Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages

Eslamloo, Khalil; Xue, Xi; Booman, Marije; Smith, Nicole C.; Rise, Matthew L.

doi:10.1016/j.dci.2016.05.021

Cited by 33 publications

(46 citation statements)

References 96 publications

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“…After overnight (16 h) cell culture at 10˚C, the culture dishes were washed 3 times using L-15+ and the non-adherent cells were discarded. Since the majority of the adherent cells in this stage were identified as macrophage-like cells (Eslamloo et al, 2016), these cells are henceforth referred to as macrophages. Atlantic cod macrophages isolated and cultured by this method were shown to have very high viability during cell culture (Eslamloo et al, 2016).…”

Section: Macrophage Isolationmentioning

confidence: 99%

“…The pIC (Sigma-Aldrich) was diluted in phosphate buffered saline (PBS) (Gibco) at 10 mg ml -1 and used as a stock solution. Starting 24 h after cell isolation, the macrophages were exposed to 50 µg ml -1 pIC or PBS (5 µl of pIC solution or PBS per ml of L-15+) at 10˚C (Eslamloo et al, 2016).…”

Section: Macrophage Stimulation and Sampling At 24 Hps For Sequencingmentioning

confidence: 99%

“…The samples were selected for miRNA sequencing of macrophages in both pIC and PBS groups at 24 and 72 HPS, based on the quality and quantity (ranging from 57-405 ng μl -1 ) of RNA as well as their immune response; the expression of isg15-1 and viperin (see Eslamloo et al 2016 for primer sequences and qPCR assay method) was assessed in all of the samples (data not shown).…”

Section: Deep Sequencing and Analysis Of Deep Sequencing Datamentioning

confidence: 99%

“…Fifty transcripts used for target gene prediction, as well as information on their function and regulation, are listed in Supplemental Table S2 [also see Table 2 in Eslamloo et al, (2016)]. The 3'UTRs of these transcripts [i.e.…”

Section: Target Gene Prediction For Pic-responsive Mirnasmentioning

confidence: 99%

“…Therefore, macrophage studies are of importance to broaden our knowledge of molecular pathways and regulatory mechanisms underlying the antiviral immune responses of fish. The pICresponsive transcripts (mRNAs) of Atlantic cod macrophages were profiled in a previously published study (Eslamloo et al, 2016). To have a better understanding of antiviral regulators in Atlantic cod, deep sequencing and real-time quantitative polymerase chain reaction (qPCR) were used in the present study to identify the pIC-responsive miRNAs in macrophages of this species.…”

Section: Introductionmentioning

confidence: 99%

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Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages

Eslamloo

Inkpen

Rise

et al. 2018

Molecular Immunology

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MicroRNAs (miRNAs) are known to play important immunoregulatory roles in teleosts, although miRNAs involved in the antiviral immune response of Atlantic cod (Gadus morhua) were previously uncharacterised. Using deep sequencing and qPCR, the present study was conducted to identify miRNAs responsive to the viral mimic, polyriboinosinic polyribocytidylic acid (pIC) in Atlantic cod macrophages. Macrophage samples isolated from Atlantic cod (n=3) and treated with pIC or phosphate buffered saline (PBS control) for 24 and 72h were used for miRNA profiling. Following deep sequencing, DESeq2 analyses identified four (miR-731-3p, miR-125b-3-3p, miR-150-3p and miR-462-3p) and two (miR-2188-3p and miR-462-3p) significantly differentially expressed miRNAs at 24 and 72h post-stimulation (HPS), respectively. Sequencing-identified miRNAs were subjected to qPCR validation using a larger number of biological replicates (n=6) exposed to pIC or PBS over time (i.e. 12, 24, 48 and 72 HPS). As in sequencing, miR-731-3p, miR-462-3p and miR-2188-3p showed significant up-regulation by pIC. The sequencing results were not qPCR-validated for miR-125b-3-3p and miR-150-3p as up- and down-regulated miRNAs at 24 HPS, respectively; however, qPCR results showed significant up-regulation in response to pIC stimulation at later time points (i.e. 48 and/or 72 HPS). We also used qPCR to assess the expression of other miRNAs that were previously shown as immune responsive in other vertebrates. qPCR results at 48 and/or 72 HPS revealed that miR-128-3-5p, miR-214-1-5p and miR-451-3p were induced by pIC, whereas miR-30b-3p and miR-199-1-3p expression were repressed in response to pIC. The present study identified ten pIC-stimulated miRNAs, suggesting them as important in antiviral immune responses of Atlantic cod macrophages. Some pIC-responsive miRNAs identified in this study were predicted to target putative immune-related genes of Atlantic cod (e.g. miR-30b-3p targeting herc4), although the regulatory functions of these miRNAs need to be validated by future studies.

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Section: Macrophage Isolationmentioning

confidence: 99%

Section: Macrophage Stimulation and Sampling At 24 Hps For Sequencingmentioning

confidence: 99%

Section: Deep Sequencing and Analysis Of Deep Sequencing Datamentioning

confidence: 99%

Section: Target Gene Prediction For Pic-responsive Mirnasmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages

Eslamloo

Inkpen

Rise

et al. 2018

Molecular Immunology

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Comprehensive transcriptomic analysis reveals insights into the gill response to hypoxia and Poly I:C in Qihe crucian carp Carassius auratus

Yun-feng

et al. 2022

Aquaculture Reports

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Dynamic immune response in the spleens of rainbow trout (Oncorhynchus mykiss) to infectious hematopoietic necrosis virus revealed by transcriptome and immune-related genes expression analysis

Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages

Cited by 33 publications

References 96 publications

Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages

Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages

Comprehensive transcriptomic analysis reveals insights into the gill response to hypoxia and Poly I:C in Qihe crucian carp Carassius auratus

Dynamic immune response in the spleens of rainbow trout (Oncorhynchus mykiss) to infectious hematopoietic necrosis virus revealed by transcriptome and immune-related genes expression analysis

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