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Puente-Marin S, Nombela I, Ciordia S, et al. In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling. Genes (Basel). 2018;9(4)doi: 10.3390/genes9040202.
Puente-Marin, S., Nombela, I., Ciordia, S., Mena, M. C., Chico, V., Coll, J., & Ortega-Villaizan, M. D. M. (2018). In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling. Genes, 9(4), . https://doi.org/10.3390/genes9040202
Puente-Marin, Sara, et al. "In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling." Genes vol. 9,4 (2018). doi: https://doi.org/10.3390/genes9040202
Puente-Marin S, Nombela I, Ciordia S, Mena MC, Chico V, Coll J, Ortega-Villaizan MDM. In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling. Genes (Basel). 2018 Apr 09;9(4). doi: 10.3390/genes9040202. PMID: 29642539; PMCID: PMC5924544.
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Genes (Basel). 2018 Apr 09;9(4). doi: 10.3390/genes9040202.

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

Genes

Sara Puente-Marin, Iván Nombela, Sergio Ciordia, María Carmen Mena, Verónica Chico, Julio Coll, María Del Mar Ortega-Villaizan

Affiliations

  1. Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain. [email protected].
  2. Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain. [email protected].
  3. Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain. [email protected].
  4. Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain. [email protected].
  5. Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain. [email protected].
  6. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain. [email protected].
  7. Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain. [email protected].

PMID: 29642539 PMCID: PMC5924544 DOI: 10.3390/genes9040202

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: LC ESI-MSMS; RNA-seq; de novo assembly; functional network; immune response; peptide fractionation; proteome; rainbow trout; red blood cells; transcriptome

Conflict of interest statement

The authors declare no conflict of interest.

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