Please use this identifier to cite or link to this item: http://dspace.umh.es/handle/11000/7002

In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling


Thumbnail

View/Open:
 10-Puente-Marin et al_2018_Genes.pdf
9,39 MB
Adobe PDF
Title:
In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling
Authors:
Puente Marín, Sara
Nombela Díaz, Iván
Ciordia, Sergio
Mena, María Carmen
Chico, Verónica
Coll, Julio
Ortega-Villaizan, María del Mar
Issue Date:
2021-01-25
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
Keywords/Subjects:
rainbow trout
red blood cells
RNA-seq
de novo assembly
transcriptome
peptide fractionation
LC ESI-MSMS
proteome
functional network
immune response
Type of document:
application/pdf
Access rights:
info:eu-repo/semantics/openAccess
Appears in Collections:
Instituto de Biología Molecular y Celular



This item is licensed under a Creative Commons License Creative Commons