miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection
Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host mi...
Published in: | Frontiers in Immunology |
---|---|
Main Authors: | , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Frontiers Media
2020
|
Subjects: | |
Online Access: | https://hdl.handle.net/10037/19391 https://doi.org/10.3389/fimmu.2020.02113 |
id |
ftunivtroemsoe:oai:munin.uit.no:10037/19391 |
---|---|
record_format |
openpolar |
spelling |
ftunivtroemsoe:oai:munin.uit.no:10037/19391 2023-05-15T15:33:07+02:00 miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection Woldemariam, Nardos Tesfaye Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn Houston, Ross D. Robledo, Diego Bron, James E. Andreassen, Rune 2020-09-11 https://hdl.handle.net/10037/19391 https://doi.org/10.3389/fimmu.2020.02113 eng eng Frontiers Media Frontiers in Immunology Norges forskningsråd: 254849 info:eu-repo/grantAgreement/RCN/HAVBRUK2/254849/Norway/miRNAs and their role in virus disease and immune response in Atlantic salmon// Woldemariam NT, Agafonov O, Sindre H, Høyheim B, Houston RD, Robledo D, Bron JE, Andreassen R. miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection. Frontiers in Immunology. 2020;11:2113 FRIDAID 1830183 https://doi.org/10.3389/fimmu.2020.02113 1664-3224 https://hdl.handle.net/10037/19391 openAccess Copyright 2020 The Author(s) VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 Journal article Tidsskriftartikkel Peer reviewed publishedVersion 2020 ftunivtroemsoe https://doi.org/10.3389/fimmu.2020.02113 2021-06-25T17:57:41Z Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or homozygous susceptible (SS) for the IPN-QTL. Small RNA-sequenced control samples were compared to samples collected at 1, 7, and 20 days post challenge (dpc). This revealed 72 differentially expressed miRNAs (DE miRNAs). Viral load (VL) was lower in RR vs. SS individuals at 7 and 20 dpc. However, analysis of miRNA expression changes revealed no differences between RR vs. SS individuals in controls, at 1 or 7 dpc, while 38 “high viral load responding” miRNAs (HVL-DE miRNAs) were identified at 20 dpc. Most of the HVL-DE miRNAs showed changes that were more pronounced in the high VL SS group than in the low VL RR group when compared to the controls. The absence of differences between QTL groups in controls, 1 and 7 dpc indicates that the QTL genotype does not affect miRNA expression in healthy fish or their first response to viral infections. The miRNA differences at 20 dpc were associated with the QTL genotype and could, possibly, contribute to differences in resistance/susceptibility at the later stage of infection. In silico target gene predictions revealed that 180 immune genes were putative targets, and enrichment analysis indicated that the miRNAs may regulate several major immune system pathways. Among the targets of HVL-DE miRNAs were IRF3, STAT4, NFKB2, MYD88, and IKKA. Interestingly, TNF-alpha paralogs were targeted by different DE miRNAs. Most DE miRNAs were from conserved miRNA families that respond to viral infections in teleost (e.g., miR-21, miR-146, miR-181, miR-192, miR-221, miR-462, miR-731, and miR-8159), while eight were species specific. The miRNAs showed dynamic temporal changes implying they would affect their target genes differently throughout disease progression. This shows that miRNAs are sensitive to VL and disease progression, and may act as fine-tuners of both immediate immune response activation and the later inflammatory processes. Article in Journal/Newspaper Atlantic salmon University of Tromsø: Munin Open Research Archive Ikka ENVELOPE(-48.100,-48.100,61.150,61.150) Frontiers in Immunology 11 |
institution |
Open Polar |
collection |
University of Tromsø: Munin Open Research Archive |
op_collection_id |
ftunivtroemsoe |
language |
English |
topic |
VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 |
spellingShingle |
VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 Woldemariam, Nardos Tesfaye Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn Houston, Ross D. Robledo, Diego Bron, James E. Andreassen, Rune miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
topic_facet |
VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 |
description |
Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or homozygous susceptible (SS) for the IPN-QTL. Small RNA-sequenced control samples were compared to samples collected at 1, 7, and 20 days post challenge (dpc). This revealed 72 differentially expressed miRNAs (DE miRNAs). Viral load (VL) was lower in RR vs. SS individuals at 7 and 20 dpc. However, analysis of miRNA expression changes revealed no differences between RR vs. SS individuals in controls, at 1 or 7 dpc, while 38 “high viral load responding” miRNAs (HVL-DE miRNAs) were identified at 20 dpc. Most of the HVL-DE miRNAs showed changes that were more pronounced in the high VL SS group than in the low VL RR group when compared to the controls. The absence of differences between QTL groups in controls, 1 and 7 dpc indicates that the QTL genotype does not affect miRNA expression in healthy fish or their first response to viral infections. The miRNA differences at 20 dpc were associated with the QTL genotype and could, possibly, contribute to differences in resistance/susceptibility at the later stage of infection. In silico target gene predictions revealed that 180 immune genes were putative targets, and enrichment analysis indicated that the miRNAs may regulate several major immune system pathways. Among the targets of HVL-DE miRNAs were IRF3, STAT4, NFKB2, MYD88, and IKKA. Interestingly, TNF-alpha paralogs were targeted by different DE miRNAs. Most DE miRNAs were from conserved miRNA families that respond to viral infections in teleost (e.g., miR-21, miR-146, miR-181, miR-192, miR-221, miR-462, miR-731, and miR-8159), while eight were species specific. The miRNAs showed dynamic temporal changes implying they would affect their target genes differently throughout disease progression. This shows that miRNAs are sensitive to VL and disease progression, and may act as fine-tuners of both immediate immune response activation and the later inflammatory processes. |
format |
Article in Journal/Newspaper |
author |
Woldemariam, Nardos Tesfaye Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn Houston, Ross D. Robledo, Diego Bron, James E. Andreassen, Rune |
author_facet |
Woldemariam, Nardos Tesfaye Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn Houston, Ross D. Robledo, Diego Bron, James E. Andreassen, Rune |
author_sort |
Woldemariam, Nardos Tesfaye |
title |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_short |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_full |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_fullStr |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_full_unstemmed |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_sort |
mirnas predicted to regulate host anti-viral gene pathways in ipnv-challenged atlantic salmon fry are affected by viral load, and associated with the major ipn resistance qtl genotypes in late infection |
publisher |
Frontiers Media |
publishDate |
2020 |
url |
https://hdl.handle.net/10037/19391 https://doi.org/10.3389/fimmu.2020.02113 |
long_lat |
ENVELOPE(-48.100,-48.100,61.150,61.150) |
geographic |
Ikka |
geographic_facet |
Ikka |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
Frontiers in Immunology Norges forskningsråd: 254849 info:eu-repo/grantAgreement/RCN/HAVBRUK2/254849/Norway/miRNAs and their role in virus disease and immune response in Atlantic salmon// Woldemariam NT, Agafonov O, Sindre H, Høyheim B, Houston RD, Robledo D, Bron JE, Andreassen R. miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection. Frontiers in Immunology. 2020;11:2113 FRIDAID 1830183 https://doi.org/10.3389/fimmu.2020.02113 1664-3224 https://hdl.handle.net/10037/19391 |
op_rights |
openAccess Copyright 2020 The Author(s) |
op_doi |
https://doi.org/10.3389/fimmu.2020.02113 |
container_title |
Frontiers in Immunology |
container_volume |
11 |
_version_ |
1766363582105124864 |