Type I interferon related genes are common genes on the early stage after vaccination by meta-analysis of microarray data

Figures & data

Table 1. Characteristics of studies included in the meta-analysis

First author （year）[reference]	PubMed ID	Vaccine	Subject number	Platform	Total Probe
Nakaya HI et al. (2011)^2	21743478	Influenza	65/124	HGU133 plus 2	54675
Nakaya HI et al. (2011)^2	21743478	Influenza	65/124	HTHGU133 plus PM	54715
Vahey MT et al. (2010)^23	20078211	malaria	12/24	HGU133A 2.0	22277
Querec TD et al. (2009)^3	19029902	yellow fever	15/36	HGU133 plus 2	54675
Gaucher D et al. (2008)^4	19047440	yellow fever	15/29	Illumina HRef8v2.0	22185
Obermoser G et al. (2013)^22	23601689	pneumovax	9/23	Illumina HHT12v3.0	49576
Obermoser G et al. (2013)^22	23601689	influenza	29/66	Illumina HHT12v3.0	49576

Note: Subject number shows pre/post vaccination.

Figure 1. Data identification and acquisition.

Table 2. Differentially expressed up-regulated genes within 7d after vaccination using meta-analysis

Gene Classification	Gene Symbol	Gene Name	Fold Change
Type I IFN related genes	LY6E	lymphocyte antigen 6 complex, locus E	2.59
	MX1	interferon-induced GTP-binding protein Mx1	2.03
	IFI44L	interferon-induced protein 44-like	1.81
	IFI6	interferon, α-inducible protein 6	1.75
	OAS3	2'-5'-oligoadenylate synthetase 3	1.59
	IFITM3	interferon-induced transmembrane protein 3	1.56
Other genes	XAF1	x-linked inhibitor of apoptosis associated factor 1	1.60
	TNFRSF17	tumor necrosis factor receptor superfamily member	1.80
	RSAD2	radical S-adenosyl methionine domain containing 2	1.84
	OTOF	Otoferlin	1.57

Table 3. Differentially expressed down-regulated genes within 7d after vaccination using meta-analysis

Gene Classification	Gene Symbol	Gene Name	Fold Change
Metabolic enzyme related genes	MGAM	maltase-glucoamylase encoding gene	−1.70
	ZNF331	zinc finger protein 331	−1.57
	PTGS2	prostaglandin G/H synthase 2 precursor	−1.54
	MME	melanin metabolic enzyme encoding gene	−1.52
Inflammation related genes	IL1R2	interleukin 1 receptor,type II	−1.63
	IL8	interleukin 8	−1.53
Chemokines	CXCL1	chemokine(C-X-C motif)ligand 1	−1.51
Cell cycle related genes	GOS2	G0/G1 switch protein 2	−2.15
Receptor associated genes	NR4A2	orphan nuclear receptor NURR1	−1.69
	NR4A3	nuclear hormone receptor NOR-1	−1.64

Table 4. The pathway distribution of DEGs within 7d after vaccination

Term	Count	P Value
Upregulated pathways:
GO:0006955∼immune response	6	0.000036
Downregulated pathways:
GO:0007610∼behavior	5	0.000156
GO:0007626∼locomotory behavior	3	0.013395
GO:0008285∼negative regulation of cell proliferation	3	0.022582
GO:0009719∼response to endogenous stimulus	3	0.028001
GO:0006928∼cell motion	3	0.037607
GO:0010243∼response to organic nitrogen	2	0.041153

Figure 2. Number of DEGs with upregulation on days 3 and 7 after vaccination. Note：There were 36 upregulated genes in 3 days, including 32 specific genes and there were 20 up-regulated genes in 7 days, including 16 specific genes. Four genes were commonly upregulated between days 3 and 7 after vaccination, among them 2 were type I IFN related genes.

Figure 3. The meta-analysis and EV71 vaccinated group validation results of 6 type I IFN related genes. Note: PBMC for baseline and day 3 after the vaccination from 8 EV71 vaccinees were assayed by RT-PCR. FC of each gene was the arithmetic average of the expression of 3 day post-vaccination/ 0 day pre-vaccination. FC greater than 1.5 is shown in red in the figure.

Nakaya HI, Wrammert J, Lee EK, Racioppi L, Marie-Kunze S, Haining WN, Means AR, Kasturi SP, Khan N, Li GM, et al. Systems biology of vaccination for seasonal influenza in humans. Nat Immunol 2011; 12:786-95; PMID:21743478; http://dx.doi.org/10.1038/ni.2067

 PubMed Web of Science ®Google Scholar

Vahey MT, Wang Z, Kester KE, Cummings J, Heppner DG, Jr., Nau ME, Ofori-Anyinam O, Cohen J, Coche T, Ballou WR, et al. Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine. J Infect Dis 2010; 201:580-9; PMID:20078211; http://dx.doi.org/10.1086/650310

 PubMed Web of Science ®Google Scholar

Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B, et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 2009; 10:116-25; PMID:19029902; http://dx.doi.org/10.1038/ni.1688

 PubMed Web of Science ®Google Scholar

Gaucher D, Therrien R, Kettaf N, Angermann BR, Boucher G, Filali-Mouhim A, Moser JM, Mehta RS, Drake DR, 3rd, Castro E, et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 2008; 205:3119-131; PMID:19047440; http://dx.doi.org/10.1084/jem.20082292

 PubMed Web of Science ®Google Scholar

Obermoser G, Presnell S, Domico K, Xu H, Wang Y, Anguiano E, Thompson-Snipes L, Ranganathan R, Zeitner B, Bjork A, et al. Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines. Immunity 2013; 38:831-44; PMID:23601689; http://dx.doi.org/10.1016/j.immuni.2012.12.008

 PubMed Web of Science ®Google Scholar