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We are analyzing https://www.nature.com/articles/ncomms8545.

Title:
Genomic modulators of gene expression in human neutrophils | Nature Communications
Description:
Neutrophils form the most abundant leukocyte subset and are central to many disease processes. Technical challenges in transcriptomic profiling have prohibited genomic approaches to date. Here we map expression quantitative trait loci (eQTL) in peripheral blood CD16+ neutrophils from 101 healthy European adults. We identify cis-eQTL for 3281 neutrophil-expressed genes including many implicated in neutrophil function, with 450 of these not previously observed in myeloid or lymphoid cells. Paired comparison with monocyte eQTL demonstrates nuanced conditioning of genetic regulation of gene expression by cellular context, which relates to cell-type-specific DNA methylation and histone modifications. Neutrophil eQTL are markedly enriched for trait-associated variants particularly autoimmune, allergy and infectious disease. We further demonstrate how eQTL in PADI4 and NOD2 delineate risk variant function in rheumatoid arthritis, leprosy and Crohn’s disease. Taken together, these data help advance understanding of the genetics of gene expression, neutrophil biology and immune-related diseases. Neutrophils are the most abundant subset of leukocyte and central to many diseases. Here by mapping expression quantitative trait loci (eQTL) in the context of epigenetic marks in neutrophils and monocytes of 101 healthy European adults, the authors provide a resource to advance understanding of immune-related trait-associated genetic variants.
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Keywords {🔍}

neutrophils, eqtl, gene, expression, article, google, scholar, cell, data, monocytes, genes, cas, variants, neutrophil, human, supplementary, disease, cells, nature, fig, genetic, regions, enrichment, variant, regulatory, types, analysis, rheumatoid, study, blood, padi, arthritis, effect, function, association, nod, involved, stat, individuals, ciseqtl, transcription, type, binding, shown, nat, genet, observed, variation, primary, fold,

Topics {✒️}

nature portfolio tertiary soluble-defence-mediator-filled granules e-mtab-2232 & e-mtab-3536 privacy policy manuscript editing trained professional nurse author information authors regional association plots advertising european research council medical research council fine-map genotype-phenotype associations45 social media 0/ reprints library cell-type-specific epigenetic data cell-type-specific dna methylation cell-type-specific cis-eqtl simple insertion/deletion genotypes late-stage phenotypic outcome step sequential gradient-density mass-spectrometry-based draft expression-qtls yields insight chemokine receptors ccr1 nature 509 nature 501 nature 464 nature 507 nature 506 nature 491 nature 511 nature cell type-dependent manner cell-type constraint include fine-map causal variants large-scale genomic data monocyte-derived dendritic cells16 monocyte-derived dendritic cells14 magnetic-activated cell sorting chromatin-immunoprecipitation sequencing data granulocyte–monocyte progenitor cells allele-specific stat3 binding cell-type-specific effects genome-wide significant correlate column-based isolation techniques 1 μg ml−1 muramyl dipeptide apparent cell-type constraint permissions connect trans-acting variants neutrophil development

Questions {❓}

  • Isolation of granulocytes: which transcriptome do we analyse—neutrophils or eosinophils?

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      headline:Genomic modulators of gene expression in human neutrophils
      description:Neutrophils form the most abundant leukocyte subset and are central to many disease processes. Technical challenges in transcriptomic profiling have prohibited genomic approaches to date. Here we map expression quantitative trait loci (eQTL) in peripheral blood CD16+ neutrophils from 101 healthy European adults. We identify cis-eQTL for 3281 neutrophil-expressed genes including many implicated in neutrophil function, with 450 of these not previously observed in myeloid or lymphoid cells. Paired comparison with monocyte eQTL demonstrates nuanced conditioning of genetic regulation of gene expression by cellular context, which relates to cell-type-specific DNA methylation and histone modifications. Neutrophil eQTL are markedly enriched for trait-associated variants particularly autoimmune, allergy and infectious disease. We further demonstrate how eQTL in PADI4 and NOD2 delineate risk variant function in rheumatoid arthritis, leprosy and Crohn’s disease. Taken together, these data help advance understanding of the genetics of gene expression, neutrophil biology and immune-related diseases. Neutrophils are the most abundant subset of leukocyte and central to many diseases. Here by mapping expression quantitative trait loci (eQTL) in the context of epigenetic marks in neutrophils and monocytes of 101 healthy European adults, the authors provide a resource to advance understanding of immune-related trait-associated genetic variants.
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      name:Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
      name:Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
      name:Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
      name:Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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