in silico functional networks identified in fish nucleated red blood cells by means of transcriptomic and proteomic profiling

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ID: 181020
2018
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Abstract
Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activation.
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puente-marin2018genesin Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Sara Puente-Marin;Iván Nombela;Sergio Ciordia;María Carmen Mena;Verónica Chico;Julio Coll;María del Mar Ortega-Villaizan
Journal thermal science and engineering progress
Year 2018
DOI
10.3390/genes9040202
URL
http://www.mdpi.com/2073-4425/9/4/202
Keywords
transcriptome proteome rna-seq de novo assembly functional network rainbow trout red blood cells

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