and fish. Comparison of the mouse and human GFAP exons showed an increased rate of nonsynonymous nucleotide substitutions in exon 7a compared to the other exons. This resulted in 10 nonconservative and 2 conservative amino acid substitutions and suggests that exon 7a has evolved under different functional constraints. Exons 7a of humans and higher primates are 100% identical apart from alanine codon 426, which is conserved in only 9% of the human alleles, while 21 and 70% of the alleles, respectively, have a valine or a threonine codon at that position. Threonine represents a potential phosphorylation site, and positive selection of that effect could explain the high allele frequency.
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Affiliation(s)
- Ripudaman Singh
- Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark
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Nielsen AL, Jørgensen P, Jørgensen AL. Mutations associated with a childhood leukodystrophy, Alexander disease, cause deficiency in dimerization of the cytoskeletal protein GFAP. J Neurogenet 2002; 16:175-9. [PMID: 12696672 DOI: 10.1080/01677060215305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Heterozygous, de novo mutations in the glial fibrillary acidic protein (GFAP) gene were recently found to be associated with Alexander disease. We examined the functional effect of such mutations, and observed a decrease in GFAP dimerization. This effect behaves in a dominant fashion and points towards a potential mechanism in pathogenesis.
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Affiliation(s)
- Anders L Nielsen
- Department of Human Genetics, The Bartholin Building, University of Aarhus, DK-8000 Aarhus C, Denmark.
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Abstract
OBJECTIVE This study examines whether the adult social roles perspective. an approach that explains drinking behaviors for Anglos, similarly affects alcohol use by Cubans, Mexican Americans, Puerto Ricans and Other Hispanics (Central and South Americans). METHOD The 1993 National Household Survey on Drug Abuse, a national probability sample of the household population in the United States, is used. The sample utilized here (N= 13,822; 56.2% female) consisted of 9,388 Anglos, 611 Cubans, 2,459 Mexican Americans, 611 Puerto Ricans and 753 Central/South Americans age 18 and older. The outcome measures include past-year drinking, and for drinkers, heavy drinking and alcohol-related problems. Logistic regression analyses are conducted using Stata. RESULTS The results show that there are some ethnic differences in the effects of the adult social roles. Of particular importance is the finding that being married has anomalous effects for Cubans (heavy drinking), Mexican Americans (problems) and Other Hispanics (problems) compared with Anglos and the other Hispanic ethnic groups. CONCLUSIONS The adult social roles perspective has some utility for explaining Hispanic drinking patterns. Future research should consider not only traditional predictors of drinking but also such socio-cultural factors as acculturation and familism, to better understand adult alcohol use by members of Hispanic ethnic groups.
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Affiliation(s)
- A L Nielsen
- Department of Sociology, University of Miami, Coral Gables, Florida 33124, USA.
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Abstract
OBJECTIVE This is one of the first studies to examine and compare alcohol use for adolescent Cubans, Mexican Americans, Puerto Ricans and other Hispanics. METHOD The data come from the 1993 National Household Survey on Drug Abuse (NHSDA), a national probability sample of the U.S. household population. The sample examined here (N = 1,865, 52% male) comprises 200 Cubans, 1,133 Mexican Americans, 255 Puerto Ricans and 277 Central/South Americans who were 12 to 17 years old. Drinking patterns are measured using a quantity-frequency index, and analyses are conducted using Stata. RESULTS In the cross-tabulations, no ethnic differences in drinking patterns are found for males or females, nor is there evidence of gender differences within ethnic groups, although there are some age differences in alcohol use. In the logistic regression analyses, two ethnic differences emerge, although the factors most consistently associated with drinking behaviors in these analyses are age, Spanish language use and urban residence. Additional analyses using the 1998 NHSDA suggest that ethnic differences in alcohol use may emerge in late adolescence/early adulthood. CONCLUSIONS Given the established findings of ethnic and gender differences in drinking among adult Hispanics, it is surprising that few differences are evidenced in adolescence. Future research should explore whether such differences emerge during the transition into adulthood and, if so, identify factors that produce them. In addition, to increase understanding of these ethnic groups' drinking patterns, future research should further investigate the factors associated with Hispanic adolescents' alcohol use, including both consideration of whether the predictors are the same across groups and of the role of sociocultural factors.
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Affiliation(s)
- A L Nielsen
- Department of Sociology, University of Miami, Coral Gables, Florida 33124-2208, USA.
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Nielsen AL, Oulad-Abdelghani M, Ortiz JA, Remboutsika E, Chambon P, Losson R. Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol Cell 2001; 7:729-39. [PMID: 11336697 DOI: 10.1016/s1097-2765(01)00218-0] [Citation(s) in RCA: 304] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Members of the heterochromatin protein 1 (HP1) family are silencing nonhistone proteins. Here, we show that in P19 embryonal carcinoma (EC) nuclei, HP1 alpha, beta, and gamma form homo- and heteromers associated with nucleosomal core histones. In vitro, all three HP1s bind to tailed and tailless nucleosomes and specifically interact with the histone-fold of histone H3. Furthermore, HP1alpha interacts with the linker histone H1. HP1alpha binds to H3 and H1 through its chromodomain (CD) and hinge region, respectively. Interestingly, the Polycomb (Pc1/M33) CD also interacts with H3, and HP1alpha and Pc1/M33 binding to H3 is severely impaired by CD mutations known to abrogate HP1 and Polycomb silencing in Drosophila. These results define a novel function for the conserved CD and suggest that HP1 self-association and histone binding may play a crucial role in HP1-mediated heterochromatin assembly.
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Affiliation(s)
- A L Nielsen
- Department of Molecular and Structural Biology and Institute of Human Genetics, Aarhus University, C. F. Mollersalle 130, DK-8000 C, Aarhus, Denmark
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Holm IE, Abelskov K, Bojsen-Møller M, Nielsen AL, Jørgensen AL. Creutzfeldt-Jakob disease segregating in a three generation Danish family. Acta Neurol Scand 2001; 103:139-47. [PMID: 11240560 DOI: 10.1034/j.1600-0404.2001.103003139.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A three generation family is presented in which rapidly progressive, early-onset Creutzfeldt-Jakob disease without typical EEG changes segregates as an autosomal dominant disease. An aspartic acid to asparagine mutation at codon 178 of the prion gene, PRNP, co-segregates with the disease. As expected, the disease allele also carries the valine codon of the polymorphic valine/methionine codon 129 of the gene. In family members homozygous for this valine codon the disease was more rapidly progressive than in a heterozygous family member, who had a variant clinical phenotype. Definite neuropathological diagnosis required prion staining with specific antibodies.
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Affiliation(s)
- I E Holm
- Department of Pathology, Aarhus University Hospital, Denmark
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Lundstrøm MS, Høgdall CK, Nielsen AL, Nyholm HC. Serum tetranectin and CA125 in endometrial adenocarcinoma. Anticancer Res 2000; 20:3903-6. [PMID: 11268474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
BACKGROUND CA125 and tetranectin (TN) are prognostic markers in ovarian cancer. This study examines the values of these markers in endometrial cancer. MATERIALS AND METHODS TN and CA125 were determined preoperatively in 99 patients with primary endometrioid adenocarcinoma and evaluated in relation to tumor grade, stage and cancer survival. RESULTS The CA125 levels correlated significantly with tumor stage. Dichotomized according to a cut-off level of 35 U/ml, CA125 significantly correlated with cancer death. Multivariate regression analysis of cancer survival time showed that CA125 > 35 U/ml was not an independent factor when stage was introduced. TN levels were within the normal range in all patients and did not show any association with tumor grade, stage or survival. CONCLUSIONS The study confirmed the role of CA125 as a prognostic factor in endometrial cancer and may be of aid in pointing out patients at high risk, whereas tetranectin did not show any prognostic effect.
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Affiliation(s)
- M S Lundstrøm
- Department of Gynecology and Obstetrics, University of Copenhagen, Hvidovre Hospital, Copenhagen, Denmark
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Abstract
OBJECTIVE This study examines and compares the drinking patterns and problems of members of four Hispanic groups (Cubans, Mexican Americans, Puerto Ricans and other Hispanics) in the United States, with information presented by gender and age. METHOD The 1993 National Household Survey on Drug Abuse, a recent national probability sample of the household population aged 18 and over in the United States, is used. Data are obtained through in-person interviews. The sample includes 4,462 Hispanics of Cuban (n = 620), Mexican (n = 2,467), Puerto Rican (n = 619) and Central and South American (n = 756) origin. Analyses are conducted using SUDAAN. RESULTS There are significant differences across the Hispanic groups in their drinking patterns and problems. Among men, Mexican Americans report the most frequent and heavy drinking, and the greatest prevalence of drunkenness and alcohol-related problems. Cubans report the lowest percentages of such respondents, and Puerto Ricans and other Hispanics are in between the other two groups. For women, fewer ethnic differences are evidenced than for men. In general, Puerto Ricans and Mexican Americans drink more often and heavily and experience more problems than the other groups. Even after controlling for predictors of adult alcohol use, some ethnic differences in drinking persist. CONCLUSIONS The four Hispanic groups have different drinking patterns. More research is necessary to determine the factors associated with differences in drinking across Hispanic groups.
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Affiliation(s)
- A L Nielsen
- Department of Sociology, University of Miami, Coral Gables, Florida 33146, USA
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Nielsen AL, Ortiz JA, You J, Oulad-Abdelghani M, Khechumian R, Gansmuller A, Chambon P, Losson R. Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family. EMBO J 1999; 18:6385-95. [PMID: 10562550 PMCID: PMC1171701 DOI: 10.1093/emboj/18.22.6385] [Citation(s) in RCA: 288] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mammalian TIF1alpha and TIF1beta (KAP-1/KRIP-1) are related transcriptional intermediary factors that possess intrinsic silencing activity. TIF1alpha is believed to be a euchromatic target for liganded nuclear receptors, while TIF1beta may serve as a co-repressor for the large family of KRAB domain-containing zinc finger proteins. Here, we report an association of TIF1beta with both heterochromatin and euchromatin in interphase nuclei. Co-immunoprecipitation of nuclear extracts shows that endogenous TIF1beta, but not TIF1alpha, is associated with members of the heterochromatin protein 1 (HP1) family. However, in vitro, both TIF1alpha and TIF1beta interact with and phosphorylate the HP1 proteins. This interaction involves a conserved amino acid motif, which is critical for the silencing activity of TIF1beta but not TIF1alpha. We further show that trichostatin A, an inhibitor of histone deacetylases, can interfere with both TIF1 and HP1 silencing. The silencing activity of TIF1alpha appears to result chiefly from histone deacetylation, whereas that of TIF1beta may be mediated via both HP1 binding and histone deacetylation.
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Affiliation(s)
- A L Nielsen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de France, BP 163, 67404 Illkirch-Cedex, France
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Nielsen AL, Thunedborg P, Brinkenfeldt H, Hegbrant J, Jensen HA, Wandrup JH. Assessment of pH and oxygen status during hemodialysis using the arterial blood line in patients with an arteriovenous fistula. Blood Purif 1999; 17:206-12. [PMID: 10494023 DOI: 10.1159/000014397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND In patients with arteriovenous fistulas, assessment of pH and oxygen status during hemodialysis (HD) using the extracorporeal dialysis arterial blood line is widely used both in daily routine and in most studies investigating hypoxia during HD. We designed this study to evaluate whether results of blood gas samples drawn from the extracorporeal arterial line were clinically acceptable in assessing oxygen status. METHODS We compared samples drawn from the extracorporeal arterial line with conventionally arterial punctures during 18 routine HD sessions. The samples were drawn simultaneously and analyzed immediately for blood gases, pH and hemoximetry values. RESULTS No significant difference was found between the values from the radial artery and the extracorporeal arterial blood line except for FMetHb. CONCLUSION Thus, obtaining samples from the extracorporeal dialysis arterial blood line to evaluate the parameters of the oxygen status (pH, pO(2), pCO(2), ctHb, sO(2), FCOHb and ctO(2)) during routine HD is a clinically convenient and accurate sampling approach.
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Affiliation(s)
- A L Nielsen
- Department of Nephrology, Hvidovre University Hospital, Hvidovre, Denmark.
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Sørensen JB, Bergman B, Nielsen AL, Krarup M, Dombernowsky P, Hansen HH. Phase II study of gemcitabine and vindesine in patients with previously untreated non-resectable non-small-cell lung cancer. Br J Cancer 1999; 79:875-81. [PMID: 10070884 PMCID: PMC2362682 DOI: 10.1038/sj.bjc.6690140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Because both vindesine and gemcitabine are active drugs in advanced non-small-cell lung cancer (NSCLC), with different modes of action and only partly overlapping toxicity, a phase II study was performed. Gemcitabine 1000 mg m(-2) was given on days 1, 8 and 15 every 4 weeks, while vindesine 3 mg m(-2) was administered weekly for 7 weeks, then every 2 weeks. A total of 42 patients with nonresectable NSCLC were included. The median age of patients was 56 years; 57% were men, 52% had adenocarcinoma, 31% squamous cell carcinoma and 17% had large-cell carcinoma. The performance status ranged from 0 to 2 with 83% in performance status 1. The majority (55%) had stage IV disease, while 40% had stage III B and 5% stage III A disease. WHO grade 3-4 leucopenia occurred in five patients (12%) and 9% had grade 4 neutropenia. Thrombocytopenia grade 3-4 was observed in six patients (15%). There were no septic death or bleeding episodes. One patient had a transient WHO grade 4 increase in bilirubin, and four patients had a decrease in glomerular filtration rate below the normal limit; one of these patients developed a non-reversible renal insufficiency. Ten patients (24%) complained of dyspnoea of uncertain mechanism, possibly involving bronchoconstriction. There were one complete and seven partial responses among 40 assessable patients (20%, 95% confidence limits 9-36%). Median response duration was 31 weeks (range 11-83 weeks) and median survival time 31 weeks (range 2-171 weeks). The current combination of gemcitabine and vindesine does not appear to be promising for further examination because of the toxicity and somewhat disappointing activity.
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Affiliation(s)
- J B Sørensen
- Department of Oncology, Finsen Center, National University Hospital, Copenhagen, Denmark
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Abstract
Eleven patients with chronic renal failure who were being treated with haemodialysis three times a week were monitored for a total of 34 haemodialysis sessions. Erythrocyte 2,3-biphosphoglycerate (2,3-BPG) concentration was analysed immediately before initiation of bicarbonate haemodialysis and 1 h afterwards. The 2,3-BPG concentration was expressed relative to the haemoglobin tetramer (Hb4) concentration as the 2,3-BPG/Hb4 ratio and compared with blood gas analyses and biochemical variables important for characterizing uraemia. During the first hour of haemodialysis the 2,3-BPG/Hb4 ratio decreased (p < 0.002), but the magnitude of the decrease did not significantly correlate with the 2,3-BPG/Hb4 ratio measured before haemodialysis (p=0.104). The decrease is most likely to be caused by the haemodialysis procedure itself. Mechanical stress on the erythrocytes is believed to cause the 2,3-BPG to escape; it is then removed by haemodialysis. Physiologically, an increase in 2,3-BPG would be expected to counteract the hypoxia which is frequently observed during haemodialysis. However, the present results show the opposite, a decrease in 2,3-BPG. No significant correlation was shown between the haemoglobin concentration and the 2,3-BPG/Hb4 ratio before dialysis (p=0.414). The pH showed a significant positive correlation with the 2,3-BPG/Hb4 ratio before dialysis, whereas the arterial pO2 and the 2,3-BPG/Hb4 ratio before dialysis were insignificantly negatively correlated. The concentrations of calcium, phosphate, creatinine, urea and albumin did not correlate significantly with the change in 2,3-BPG/Hb4-ratio after 1 h. The 2,3-BPG/Hb4 ratio (p=0.03) sampled just before dialysis correlated significantly and positively with the total weekly dosage of erythropoietin given to the patients.
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Affiliation(s)
- A L Nielsen
- Department of Nephrology, Hvidovre University Hospital, Denmark.
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Abstract
Ligand-induced gene activation by nuclear receptors (NRs) is thought to be mediated by transcriptional intermediary factors (TIFs), that interact with their ligand-dependent AF-2 activating domain. Included in the group of the putative AF-2 TIFs identified so far is TIF1alpha, a member of a new family of proteins which contains an N-terminal RBCC (RING finger-B boxes-coiled coil) motif and a C-terminal bromodomain preceded by a PHD finger. In addition to these conserved domains present in a number of transcriptional regulatory proteins, TIF1alpha was found to contain several protein-protein interaction sites. Of these, one specifically interacts with NRs bound to their agonistic ligand and not with NR mutants that are defective in the AF-2 activity. Immediately adjacent to this 'NR box', TIF1alpha contains an interaction site for members of the chromatin organization modifier (chromo) family, HP1alpha and MOD1, which both are heterochromatinic proteins. Finally, TIF1alpha also has a binding site for KRAB silencing domains of C2H2 zinc finger proteins. TIF1beta, another member of the TIF1 gene family, has some interacting partners in common with TIF1alpha. TIF1beta can interact with HP1alpha, MOD1 and KRAB domains, but apparently not with NRs. Both TIF1alpha and TIF1beta repress transcription when fused to a DNA binding domain in transiently transfected mammalian cells. A model discussing the potential function(s) of TIF1s in the control of transcription at the level of the chromatin template will be presented.
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Affiliation(s)
- B Le Douarin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Collège de France, Illkirch
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Le Douarin B, Nielsen AL, You J, Chambon P, Losson R. TIF1 alpha: a chromatin-specific mediator for the ligand-dependent activation function AF-2 of nuclear receptors? Biochem Soc Trans 1997; 25:605-12. [PMID: 9191165 DOI: 10.1042/bst0250605] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- B Le Douarin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Collège de France, Illkirch, France
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Nyholm HC, Christensen IJ, Nielsen AL. [The prognostic significance of progesterone receptor level in endometrial cancer]. Ugeskr Laeger 1997; 159:601-4. [PMID: 9045451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Oestrogen receptor (ER) and progesterone receptor (PR) contents were determined by biochemical (dextran charcoal-coated (DCC) assay) and immunohistochemical (ICA) methods in biopsies from 145 primary endometrial adenocarcinomas. Correlations between receptor contents and cancer specific survival were examined in a multivariate analysis including histopathological characteristics. Median patient follow-up time was 67 months with 18 cancer deaths. "High" PR levels correlated significantly (p = 0.004) with survival, independently of stage risk group (stages Ia-Ib vs Ic-IV). Patient age and histological grade were prognostic factors in a univariate setting but these parameters were eliminated in the multivariate model. The association between PR contents and cancer survival suggests that determination of PR can be of importance in the evaluation of endometrial cancer.
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Affiliation(s)
- H C Nyholm
- Gynaekologisk-obstetrisk afdeling, H:S Hvidovre Hospital
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