Impact of selenium supplementation on fish antiviral responses: a whole transcriptomic analysis in rainbow trout (Oncorhynchus mykiss) fed supranutritional levels of Sel-Plex®

Pacitti, D.; Lawan, M. M.; Feldmann, J.; Sweetman, J.; Wang, T.; Martin, S. A. M.; Secombes, C. J.

doi:10.1186/s12864-016-2418-7

Table 5 List of selected transcripts significantly modulated in the HK of fish injected with poly(I:C) and dependant on prior feeding regime. The selection was based on the results of the GO analysis (Fig. 7)

From: Impact of selenium supplementation on fish antiviral responses: a whole transcriptomic analysis in rainbow trout (Oncorhynchus mykiss) fed supranutritional levels of Sel-Plex®

Trait	SeC	SeP	CP	SeP⁵	Acc. Number⁶	Identity⁷	HGNC	Gene Function⁹
Identifier¹	HK²	HK³	HK⁴	CP	Acc. Number⁶	Identity⁷	symbol⁸	Gene Function⁹
CUST_201_	−1.2	19.2	5.9	2.7	FM864346.1	Interferon gamma2	IFNG	Positive regulation of interleukin-12 production
PI429021944	−1.2	19.2	5.9	2.7	FM864346.1	Interferon gamma2	IFNG	Positive regulation of interleukin-12 production
IMM 478	−1.1	15.1	8.0	1.7	NM_001124446	Glycogen synthase kinase binding protein	GBP1	Response to interferon-gamma
IMM 851	1.0	13.5	6.8	2.0	AF401631	TNF decoy receptor	TNFRSF6B	Regulation of cellular response to stress
TC151161	−1.1	9.4	4.9	1.7	BT072291	Salmo salar clone ssal-rgf-519–364,	MAVS	Positive regulation of chemokine production
TC151161	−1.1	9.4	4.9	1.7	BT072291	unknown large open reading frame	MAVS	Response to exogenous dsRNA
TC160031	−1.3	7.6	2.8	2.1	BT058838	Metalloproteinase inhibitor 3	TIMP3	Response to organic substance
TC132324	−1.1	5.6	3.3	1.5	NM_001124412	Toll-like receptor 22	TLR3	Positive regulation of interleukin-12 production
TC132324	−1.1	5.6	3.3	1.5	NM_001124412	Toll-like receptor 22	TLR3	Positive regulation of chemokine production
TC144460	−1.2	5.5	2.7	1.7	BT074153	Sorcin	SRI	Regulation of transcription factor import into nucleus
TC144460	−1.2	5.5	2.7	1.7	BT074153	Sorcin	SRI	Cellular transition metal ion homeostasis
TC138806	−2.5	5.4	2.0	1.1	EU481821	Salmo salar physical map contig 483 genomic sequence	NR2F2	Positive regulation of macromolecule metabolic process
TC138806	−2.5	5.4	2.0	1.1	EU481821	Salmo salar physical map contig 483 genomic sequence	NR2F2	Regulation of DNA binding
TC142451	−1.5	4.5	1.8	1.6	BT048169	Lipopolysaccharide-induced tumor necrosis factor-alpha factor	LITAF	Regulation of transcription factor import into nucleus
TC142451	−1.5	4.5	1.8	1.6	BT048169		LITAF	Regulation of NF-kappaB import into nucleus
TC144371	−1.3	4.1	2.4	1.3	NM_001124746	Transducer/activator of transcription	STAT1	Response to exogenous dsRNA
TC144371	−1.3	4.1	2.4	1.3	NM_001124746	Transducer/activator of transcription	STAT1	Response to interferon-gamma
TC155255	−1.4	3.9	1.3	2.2	BT072728	B-cell lymphoma 3-encoded protein	BCL3	Regulation of transcription factor import into nucleus
TC155255	−1.4	3.9	1.3	2.2	BT072728	B-cell lymphoma 3-encoded protein	BCL3	Regulation of NF-kappaB import into nucleus
TC155255	−1.4	3.9	1.3	2.2	BT072728	B-cell lymphoma 3-encoded protein	BCL3	Regulation of transcription factor import into nucleus
TC155255	−1.4	3.9	1.3	2.2	BT072728	B-cell lymphoma 3-encoded protein	BCL3	Regulation of NF-kappaB import into nucleus
TC148036	−1.2	3.4	2.5	1.2	NM_001165385	Macrosialin	SSC5D	Response to molecule of bacterial origin
TC164429	−1.2	2.4	1.4	1.5	FR751081	Caspase 3	CASP3	Neurotrophin TRK receptor signaling pathway
CUST_118_	−1.1	2.4	1.5	1.5	NM_001124438	Interferon regulatory factor 2	IRF2	Response to interferon-gamma
_PI420312184	−1.1	2.4	1.5	1.5	NM_001124438	Interferon regulatory factor 2	IRF2	Response to interferon-gamma
TC162287	−1.2	2.4	1.7	1.2	not-annotated	not-annotated	RIPK2	Positive regulation of interleukin-12 production
TC162287	−1.2	2.4	1.7	1.2	not-annotated	not-annotated	RIPK2	Positive regulation of chemokine production
TC161320	−1.2	2.2	1.5	1.2	BT057463	Proteasome subunit alpha type-6 putative	PSMA6	Regulation of G1/S transition of mitotic cell cycle
CUST_75	−1.0	2.1	1.6	1.3	GQ169787.1	TNF receptor superfamily member 5A	CD40	Positive regulation of interleukin-12 production
_PI429021944	−1.0	2.1	1.6	1.3	GQ169787.1	TNF receptor superfamily member 5A	CD40	Positive regulation of interleukin-12 production
TC137335	−1.5	−1.2	−2.2	1.2	not-annotated	not-annotated	ECT2	Maintenance of protein location in cell
TC137335	−1.5	−1.2	−2.2	1.2	not-annotated	not-annotated	ECT2	Positive regulation of I-kappaB kinase/NF-kappaB signaling
TC141297	−1.6	−1.2	−2.4	1.2	BT073959	Proteasome subunit beta type 1-A	PSMB1	Regulation of G1/S transition of mitotic cell cycle
TC141297	−1.6	−1.2	−2.4	1.2	BT073959	Proteasome subunit beta type 1-A	PSMB1	Antigen processing and presentation of peptide antigen
TC144499	−1.2	−1.4	−2.2	1.3	NM_001165391	Cyclin D1	CCND1	Regulation of G1/S transition of mitotic cell cycle
TC144499	−1.2	−1.4	−2.2	1.3	NM_001165391	Cyclin D1	CCND1	response to nutrient
TC134399	−1.3	−1.5	−2.1	1.1	BT072801	Mitogen-activated protein kinase 7-interacting protein homolog 2	TAB2	Toll-like receptor signaling pathway
TC134399	−1.3	−1.5	−2.1	1.1	BT072801		TAB2	MyD88-dependent toll-like receptor signaling pathway
TC145638	−1.4	−1.5	−2.4	1.1	BT027690	CGX87-B08	TTK	Positive regulation of signal transduction
TC145638	−1.4	−1.5	−2.4	1.1	BT027690	CGX87-B08	TTK	Positive regulation of cell proliferation
TC142766	−1.4	−1.5	−2.4	1.1	FP236858	Zebrafish DNA sequence from clone CH73-339E3	TJP1	Response to molecule of bacterial origin
TC142766	−1.4	−1.5	−2.4	1.1	FP236858	Zebrafish DNA sequence from clone CH73-339E3	TJP1	Response to lipopolysaccharide
TC168733	−1.5	−1.5	−2.5	1.1	BT059118	Choline transporter-like protein 2	SLC44A2	Regulation of I-kappaB kinase/NF-kappaB signaling
TC168733	−1.5	−1.5	−2.5	1.1	BT059118	Choline transporter-like protein 2	SLC44A2	Positive regulation of I-kappaB kinase/NF-kappaB signaling
TC159957	−1.7	−1.7	−3.1	1.1	BT072217	Fibronectin	FN1	Defence response
TC159957	−1.7	−1.7	−3.1	1.1	BT072217	Fibronectin	FN1	Response to wounding
TC132905	3.0	1.5	3.4	1.3	NM_001124288	Hypoxia-inducible factor 1 alpha subunit	HIF1A	Regulation of chemokine production
TC132905	3.0	1.5	3.4	1.3	NM_001124288	Hypoxia-inducible factor 1 alpha subunit	HIF1A	positive regulation of chemokine production
TC156038	1.5	1.5	2.5	−1.2	BT044876	Ras-related C3 botulinum toxin substrate 1 precursor	RAC1	Positive regulation of protein polymerization
TC169458	1.9	1.8	2.5	1.4	BT074060	NF-kappa-B inhibitor alpha	NFKBIA	Regulation of NF-kappaB import into nucleus
TC169458	1.9	1.8	2.5	1.4	BT074060	NF-kappa-B inhibitor alpha	NFKBIA	Response to exogenous dsRNA
TC135280	1.5	1.6	2.4	1.0	BT044949	Tyrosine-protein kinase HCK	HCK	Positive regulation of protein polymerization
TC135280	1.5	1.6	2.4	1.0	BT044949	Tyrosine-protein kinase HCK	HCK	Regulation of actin filament polymerization
TC151093	1.2	1.5	2.3	−1.2	BT044981	Histone deacetylase 3	HDAC3	Neurotrophin TRK receptor signaling pathway
TC137681	1.7	1.3	2.3	−1.1	BT045910	Mitogen-activated protein kinase-activated	MAPKA	Regulation of tumor necrosis factor production
TC137681	1.7	1.3	2.3	−1.1	BT045910	Mitogen-activated protein kinase-activated	MAPKA	Regulation of interleukin-6 production
TC148701	1.7	−1.0	2.1	−1.2	NM_001171899	Red cell arrestin 2	ARRB2	Regulation of interleukin-12 production
TC148701	1.7	−1.0	2.1	−1.2	NM_001171899	Red cell arrestin 2	ARRB2	Regulation of tumor necrosis factor production
TC135368	1.4	1.0	2.1	−1.4	NM_001172498	CCAAT/enhancer binding protein beta2	CEBPB	Regulation of interleukin-6 production
IMM 136	1.8	1.1	2.0	−1.0	AJ620466	Complement receptor-like protein 1 splice variant 2	CD55	Response to molecule of bacterial origin
								Response to lipopolysaccharide
IMM 505	1.6	1.1	2.0	−1.1	DQ399551	Dual specificity phosphatase 6 (dusp6)	DUSP6	Toll-like receptor signaling pathway
IMM 505	1.6	1.1	2.0	−1.1	DQ399551	Dual specificity phosphatase 6 (dusp6)	DUSP6	MyD88-dependent toll-like receptor signaling pathway
TC167434	1.8	1.1	2.0	1.0	NM_001140341	Sequestosome-1	SQSTM1	regulation of I-kappaB kinase/NF-kappaB signaling
TC167434	1.8	1.1	2.0	1.0	NM_001140341	Sequestosome-1	SQSTM1	neurotrophin TRK receptor signaling pathway
TC132407	1.5	1.2	2.0	−1.1	NM_001124559	cAMP-dependent transcription factor	ATF1	toll-like receptor signaling pathway
TC132407	1.5	1.2	2.0	−1.1	NM_001124559	cAMP-dependent transcription factor	ATF1	MyD88-dependent toll-like receptor signaling pathway
IMM 223	1.5	−2.0	−1.2	−1.1	BT047880	Heme oxygenase putative mRNA	HMOX1	regulation of chemokine production
IMM 223	1.5	−2.0	−1.2	−1.1	BT047880	Heme oxygenase putative mRNA	HMOX1	cellular transition metal ion homeostasis

Genes with corresponding microarray feature code¹ found involved in a biological process significantly altered by the experimental diet in the HK were selected. If the transcripts were significantly modulated also in fish fed the experimental diet enriched with 4 mg Se Kg⁻¹ and injected with poly(I:C)³, or in the same tissue of fish fed the control diet and injected with poly(I:C)⁴, these values are given. Also the fold change of the expression of the same targets between these last two groups is reported, as given from Genespring software⁵. All the transcripts shown were significantly modulated at p < 0.05 following the Benjamini–Hochberg correction and had a fold change ≥2. Accession numbers of the cDNA sequences⁶, their identity⁷ and the corresponding human orthologue⁸ determined by BLASTx within the Ensemble database are reported. For each gene the function assigned by ClueGO software is also indicated. SeC represents the groups comparison addressed to analyse the effects of the 4 mg Se Kg⁻¹ diet. CP and SeP instead represent the comparisons addressed to analyse the effect of poly(I:C) stimulation on fish fed either a control diet or the experimental diet respectively

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ISSN: 1471-2164

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