Insights into TREM2 biology by network analysis of human brain gene expression data

Neurobiology of Aging - Tập 34 - Trang 2699-2714 - 2013
Paola Forabosco1, Adaikalavan Ramasamy2,3, Daniah Trabzuni2,4, Robert Walker5, Colin Smith5, Jose Bras2, Adam P. Levine6, John Hardy2, Jennifer M. Pocock7, Rita Guerreiro2, Michael E. Weale3, Mina Ryten2
1Istituto di Genetica delle Popolazioni—CNR, Sassari, Italy
2Reta Lila Weston Institute and Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, UK
3Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
4Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
5MRC Sudden Death Brain Bank Project, Department of Neuropathology, University of Edinburgh, Edinburgh, UK
6Division of Medicine, University College London, London, UK
7Department of Neuroinflammation, University College London Institute of Neurology, London, UK

Tài liệu tham khảo

Barbosa-Morais, 2010, A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data, Nucleic Acids Res., 38, e17, 10.1093/nar/gkp942 Barreiro, 2012, Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection, Proc. Natl. Acad. Sci. U.S.A, 109, 1204, 10.1073/pnas.1115761109 Chan, 2007, The origin and cell lineage of microglia: new concepts, Brain Res. Rev., 53, 344, 10.1016/j.brainresrev.2006.11.002 Colantuoni, 2011, Temporal dynamics and genetic control of transcription in the human prefrontal cortex, Nature, 478, 519, 10.1038/nature10524 Colonna, 2003, TREMs in the immune system and beyond, Nat. Rev. Immunol., 3, 445, 10.1038/nri1106 Conde, 2006, Microglia in the aging brain, J. Neuropathol. Exp. Neurol., 65, 199, 10.1097/01.jnen.0000202887.22082.63 David, 2011, Repertoire of microglial and macrophage responses after spinal cord injury, Nat. Rev. Neurosci., 12, 388, 10.1038/nrn3053 Daws, 2003, Pattern recognition by TREM-2: binding of anionic ligands, J. Immunol., 171, 594, 10.4049/jimmunol.171.2.594 Edgar, 2002, Gene Expression Omnibus: NCBI gene expression and hybridization array data repository, Nucleic Acids Res., 30, 207, 10.1093/nar/30.1.207 Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. U.S.A, 95, 14863, 10.1073/pnas.95.25.14863 Fairfax, 2012, Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles, Nat. Genet., 44, 502, 10.1038/ng.2205 Geschwind, 2009, Neuroscience in the era of functional genomics and systems biology, Nature, 461, 908, 10.1038/nature08537 Ginhoux, 2010, Fate mapping analysis reveals that adult microglia derive from primitive macrophages, Science, 330, 841, 10.1126/science.1194637 Gordon, 2003, Alternative activation of macrophages, Nat Rev Immunol., 3, 23, 10.1038/nri978 Griggs, 2008, Dedicator of cytokinesis 8 is disrupted in two patients with mental retardation and developmental disabilities, Genomics, 91, 195, 10.1016/j.ygeno.2007.10.011 Guerreiro, 2012, TREM2 variants in Alzheimer's disease, N. Engl. J. Med, 368, 117, 10.1056/NEJMoa1211851 Hanisch, 2007, Microglia: active sensor and versatile effector cells in the normal and pathologic brain, Nat. Neurosci., 10, 1387, 10.1038/nn1997 Harada, 2012, DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses, Blood, 119, 4451, 10.1182/blood-2012-01-407098 Haynes, 2006, The P2Y12 receptor regulates microglial activation by extracellular nucleotides, Nat. Neurosci., 9, 1512, 10.1038/nn1805 Hernandez-Varas, 2011, Rap1-GTP-interacting adaptor molecule (RIAM) protein controls invasion and growth of melanoma cells, J. Biol. Chem., 286, 18492, 10.1074/jbc.M110.189811 Hollingworth, 2011, Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease, Nat. Genet., 43, 429, 10.1038/ng.803 Huang da, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923 Huang da, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Hynes, 1992, Integrins: versatility, modulation, and signaling in cell adhesion, Cell, 69, 11, 10.1016/0092-8674(92)90115-S Jabara, 2012, DOCK8 functions as an adaptor that links TLR-MyD88 signaling to B cell activation, Nat. Immunol., 13, 612, 10.1038/ni.2305 Jonsson, 2012, Variant of TREM2 associated with the risk of Alzheimer's disease, N. Engl. J. Med, 368, 107, 10.1056/NEJMoa1211103 Kanehisa, 2000, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27 Kanehisa, 2012, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res., 40, D109, 10.1093/nar/gkr988 Kang, 2011, Spatio-temporal transcriptome of the human brain, Nature, 478, 483, 10.1038/nature10523 Kettenmann, 2013, Microglia: new roles for the synaptic stripper, Neuron, 77, 10, 10.1016/j.neuron.2012.12.023 Konopka, 2011, Human-specific transcriptional networks in the brain, Neuron, 75, 601, 10.1016/j.neuron.2012.05.034 Lafuente, 2004, RIAM, an Ena/VASP and Profilin ligand, interacts with Rap1-GTP and mediates Rap1-induced adhesion, Dev. Cell, 7, 585, 10.1016/j.devcel.2004.07.021 Lambe, 2011, DOCK8 is essential for T-cell survival and the maintenance of CD8+ T-cell memory, Eur. J. Immunol., 41, 3423, 10.1002/eji.201141759 Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, 9, 559, 10.1186/1471-2105-9-559 Langfelder, 2011, Is my network module preserved and reproducible?, PLoS Comput. Biol., 7, e1001057, 10.1371/journal.pcbi.1001057 Lee, 2004, Coexpression analysis of human genes across many microarray data sets, Genome Res., 14, 1085, 10.1101/gr.1910904 Linnartz, 2010, Microglial immunoreceptor tyrosine-based activation and inhibition motif signaling in neuroinflammation, Int. J. Alzheimers Dis., 2010 Mason, 2009, Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells, BMC Genomics, 10, 327, 10.1186/1471-2164-10-327 Millar, 2007, Tissue and organ donation for research in forensic pathology: the MRC Sudden Death Brain and Tissue Bank, J. Pathol., 213, 369, 10.1002/path.2247 Miller, 2008, A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging, J. Neurosci., 28, 1410, 10.1523/JNEUROSCI.4098-07.2008 Miller, 2007, The effects of aging, injury and disease on microglial function: a case for cellular senescence, Neuron Glia Biol., 3, 245, 10.1017/S1740925X08000136 Mittelbronn, 2001, Local distribution of microglia in the normal adult human central nervous system differs by up to one order of magnitude, Acta Neuropathol., 101, 249, 10.1007/s004010000284 Mizesko, 2013, Defective actin accumulation impairs human natural killer cell function in patients with dedicator of cytokinesis 8 deficiency, J. Allergy Clin. Immunol, 131, 840, 10.1016/j.jaci.2012.12.1568 Morgan, 2007, Association studies of 23 positional/functional candidate genes on chromosome 10 in late-onset Alzheimer's disease, Am. J. Med. Genet. B Neuropsychiatr. Genet., 144B, 762, 10.1002/ajmg.b.30509 Naj, 2011, Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease, Nat. Genet., 43, 436, 10.1038/ng.801 N'Diaye, 2009, TREM-2 (triggering receptor expressed on myeloid cells 2) is a phagocytic receptor for bacteria, J. Cell Biol., 184, 215, 10.1083/jcb.200808080 Nimmerjahn, 2005, Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo, Science, 308, 1314, 10.1126/science.1110647 Oldham, 2006, Conservation and evolution of gene coexpression networks in human and chimpanzee brains, Proc. Natl. Acad. Sci. U.S.A, 103, 17973, 10.1073/pnas.0605938103 Oldham, 2008, Functional organization of the transcriptome in human brain, Nat. Neurosci., 11, 1271, 10.1038/nn.2207 Otero, 2009, Macrophage colony-stimulating factor induces the proliferation and survival of macrophages via a pathway involving DAP12 and beta-catenin, Nat. Immunol., 10, 734, 10.1038/ni.1744 Paloneva, 2002, Mutations in two genes encoding different subunits of a receptor signaling complex result in an identical disease phenotype, Am. J. Hum. Genet., 71, 656, 10.1086/342259 Parkinson, 2011, ArrayExpress update–an archive of microarray and high-throughput sequencing-based functional genomics experiments, Nucleic Acids Res., 39, D1002, 10.1093/nar/gkq1040 Pocock, 2007, Neurotransmitter receptors on microglia, Trends Neurosci., 30, 527, 10.1016/j.tins.2007.07.007 Rademakers, 2011, Mutations in the colony stimulating factor 1 receptor (CSF1R) gene cause hereditary diffuse leukoencephalopathy with spheroids, Nat. Genet., 44, 200, 10.1038/ng.1027 Ravasz, 2003, Hierarchical organization in complex networks, Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 67, 026112, 10.1103/PhysRevE.67.026112 Rosen, 2011, Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling, Neuron, 71, 1030, 10.1016/j.neuron.2011.07.021 Sanui, 2003, DOCK2 regulates Rac activation and cytoskeletal reorganization through interaction with ELMO1, Blood, 102, 2948, 10.1182/blood-2003-01-0173 Schoenwaelder, 1999, Bidirectional signaling between the cytoskeleton and integrins, Curr. Opin. Cell Biol., 11, 274, 10.1016/S0955-0674(99)80037-4 Smith, 2009, Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease, J. Exp. Med., 206, 1883, 10.1084/jem.20091233 Stuart, 2003, A gene-coexpression network for global discovery of conserved genetic modules, Science, 302, 249, 10.1126/science.1087447 Trabzuni, 2011, Quality control parameters on a large dataset of regionally dissected human control brains for whole genome expression studies, J. Neurochem., 119, 275, 10.1111/j.1471-4159.2011.07432.x van Lookeren Campagne, 2007, Macrophage complement receptors and pathogen clearance, Cell Microbiol., 9, 2095, 10.1111/j.1462-5822.2007.00981.x Weiner, 2006, Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis, PLoS Biol., 4, e38, 10.1371/journal.pbio.0040038 Winden, 2009, The organization of the transcriptional network in specific neuronal classes, Mol. Syst. Biol., 5, 291, 10.1038/msb.2009.46 Wu, 2004, A model-based background adjustment for oligonucleotide expression arrays, J. Am. Stat. Assoc., 99, 909, 10.1198/016214504000000683 Yip, 2007, Gene network interconnectedness and the generalized topological overlap measure, BMC Bioinformatics, 8, 22, 10.1186/1471-2105-8-22 Yu, 2008, A navigator for human genome epidemiology, Nat. Genet., 40, 124, 10.1038/ng0208-124 Zhang, 2005, A general framework for weighted gene co-expression network analysis, Stat. Appl. Genet. Mol. Biol., 4, 10.2202/1544-6115.1128