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Schlachetzki JCM, Prots I, Tao J, Chun HB, Saijo K, Gosselin D, Winner B, Glass CK, Winkler J. Author Correction: A monocyte gene expression signature in the early clinical course of Parkinson's disease. Sci Rep 2020; 10:6261. [PMID: 32253373 PMCID: PMC7136204 DOI: 10.1038/s41598-020-62928-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Johannes C M Schlachetzki
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany. .,Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, 92093-0651, CA, USA.
| | - Iryna Prots
- Department of Stem Cell Biology, FAU Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, 92093-0651, CA, USA
| | - Hyun B Chun
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, 92093-0651, CA, USA
| | - Kaoru Saijo
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, 94720-3200, CA, USA
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, 92093-0651, CA, USA.,Department of Molecular Medicine, Centre de Recherche du CHU de Québec - Université Laval, Québec, G1V 4G2, Canada
| | - Beate Winner
- Department of Stem Cell Biology, FAU Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, 92093-0651, CA, USA
| | - Jürgen Winkler
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany.
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Schlachetzki JCM, Prots I, Tao J, Chun HB, Saijo K, Gosselin D, Winner B, Glass CK, Winkler J. A monocyte gene expression signature in the early clinical course of Parkinson's disease. Sci Rep 2018; 8:10757. [PMID: 30018301 PMCID: PMC6050266 DOI: 10.1038/s41598-018-28986-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 02/13/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
Microglia are the main immune cells of the brain and express a large genetic pattern of genes linked to Parkinson’s disease risk alleles. Monocytes like microglia are myeloid-lineage cells, raising the questions of the extent to which they share gene expression with microglia and whether they are already altered early in the clinical course of the disease. To decipher a monocytic gene expression signature in Parkinson’s disease, we performed RNA-seq and applied the two-sample Kolmogorov-Smirnov test to identify differentially expressed genes between controls and patients with Parkinson's disease and changes in gene expression variability and dysregulation. The gene expression profiles of normal human monocytes and microglia showed a plethora of differentially expressed genes. Additionally, we identified a distinct gene expression pattern of monocytes isolated from Parkinson’s disease patients at an early disease stage compared to controls using the Kolmogorov-Smirnov test. Differentially expressed genes included genes involved in immune activation such as HLA-DQB1, MYD88, REL, and TNF-α. Our data suggest that future studies of distinct leukocyte subsets are warranted to identify possible surrogate biomarkers and may lead to the identification of novel interventions early in the disease course.
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Affiliation(s)
- Johannes C M Schlachetzki
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany. .,Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, CA, 92093-0651, USA.
| | - Iryna Prots
- Department of Stem Cell Biology, FAU Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, CA, 92093-0651, USA
| | - Hyun B Chun
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, CA, 92093-0651, USA
| | - Kaoru Saijo
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720-3200, USA
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, CA, 92093-0651, USA.,Department of Molecular Medicine, Centre de Recherche du CHU de Québec - Université Laval, Québec, G1V 4G2, Canada
| | - Beate Winner
- Department of Stem Cell Biology, FAU Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego at La Jolla, CA, 92093-0651, USA
| | - Jürgen Winkler
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany.
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Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell 2018; 173:1796-1809.e17. [PMID: 29779944 PMCID: PMC6003872 DOI: 10.1016/j.cell.2018.04.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [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: 01/03/2018] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
Non-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites, and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluating genetic variation provided evidence for roles of ∼100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 datasets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.
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Affiliation(s)
- Verena M Link
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Sascha H Duttke
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hyun B Chun
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emma Westin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dylan Skola
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gregory J Fonseca
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Dirk Metzler
- Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Bing Ren
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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Kaikkonen MU, Spann N, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 2013; 51:310-25. [PMID: 23932714 PMCID: PMC3779836 DOI: 10.1016/j.molcel.2013.07.010] [Citation(s) in RCA: 493] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 05/06/2013] [Accepted: 07/11/2013] [Indexed: 11/20/2022]
Abstract
Recent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell-type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ∼3,000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. Unexpectedly, we find that enhancer transcription precedes local mono- and dimethylation of histone H3 lysine 4 (H3K4me1/2). H3K4 methylation at de novo enhancers is primarily dependent on the histone methyltransferases Mll1, Mll2/4, and Mll3 and is significantly reduced by inhibition of RNA polymerase II elongation. Collectively, these findings suggest an essential role of enhancer transcription in H3K4me1/2 deposition at de novo enhancers that is independent of potential functions of the resulting eRNA transcripts.
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Affiliation(s)
- Minna U Kaikkonen
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
- A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Nathanael Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
| | - Sven Heinz
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
| | - Casey E. Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
| | - Karmel A. Allison
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
| | - Joshua D. Stender
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
| | - Hyun B. Chun
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
| | - David F. Tough
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Rab K. Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Christopher Benner
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, USA 92037
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA
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