Elsevier

Vaccine

Volume 28, Issue 16, 1 April 2010, Pages 2865-2876
Vaccine

A whole genome transcriptional analysis of the early immune response induced by live attenuated and inactivated influenza vaccines in young children

https://doi.org/10.1016/j.vaccine.2010.01.060Get rights and content

Abstract

The protective mechanisms of influenza vaccines in young children are not completely understood. A phase 2 clinical study was conducted in 85 children 12–35 months of age to describe and compare the immune responses to live attenuated influenza vaccine (LAIV) with trivalent inactivated influenza vaccine (TIV). To better understand the biology of vaccine effects, oligonucleotide microarrays were employed to measure the genome-wide changes in transcript profiles in whole blood at approximately 7 days after 1 dose of LAIV or TIV. Of the total 265 differentially expressed genes identified in this study, 6 clusters of genes were identified to be tightly coexpressed, many of which are likely modulated by cytokines including type 1 interferons (IFNs) and granulocyte–macrophage colony-stimulating factor. Additional functional analyses revealed that the type 1 IFN pathway and cell cycle regulation-related genes are enriched in the 6 coexpressed gene sets. Promoter characterization of these coexpressed genes also supported this conclusion. Moreover, it is suggested that the IFN-stimulated response element is likely to be a potential bidirectional promoter, and the CCAAT/enhancer-binding protein might cooperate with the E2F transcription factor family in the regulation of the cell cycle in the early immune response induced by the influenza vaccine. Overall, our study clearly indicates that the expression profile changes induced by LAIV are significantly different from those induced by TIV. These results suggest that the pattern of overexpression of type 1 IFN-stimulated genes can potentially be used as a biomarker to identify the early vaccination response of LAIV and may also explain, to a certain extent, previous clinical study observations of LAIV-induced protection against influenza-like illness in the first 2 weeks after administration.

Introduction

In the United States, annual influenza vaccination is now recommended for all children 6 months through 18 years of age [1]. The injectable trivalent inactivated influenza vaccine (TIV) and the intranasal live attenuated influenza vaccine (LAIV) are available for use in young children; LAIV is approved for use in eligible children 2 years and older and some TIV formulations are approved for use in children as young as 6 months. Both vaccines are trivalent, containing recommended influenza A (H1N1 and H3N2) and influenza B strains. Despite widespread use and significant investigation, the protective mechanisms of these vaccines in young children are not completely understood. In 3 randomized studies among children 6 months to 17 years of age, LAIV recipients had 35% to 53% fewer cases of influenza illness compared with TIV recipients, with comparable safety among children 2 years and older [2], [3], [4], [5]. In 1 study among children 6–23 months of age, an increased rate of wheezing through 6 weeks postvaccination was associated with LAIV (LAIV, 5.9%; TIV, 3.8%), and in children 6–11 months of age there was an increased rate of hospitalization through 6 months after vaccination (LAIV, 6.1%; TIV, 2.6%) [3]. Several studies have shown that TIV and LAIV are immunogenic in young children [5], [6], [7], [8], [9], although different immune mechanisms may be involved. TIV can induce a stronger serum antibody response than LAIV, measured by immunoglobulin (Ig) G and IgA antibody levels and hemagglutination inhibition, particularly in older children with previous exposure to influenza [8]. LAIV, on the other hand, has been shown to induce significantly higher levels of mucosal IgA antibody [10]. In addition, studies with LAIV and TIV have shown that both vaccines can induce cellular immune responses [7], [11], [12].

Previous studies have demonstrated that type 1 interferon (IFN)-stimulated genes (ISGs) are significantly overexpressed after RNA viral invasion or vaccination, and that the activation of the type 1 IFN signaling pathway has a critical role in the development of adaptive and innate immune responses against influenza and other viral infections [13], [14], [15], [16]. To better understand the humoral and cellular responses elicited by vaccination, microarrays have been used to survey genome-wide changes in transcriptional profiles after influenza vaccination. Prominent overexpression of type 1 ISGs was displayed in children infected with influenza virus [14], [17]; similar transcriptional profiles were also observed in animals infected with influenza virus [18], [19].

In this study, we compiled a transcriptional profile of the early immune responses induced by TIV and LAIV in young children using whole genome DNA microarrays. A series of coexpressed gene clusters induced by such vaccination were identified. These gene clusters were further characterized by both functional and promoter analyses. In addition to directly comparing the expression profiles between LAIV and TIV, we examined the responses of (1) different age groups and (2) subjects who had/had not previously received the influenza vaccine were compared to understand potential differences in transcriptional regulation. This comprehensive analysis may provide a better understanding of differences in the mechanisms of action between vaccination with TIV and LAIV as well as differences in immune responses between individual subjects.

Section snippets

Patient enrollment

Children 12–35 months of age were enrolled in a prospective, randomized, open-label, multicenter study to evaluate their immune responses to LAIV or TIV. Children with a contraindication or warning against the use of LAIV or TIV were excluded from the study. Eighty-five subjects were randomized at a 1:1 ratio to receive 1 dose of intranasal LAIV (n = 43) or intramuscular TIV (n = 42). The 2006–2007 formulations of TIV and LAIV were used; each contained A/New Caledonia/20/99 (H1N1),

Identification of the genes with significantly differential expression

Of the 85 subjects, 43 subjects were vaccinated with LAIV and 42 subjects were vaccinated with TIV. The subjects were all 12–35 months of age, and only 4 subjects had previously received an influenza vaccine. The demographic data of the 85 subjects in the study are summarized in Table 1. To identify the transcripts that were differentially expressed in subjects vaccinated with LAIV or TIV, the FC values for a subject pre- and postvaccination were calculated. A total of 246 and 39 probe sets

Identification of differentially expressed genes using a nonconventional approach

To identify differentially expressed transcripts between postdose 1 and baseline for each subject, Student's t-test was used. However, only 1 gene (IFI27) was found to be significantly differentially expressed. Because most of the differentially expressed genes identified in this study had a prevalence of <50%, few of them would be selected using a conventional approach, such as a t-test. The low prevalence may be attributed to varying responses in subjects; a subject may have a distinct

Acknowledgments

We thank Joseph Shaw and Gorazd Drozina for the manuscript preparation and Tingting Yi for technical assistance.

References (57)

  • D.M. Fleming et al.

    Comparison of the efficacy and safety of live attenuated cold-adapted influenza vaccine, trivalent, with trivalent inactivated influenza virus vaccine in children and adolescents with asthma

    Pediatr Infect Dis J

    (2006)
  • R.B. Belshe et al.

    Safety and efficacy of live attenuated influenza vaccine in children 2–7 years of age

    Vaccine

    (2008)
  • X.S. He et al.

    Cellular immune responses in children and adults receiving inactivated or live attenuated influenza vaccines

    J Virol

    (2006)
  • S. Sasaki et al.

    Comparison of the influenza virus-specific effector and memory B-cell responses to immunization of children and adults with live attenuated or inactivated influenza virus vaccines

    J Virol

    (2007)
  • T. Vesikari

    Emerging data on the safety and efficacy of influenza vaccines in children

    Pediatr Infect Dis J

    (2008)
  • B.D. Forrest et al.

    Correlation of cellular immune responses with protection against culture-confirmed influenza virus in young children

    Clin Vaccine Immunol

    (2008)
  • X.S. He et al.

    Phenotypic changes in influenza-specific CD8+ T cells after immunization of children and adults with influenza vaccines

    J Infect Dis

    (2008)
  • M.G. Katze et al.

    Innate immune modulation by RNA viruses: emerging insights from functional genomics

    Nat Rev Immunol

    (2008)
  • J. Kawada et al.

    Analysis of gene-expression profiles by oligonucleotide microarray in children with influenza

    J Gen Virol

    (2006)
  • D. Proud et al.

    Gene expression profiles during in vivo human rhinovirus infection: insights into the host response

    Am J Respir Crit Care Med

    (2008)
  • G.R. Stark et al.

    How cells respond to interferons

    Annu Rev Biochem

    (1998)
  • T. Baas et al.

    Integrated molecular signature of disease: analysis of influenza virus-infected macaques through functional genomics and proteomics

    J Virol

    (2006)
  • Bioconductor: open source software for bioinformatics. Available at: http://bioconductor.org/ [accessed...
  • R. Suzuki et al.

    Pvclust: an R package for assessing the uncertainty in hierarchical clustering

    Bioinformatics

    (2006)
  • UCSC genome browser. Available at: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/upstream1000.fa.gz [accessed...
  • T.L. Bailey et al.

    Fitting a mixture model by expectation maximization to discover motifs in biopolymers

    Proc Int Conf Intell Syst Mol Biol

    (1994)
  • T.L. Bailey et al.

    Combining evidence using p-values: application to sequence homology searches

    Bioinformatics

    (1998)
  • The MEME suite: motif-based sequence analysis tools. Available at: http://meme.nbcr.net/meme4_3_0/downloads.html...
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