Integrated Transcriptomic and Proteomic Analysis of Red Blood Cells from Rainbow Trout Challenged with VHSV Point Towards Novel Immunomodulant Targets
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Rainbow Trout Challenge with VHSV
2.3. Blood Extraction and Staining
2.4. Cell Sorting
2.5. Transcriptome Analysis
2.6. Proteome Analysis
2.7. Pathway Enrichment Analysis
2.8. RNA Isolation and cDNA Synthesis
2.9. Quantitative PCR
2.10. Antibodies
2.11. Western Blotting
2.12. Ethics Statement
2.13. Software and Statistics
3. Results
3.1. Transcriptomic Analysis of PB-RBCs and HK-RBCs from VHSV-Challenged Rainbow Trout Revealed the Upregulation of Genes Related to the Complement System and the Interferon Pathway, Respectively
3.2. Upregulated DEGs from Overrepresented Pathways Were Analyzed by RT-qPCR
3.3. Proteomic Analysis of PB-RBCs from VHSV-Challenged Rainbow Trout Showed Upregulation of Proteins Involved in the Immune Response
3.4. Antiviral Effectors Were Upregulated in VHSV-Challenged Rainbow Trout RBCs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene | Forward | Reverse | Probe | Reference or Accession Number |
---|---|---|---|---|
c4bpa | TGAGAATGGCGTTAGGATTGAA | GTTGCACTTATACGTCACAAAAGACTT | - | XM_021564396.1 |
cd55 | CGCTCAAATTAACCTGCAAAAA | GTGCCTTCCTTAAACTCATATGTCAA | - | XM_021609679.1 |
cd59 | CGGAGCCACATCCATTGG | TTACTGCATACACCACCACATCACT | - | NM_001124497.1 |
dhx58 | GCTCTCCACTTGCGTCAGTACA | GACCCTAAAGGCATCCACCAT | - | XM_021624832.1 |
ef1a | ACCCTCCTCTTGGTCGTTTC | TGATGACACCAACAGCAACA | GCTGTGCGTGACATGAGGCA | [29] |
gbp1 | TGGTTCCGCTCTAGGTTTCTTC | AGCCTAAAACCCAAAAGAGCAA | - | XM_021579826.1 |
ifi35 | CTGGTGCCCTGTCAAGTAGAGA | TTCTTGGGCAGGTTGGAAAC | - | XM_021558400.1 |
ifih1 | GAGCCCGTCCAAAGTGAAGTT | AGTGAGGTGTTTTCTCTTTGAATGAA | - | NM_001195179.1 |
ifit5 | CCCTCAATGACTCTGACAAGCA | CCCTGCCCTCATCTTTCTTCT | CCAGCTTCGGCCTGTTTCTGTTCCA | [7] |
irak1 | CAGACAGACCAACGCTCACAA | GCAGATCGCACCCACATG | - | XM_021567162.1 |
mavs | GAGGGCAGAGTGGAACAAACA | TCAGAGCTGGTAGAAGGAATTGGT | - | NM_001195181.1 |
mx1-3 | TGAAGCCCAGGATGAAATGG | TGGCAGGTCGATGAGTGTGA | ACCTCATCAGCCTAGAGATTGGCTCCCC | [30] |
nlrc5 | CTGCTATGTGCCGCCAATT | CCAGTGTAGGCCAAGGATCAC | - | XM_021570046.1 |
nlrx1 | CCTGCTTTTTACCTTCCTATTGCT | CACCTCCCCTCCAAAGTTGA | - | XM_021581927.1 |
nod2 | GAGAGACAGGAGTTGACGATTCTG | TTGTCTGACTTCTTCGAGATCATCA | - | NM_001201555.1 |
NVHSV | GACTCAACGGGACAGGAATGA | GGGCAATGCCCAAGTTGTT | TGGGTTGTTCACCCAGGCCGC | [27] |
stat1 | GCCGAGAACATCCCTGAGAA | GCTTACTCGCCAACTCCATTG | - | XM_021596980.1 |
traf3 | GGGCTTCAGGGACCACTTC | ACCAGCTTGCAGGACTCACA | - | NM_001124615.1 |
Name | Symbol | Log2FC PB-RBCs | Log2FC HK-RBCs | References 1 |
---|---|---|---|---|
Cholesterol 25-hydroxylase | ch25h | - | 8.68 | [33] |
GTPase, very large interferon inducible pseudogene 1 | gvinp1 | 8.54 | - | [34] |
Interferon induced protein 35 | ifi35 | 8.38 | 5.12 | [35] |
Interferon induced protein with tetratricopeptide repeats 5 | ifit5 | 14.58 | 4.85 | [8,36] |
Interferon-induced transmembrane protein 3 | ifitm3 | 5.00 | - | [37,38] |
Interferon-induced GTP-binding protein Mx 1 | mx1 | 10.95 | 6.76 | [39] |
Radical SAM domain-containing protein 2 | rsad2 | 11.61 | 5.47 | [40,41] |
SAM and HD domain-containing protein 1 | samhd1 | 7.74 | - | [42] |
Tripartite motif family 16 | trim16 | 8.80 | 3.95 | [43] |
Tripartite motif family 21 | trim21 | 6.65 | - | [44] |
Tripartite motif family 25 | trim25 | 9.76 | 7.90 | [45,46,47] |
Tripartite motif family 39 | trim39 | 7.01 | 8.46 | [48] |
Tripartite motif family 47 | trim47 | 3.75 | 6.15 | [49] |
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Nombela, I.; Lopez-Lorigados, M.; Salvador-Mira, M.E.; Puente-Marin, S.; Chico, V.; Ciordia, S.; Mena, M.C.; Mercado, L.; Coll, J.; Perez, L.; Ortega-Villaizan, M.d.M. Integrated Transcriptomic and Proteomic Analysis of Red Blood Cells from Rainbow Trout Challenged with VHSV Point Towards Novel Immunomodulant Targets. Vaccines 2019, 7, 63. https://doi.org/10.3390/vaccines7030063
Nombela I, Lopez-Lorigados M, Salvador-Mira ME, Puente-Marin S, Chico V, Ciordia S, Mena MC, Mercado L, Coll J, Perez L, Ortega-Villaizan MdM. Integrated Transcriptomic and Proteomic Analysis of Red Blood Cells from Rainbow Trout Challenged with VHSV Point Towards Novel Immunomodulant Targets. Vaccines. 2019; 7(3):63. https://doi.org/10.3390/vaccines7030063
Chicago/Turabian StyleNombela, Ivan, Marina Lopez-Lorigados, Maria Elizabeth Salvador-Mira, Sara Puente-Marin, Veronica Chico, Sergio Ciordia, Maria Carmen Mena, Luis Mercado, Julio Coll, Luis Perez, and Maria del Mar Ortega-Villaizan. 2019. "Integrated Transcriptomic and Proteomic Analysis of Red Blood Cells from Rainbow Trout Challenged with VHSV Point Towards Novel Immunomodulant Targets" Vaccines 7, no. 3: 63. https://doi.org/10.3390/vaccines7030063