What can we learn about influenza infection and vaccination from transcriptomics?

Figures & data

Figure 1. Steps involved in transcriptomic analyses using RNA sequencing.

Table 1. Transcription profiles of host responses to influenza infection and vaccination with potential clinical and research applications.

Outcome measure	Genes/immune pathways involved	Potential clinical/research application	References
Differentiate influenza from other respiratory viral infections	Type I interferon (IFI44, IFI44L, OAS2, IRF7) and type II interferon (IFI35, IFITM1–3) were overexpressed in children with influenza compared to children with RSV or HRV LRTI	Diagnosis of influenza infection; potential for elucidating the main pathogen in viral co-infections Target antiviral therapy	Mejias et al.^Citation21 Parnell et al.^Citation22 Zhai et al.^Citation23 Andres-Terre et al.^Citation24
Differentiate influenza infection from bacterial pneumonia and systemic inflammatory response syndrome	Influenza gene-expression profile -upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways, e.g. Cell cycle mitosis, Cell cycle core, Proteolysis Ubiquitin-proteasomal proteolysis, Cell cycle S phase, Cell cycle G2M	Identification of presence or absence of secondary bacterial infections Target therapy	Parnell et al.^Citation22
Differentiate symptomatic from asymptomatic infection	Asymptomatic infection characterized by transcriptional regulation of the inflammasome genes; transcriptional activation of suppressor of cytokine signaling (SOCS) family genes and downregulation of JAK-STAT signaling; transcriptional activation of virus interacting proteins, anti-oxidant and cell-mediated innate immune responses.	Disease surveillance Host transmission studies Identify desired host immune responses for new vaccine development	Huang et al.^Citation25
Identify transcription profiles associated with more severe clinical outcomes	Decreased type I interferon and ubiquitination gene transcription associated with severe outcome of influenza A infection Transcription of interferon-induced transmembrane protein genes associated with mild disease	Identify patients at high risk of developing severe disease and design early interventions to ameliorate the outcome	Hoang et al.^Citation26
Identify infection prior to the onset of symptoms	Transcription of genes coding for innate viral RNA sensors, interferon response elements and cytokine response pathways 24–36 hours before symptoms	Studying outbreaks, illness clusters, epidemiologic surveillance, transmission studies	Hoang et al.^Citation26
Distinctive biosignatures that represent acute and recovery phase of infection	Acute phase- activation of gene transcription on the interferon pathway and innate immunity; decreased translational elongation and protein biosynthesis gene transcription Recovery phase – activation of genes involved in antigen binding, antibody secretion and cell morphogenesis	Devise and monitor response to novel therapeutic interventions	Zhai et al.^Citation23 Huang et al.^Citation25
Human cell responses to avian influenza viruses	H7N9 infection of human epithelial cells generates a transcriptional profile intermediate between H3N2 and H5N1	Identify the potential of avian influenza viruses to spread in humans	Josset et al.^Citation27
Genome-based identification of influenza-specific immune modifiers	Kinase inhibitor SB-203580, genistein, troglitazone, minocycline, and LY-294002- capable of reverting gene transcription induced by avian influenza viruses	Identifying novel therapeutic interventions	Josset et al.^Citation27
Differences in IIV- and LAIV-induced responses	LAIV activates gene transcription of the interferon pathway TIV generates plasmablast activation and antibody response gene transcription	Novel vaccine design based on attributes of existing vaccines	Nakaya et al.^Citation28 Cao et al.^Citation29 Cole et al.^Citation30
Adjuvant-specific signatures	Adjuvanted vaccine induced higher magnitude of gene expression compared with non-adjuvanted vaccine, including antiviral interferon, dendritic cell signature, Toll-like receptor (TLR) and inflammatory signaling pathways	Identify adjuvants that elicit most protective immune response	Nakaya et al.^Citation31 Olafsdottir et al.^Citation32
Early Transcriptional signature that correlates with HAI responses to vaccines	Early upregulation of Interferon response and antigen presentation pathways is associated with a higher antibody response	Development of new vaccines and adjuvants	Tan et al.^Citation33 Bucasas et al.^Citation34

IIV, inactivated influenza vaccine; TIV, trivalent influenza vaccine; LAIV, live attenuated influenza vaccine; HAI, hemagglutinin antibody inhibition; RSV, respiratory syncytial virus; HRV, human rhinovirus; LRTI, lower respiratory tract infection.

Table 2. Summary of findings from studies evaluating the host response to influenza infection.

Study methodology	Findings	Summary of Main findings	References
Prospective observational study of infants with RSV (n = 135), HRV (n = 30), influenza (n = 16) and healthy age matched controls, using microarray analysis	Children with influenza displayed a stronger activation of genes related to interferon, inflammation, monocytes, and innate immune response compared with children with RSV or HRV. Several type I interferon (IFIH1, IFIT1–5, STAT2, MX1) and type II interferon (IFI16, CXCL10, CCL8, GBP1–5, STAT1, SOCS1) genes were only expressed in influenza and RSV infection. The magnitude of the type I interferon (IFI44, IFI44L, OAS2, IRF7) and type II interferon (IFI35, IFITM1–3) response present was 2- to 22-fold higher in children with influenza compared with children with RSV or HRV. Genes related to inflammation, monocytes, and innate immune response were overexpressed in children with influenza compared to those with RSV or HRV LRTI.	Type I interferon and type II interferon were overexpressed in children with influenza compared to children with RSV or HRV LRTI	Mejias et al.^Citation21
39 critically ill patients with severe community-acquired pneumonia, 12 patients with non-infective systemic inflammatory response syndrome and 18 healthy volunteers evaluated using microarray analysis	Biological pathway analysis of the 1,416 genes uniquely upregulated in H1N1 influenza A infection showed that the influenza gene-expression profile is characterized by upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways. In contrast, a specific gene-expression signature was not found in bacterial pneumonia. Activation and signaling pathways of interleukins (IL-8, IL-2, IL-15, IL-6, IL-10, IL-7, IL-3, IL-13, IL-17, and IL-23) were downregulated in influenza H1N1 cohort. Influenza gene-expression profile showed upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways, e.g. Cell cycle mitosis, Cell cycle core, Proteolysis Ubiquitin-proteasomal proteolysis, Cell cycle S phase and Cell cycle G2M	Gene-expression profile of H1N1 influenza A pneumonia was distinctly different from those of bacterial pneumonia and systemic inflammatory response syndrome More interleukin suppression is present in severe H1N1 influenza infection	Parnell et al.^Citation22
Prospective observational study of 1610 healthy adults; of these 133 developed influenza-like illness, and 73 had PCR-confirmed influenza and were followed for 3 weeks; changes in peripheral blood gene expression evaluated using microarray analysis	In the acute phase, there was a large increase in components of the interferon pathway and innate immunity (e.g. IFI44L, IFIT1, MX1, IFITM3, OAS2, IFI27 and IFIT3), as well as decreased expression of genes involved in translational elongation and protein biosynthesis (e.g. RPS4X, RPS18, RPS6, RPS8 and RPL5). This pattern was most intense on the first day of illness and continued for 2–4 days. This phase was followed by a characteristic recovery phase in which there was a transition to genes involved in antigen binding and antibody secretion (IGJ, LOC652694, IGLL1 and MZB1) and genes regulating cell morphogenesis (STRADB, DPYSL5, EPB42, LST1 and MAP1S).	There is upregulation of interferon pathway and innate immunity genes in the early phase of infection lasting 2–4 days, followed by cell proliferation and repair gene overexpression at days 4–6. Day 21 gene expression patterns were indistinguishable from baseline patterns. Influenza virus infection induced a higher magnitude and longer duration of the expression signature of illness compared to other viral infections. There is an intense activation of NK cells during the acute phase of infection.	Zhai et al.^Citation23
Analyses of 18 publicly available transcriptional datasets of host whole blood, PBMCs or epithelial cells of patients with viral infections, bacterial infections, SIRS, vaccinated patients	An 11-gene ‘influenza meta-signature’ was identified, that could discriminate symptomatic from asymptomatic subjects, influenza infection from other respiratory viral infections, and patients with mixed influenza and/or bacterial pneumonia from those with bacterial pneumonia alone. (CD38, HERC5, HERC6,, IFI6, IFIH1, LGALS3BP, LY6E, MX1, PARP12, RTP4, and ZBP1)	Gene signature that can differentiate influenza infections from other viral infections The host signature was predictive of response to influenza vaccine	Andres-Terre et al.^Citation24
Experimental challenge of 17 healthy adults with H3N2 and evaluation of peripheral blood gene expression at 16 timepoints over 132 hours.	Asymptomatic infection characterized by transcriptional regulation of the inflammasome genes; transcriptional activation of suppressor of cytokine signaling (SOCS) family genes and downregulation of JAK-STAT signaling; transcriptional activation of virus interacting proteins, anti-oxidant and cell-mediated innate immune responses. Early expression patterns of suppressor of cytokine signaling family genes and related JAK-STAT signaling in asymptomatic hosts with no sign of excessive inflammation Transcription of genes coding for innate viral RNA sensors, interferon response elements and cytokine response pathways 24–36 hours before symptoms	Transcriptome can differentiate symptomatic from asymptomatic infection. The host antiviral response is activated 36 hours before peak symptom time.	Huang et al.^Citation25
Evaluation of transcriptomic profiles of children and adults with influenza infection, classified as mild (N = 83) moderate (N = 40) and severe (N = 11), using microarray analysis; compared with febrile patients with unknown etiology	Patients with influenza infection had stronger induction of Toll-like receptor signaling, IL-10 signaling, and NFkB than those without influenza infection Genes in IL-1 signaling, IL-22 signaling, Production of Nitric Oxide and Reactive Oxygen Species in Macrophages and p38 MAPK signaling were only up-regulated in moderate and severe patients Transcription of interferon-induced transmembrane protein genes was associated with mild disease	Transcription profiles involving type I interferon and ubiquitination gene transcription were attenuated in patients with severe disease	Hoang et al.^Citation26
Experimental challenge of 24 healthy volunteers with influenza A H1N1 or H3N2, whole blood RNA isolated from blood samples collected every 8 hours and analyzed using microarrays	Gene signatures derived independently for the two different strains of influenza are highly similar, sharing 44 out of the top 50 genes, and characterize host response to viral infection. These genes include RSAD2, the OAS family, multiple interferon response elements, the myxovirus-resistance gene MX1, cytokine response pathways	Signature differentiates symptomatic influenza A H1N1 or H3N2 infection from asymptomatic individuals	Woods et al.^Citation35
Human bronchoepithelial cells were inoculated with influenza H3N2, H7N9 or H5N1, then extracted RNA was analyzed using microarrays	H7N9 infection of human epithelial cells generates a transcriptional profile intermediate between H3N2 and H5N1. Kinase inhibitor SB-203580, genistein, troglitazone, minocycline, and LY-294002 are capable of reverting gene transcription induced by avian influenza viruses	Higher potential of H7N9 avian influenza viruses to spread in humans Identifying several novel therapeutic interventions	Josset et al.^Citation27

RSV, respiratory syncytial virus; HRV, human rhinovirus; DNA, deoxyribonucleic acid; RNA, ribonucleic acid; NK, natural killer; PCR, polymerase chain reaction.

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