title: Bioinformatics Analysis of Chicken miRNAs Associated with Monocyte to Macrophage Differentiation and Subsequent IFNγ Stimulated Activation.
abstract: The goal of this project was to characterize the molecular and cellular roles of various gene targets regulated by miRNAs identified in differentiating and stimulating avian macrophages. Once a monocyte arrives to a site of infection, local signals induce a redistribution of resources into a macrophage phenotype. This may involve upregulating pathogen pattern recognizing receptors and increasing the efficiency of lysosomal biogenesis, while simultaneously recycling components involved in circulatory migration and leukocyte extravasation. a monocyte tooled with chemokine surface receptors and an internal cytoskeletal structure geared towards mobility may efficiently sense, react, and migrate toward a site of infection.
  
  
  
  Peripheral blood derived monocytes were purified and cultured from young chickens. RNA sequencing was performed on both peripheral blood monocytes during differentiation into macrophages and on mature macrophages following stimulation with interferon gamma. A set of microRNAs were identified and investigated using bioinformatics methods to ascertain their potential role in avian macrophage biology.
  
  
  
  Among a number of miRNAs that are found to be expressed in avian macrophages, we focused on eight specific miRNAs (miR-1618, miR-1586, miR-1633, miR-1627, miR-1646, miR-1649, miR-1610, miR-1647) associated with macrophage differentiation and activation. Expression profiles of microRNAs were characterized during differentiation and activation. Candidate miRNA targets were implicated in processes including Wnt signaling, ubiquitination, PPAR mediated macrophage function, vesicle mediated cytokine trafficking, and WD40 domain protein functions.
  
  
  
  A global theme for macrophage function that may be modulated by microRNAs is the comprehensive redistribution of the cell's protein repertoire. This redistribution involves two processes: 1) the degradation and recycling of unneeded cytoplasmic and membrane components and 2) the mobilization of newly synthesized cellular components via vesicular trafficking. Generally, it appears that macrophages need to closely regulate gene expression for differentiation to be able to activate successfully in response to a pathogen. This is a process in which miRNAs participate by affecting several pathways critical for both, differentiation and activation.
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.|College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, United States.
authors.forename: Kristopher J L
authors.initials: KJL
authors.lastname: Irizarry
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.
authors.forename: Adam
authors.initials: A
authors.lastname: Chan
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.
authors.forename: Derek
authors.initials: D
authors.lastname: Kettle
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.
authors.forename: Steven
authors.initials: S
authors.lastname: Kezian
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.
authors.forename: Dominic
authors.initials: D
authors.lastname: Ma
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.
authors.forename: Louis
authors.initials: L
authors.lastname: Palacios
authors.affiliation: The Applied Genomic Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, CA 91766, United States.
authors.forename: Qingshun Q
authors.initials: QQ
authors.lastname: Li
authors.affiliation: Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE 19716, United States.
authors.forename: Calvin L
authors.initials: CL
authors.lastname: Keeler
authors.affiliation: College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, United States.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Drechsler
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D002478:Cells, Cultured; D002645:Chickens; D019295:Computational Biology / Q000379:methods; D016207:Cytokines / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects; D007371:Interferon-gamma / Q000276:immunology / Q000494:pharmacology; D008262:Macrophage Activation / Q000187:drug effects / Q000235:genetics* / Q000276:immunology; D008264:Macrophages / Q000166:cytology* / Q000276:immunology / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics*; D009000:Monocytes / Q000166:cytology* / Q000276:immunology / Q000378:metabolism*; D005810:Multigene Family; D047492:Peroxisome Proliferator-Activated Receptors / Q000378:metabolism; D034622:RNA Interference; D022161:Transport Vesicles / Q000378:metabolism; D025801:Ubiquitin / Q000378:metabolism; D000071678:WD40 Repeats; D060449:Wnt Signaling Pathway / Q000187:drug effects
chemical_list: D016207:Cytokines; D035683:MicroRNAs; D047492:Peroxisome Proliferator-Activated Receptors; D025801:Ubiquitin; D007371:Interferon-gamma
keywords: Activation; avian; bioinformatics; differentiation; genomics; macrophage; miRNA; miRNA target; monocyte