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Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses… Lee, Suki M; Chan, Renee W; Gardy, Jennifer L; Lo, Cheuk-kin; Sihoe, Alan D; Kang, Sara S; Cheung, Timothy K; Guan, Yi; Chan, Michael C; Hancock, Robert E; Peiris, Malik J Oct 28, 2010

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RESEARCH Open AccessSystems-level comparison of host responsesinduced by pandemic and seasonal influenza AH1N1 viruses in primary human type I-likealveolar epithelial cells in vitroSuki MY Lee1†, Renee WY Chan1,2†, Jennifer L Gardy3, Cheuk-kin Lo4, Alan DL Sihoe5, Sara SR Kang1,Timothy KW Cheung1, Yi Guan1, Michael CW Chan1, Robert EW Hancock6, Malik JS Peiris1,7*AbstractBackground: Pandemic influenza H1N1 (pdmH1N1) virus causes mild disease in humans but occasionally leads tosevere complications and even death, especially in those who are pregnant or have underlying disease. Cytokineresponses induced by pdmH1N1 viruses in vitro are comparable to other seasonal influenza viruses suggesting thecytokine dysregulation as seen in H5N1 infection is not a feature of the pdmH1N1 virus. However a comprehensivegene expression profile of pdmH1N1 in relevant primary human cells in vitro has not been reported. Type I alveolarepithelial cells are a key target cell in pdmH1N1 pneumonia.Methods: We carried out a comprehensive gene expression profiling using the Affymetrix microarray platform tocompare the transcriptomes of primary human alveolar type I-like alveolar epithelial cells infected with pdmH1N1or seasonal H1N1 virus.Results: Overall, we found that most of the genes that induced by the pdmH1N1 were similarly regulated inresponse to seasonal H1N1 infection with respect to both trend and extent of gene expression. These commonlyresponsive genes were largely related to the interferon (IFN) response. Expression of the type III IFN IL29 was moreprominent than the type I IFN IFNb and a similar pattern of expression of both IFN genes was seen in pdmH1N1and seasonal H1N1 infection. Genes that were significantly down-regulated in response to seasonal H1N1 but notin response to pdmH1N1 included the zinc finger proteins and small nucleolar RNAs. Gene Ontology (GO) andpathway over-representation analysis suggested that these genes were associated with DNA binding andtranscription/translation related functions.Conclusions: Both seasonal H1N1 and pdmH1N1 trigger similar host responses including IFN-based antiviralresponses and cytokine responses. Unlike the avian H5N1 virus, pdmH1N1 virus does not have an intrinsic capacityfor cytokine dysregulation. The differences between pdmH1N1 and seasonal H1N1 viruses lay in the ability ofseasonal H1N1 virus to down regulate zinc finger proteins and small nucleolar RNAs, which are possible viraltranscriptional suppressors and eukaryotic translation initiation factors respectively. These differences may bebiologically relevant and may represent better adaptation of seasonal H1N1 influenza virus to the host.* Correspondence: malik@hkucc.hku.hk† Contributed equally1Department of Microbiology, The University of Hong Kong, Hong KongSAR, PR ChinaFull list of author information is available at the end of the articleLee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147© 2010 Lee et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited.BackgroundPandemic H1N1 remains a mild disease although occa-sionally severe complications and death may ensue,especially in those who are pregnant or have underlyingrespiratory, cardiac or endocrine diseases or morbidobesity [1]. We and others have demonstrated thatpdmH1N1 virus does not differ from seasonal influenzaviruses in its induction of cytokine responses in humanmacrophages and epithelial cells [2-4]. This suggeststhat the cytokine dysregulation seen in H5N1 infectionis not an intrinsic feature of the pdmH1N1 virus.The pdmH1N1 virus arose from genetic reassortmentbetween influenza viruses endemic in swine, a NorthAmerican triple-reassortant swine influenza virusacquiring a neuraminidase and matrix (M) gene segmentfrom viruses of the Eurasian-avian-like swine virus line-age [5,6]. Since these swine viruses have in turn origi-nated via complex genetic reassortments between swine,avian and human influenza viruses, the pdmH1N1 virushas a novel gene constellation with virus gene segmentsthat are derived from human (PB1), classical swineH1N1 (HA, NP, NS), Eurasian avian-like swine (M, NA)and avian (PB2, PA) sources. While the precursor swineviruses were clearly well adapted to circulate in pigs forperiods ranging from 11 (North American triple reassor-tant) to 90 (classical swine) years, evolutionary datinganalysis suggests that the pdmH1N1 virus transmittedin humans only a few months prior to its detection inMarch 2009 [6].Using the Affymetrix microarray platform, we hadpreviously demonstrated that avian H5N1 viruses elicithost responses that were qualitatively similar but quanti-tatively markedly different to seasonal influenza H1N1virus in human macrophages [7]. As the tracheo-bron-chial epithelium, type I and II alveolar epithelial cellsand macrophages are key target cells for pdmH1N1infection [8] and the most serious complication ofpdmH1N1 disease is primary viral pneumonia, weemployed type I-like alveolar epithelial cells as a modelto examine the host transcriptomes induced bypdmH1N1 viruses compared with that of seasonalH1N1 viruses using the same Affymetrix microarrayplatform. We aimed to identify the mechanistic differ-ences in host responses induced by these two H1N1viruses, in order to provide insights into virus pathogen-esis, which may in turn be relevant to therapeutic strate-gies for the treatment of influenza.MethodsVirusesThe viruses used were the pdmH1N1 2009 influenza Avirus (A/Hong Kong/415742/2009) and human seasonalH1N1 influenza A virus (A/Hong Kong/54/1998). Fromtheir initial isolation, the viruses were propagated inMadin-Darby canine kidney (MDCK) cells. Virus infec-tivity was determined by cytopathic assays on MDCKcells and quantified as 50% tissue culture infectious dose(TCID50). Infectious material was handled in a bio-safetylevel 3 facility at the Department of Microbiology, TheUniversity of Hong Kong.Isolation of primary human alveolar type II alveolarepithelial cellsPrimary type II alveolar epithelial cells were isolatedusing human non-malignant lung tissue as previouslydescribed [3] obtained from patients undergoing lungresection in the Department of Cardiothoracic Surgery,Queen Mary Hospital, Hong Kong SAR, under a studyapproved by the Institutional Review Board of the Uni-versity of Hong Kong and Hospital Authority HongKong West Cluster. Written informed consent was pro-vided by each patient. Briefly, after removing visiblebronchi, the lung tissue was minced into pieces of >0.5mm thickness using a tissue chopper and washed withbalanced salt solution (BSS) containing Hanks’ balancedsalt solution (Gibco) with 0.7 mM sodium bicarbonate(Gibco) at pH 7.4 for 3 times to partially remove macro-phages and blood cells. The tissue was digested using acombination of 0.5% trypsin (Gibco) and 4 U/ml elastase(Worthington Biochemical Corporation, Lakewood, NJ,USA) for 40 min at 37°C in a shaking water-bath. Thedigestion was stopped by adding DMEM/F12 medium(Gibco) with 40% FBS in and DNase I (350 U/ml)(Sigma). Cell clumps were dispersed by repeatedly pipet-ting the cell suspension for 10 min. A disposable cellstrainer (gauze size of 50 μm) (BD Science) was used toseparate large undigested tissue fragments. The singlecell suspension in the flow-through was centrifuged andresuspended in a 1:1 mixture of DMEM/F12 mediumand small airway basal medium (SABM) (Lonza) supple-mented with 0.5 ng/ml epidermal growth factor (hEGF),500 ng/ml epinephrine, 10 μg/ml transferrin, 5 μg/mlinsulin, 0.1 ng/ml retinoic acid, 6.5 ng/ml triiodothyro-nine, 0.5 μg/ml hydrocortisone, 30 μg/ml bovine pitui-tary extract and 0.5 mg/ml BSA together with 5% FBSand 350 U/ml DNase I. The cell suspension was platedon plastic flask (Corning) and incubated in a 37°Cwater-jacketed incubator with 5% CO2 supply for 90min. The non-adherent cells were layered on a discon-tinuous cold Percoll density gradient (densities 1.089and 1.040 g/ml) and centrifuged at 25×g for 20 minwithout brake. The cell layer at the interface of the twogradients was collected and washed four times with BSSto remove the Percoll. The cell suspension was incu-bated with magnetic beads coated with anti-CD14 anti-bodies at room temperature (RT) for 20 min underLee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 2 of 9constant mixing. After the removal of the beads using amagnet (MACS CD14 MicroBeads), cell viability wasassessed by trypan-blue exclusion. The purified alveolarepithelial cell suspension was resuspended in small air-way growth medium (Lonza) supplemented with 1%FBS, 100 U/ml penicillin and 100 μg/ml streptomycin,and plated at a cell density of 3×105 cells/cm2. The cellswere maintained in a humidified atmosphere (5% CO2,37°C) under liquid-covered conditions, and growth med-ium was changed daily starting from 60 h after platingthe cells.Type I-like alveolar epithelial cell differentiationThe purified type II alveolar epithelial cell pellet (pas-sage 1 or 2) was resuspended in medium to a final con-centration that allowed seeding at 5 × 105 cells/cm2onto culture flask and cultured for 14 to 20 days withthe small airway culture medium SAGM (Lonza). Thecells spread to form a confluent monolayer and the cul-ture medium was changed every 48 hbefore being usedfor virus infection experiments.Virus infection of type I-like alveolar epithelial cellsType I-like alveolar epithelial cells were infected withpdmH1N1 and seasonal H1N1 at a multiplicity of infec-tion (MOI) of two. Minimum Essential Medium (MEM)(Gibco) with 100 U/ml penicillin and 100 μg/ml strepto-mycin was used as inoculum in the mock infected cells.The cells were incubated with the virus inoculum for 1h in a water-jacketed 37°C incubator with 5% CO2.Then the cells were rinsed 3 times with warm PBS andreplenished with the appropriate growth medium. Theinfected cells were harvested for mRNA collection at 8h post-infection and viral M gene was quantified usingreal-time PCR. Total RNA was extracted from cells after8 h post-infection using the RNeasy Mini kit (Qiagen)according to the manufacturer’s recommended protocol.Microarray AnalysisHuman gene expression was examined with the Gene-Chip Human Gene 1.0 ST array (Affymetrix). TheHuman Gene 1.0 ST array comprises more than 750,000unique 25-mer oligonucleotide features, constitutingover 28,000 gene-level probe sets. RNA quality control,sample labelling, GeneChip hybridization and dataacquisition were performed at the Genome ResearchCentre, The University of Hong Kong. The quality oftotal RNA was checked by the Agilent 2100 bioanalyzer.The RNA was then amplified and labeled with Gene-Chip® WT Sense Target Labeling and Control Reagentskit (Affymetrix). cDNA was synthesized, labeled andhybridized to the GeneChip array according to the man-ufacturer’s protocol. The GeneChips were finally washedand stained using the GeneChip Fluidics Station 450(Affymetrix) and then scanned with the GeneChip Scan-ner 3000 7G (Affymetrix).GeneSpring GX 11 (Agilent) was used for the normali-zation, filtering and statistical data analysis of the Affy-metrix microarray data. The linear data was firstsummarized using Exon Robust Multichip Average(RMA) summarization algorithm on the CORE probe-sets and Baseline Transformation to Median of all sam-ples for three major tasks including BackgroundCorrection, Normalization and Probe Summarization.Briefly, Exon RMA performed a GC based backgroundcorrection followed by Quantile Normalization and sub-sequently performed a Median Polish probe summariza-tion. Next, quality control on samples was performed atdifferent levels including 1) internal controls to checkthe RNA sample quality, 2) hybridization controls toassess the hybridization quality and 3) Principal Compo-nent Analysis (PCA) to check the data quality. Onlysamples that found to be satisfactory in all quality con-trol tests were included in further analysis. In the pro-cess of data filtering, probesets with an intensity valueof the lowest 20th percentile of all the intensity valueswere removed. The filtered entities resulted in a workingtranscript list used for statistical analysis. An analysis ofvariance (ANOVA) was performed to identify genes sig-nificantly expressed (p < 0.05) in response to virus infec-tion. In order to reduce the overall false positive hits,Benjamini and Hochberg multiple testing correction wasemployed. Significantly differentially expressed geneswith fold change ≥1.5 in response to pdmH1N1 and sea-sonal H1N1 infection compared with mock were thenmerged into a gene list for further GO and pathwayanalysis.GO and pathway over-representation analysis as wellas further analysis of protein-protein interactions andtranscription factor regulation were carried out usingthe InnateDB platform [9,10]. Over-representation ana-lyses were performed using a hypergeometric algorithm,and over-represented GO terms or pathways withp-values ≤ 0.05 were retained provided at least twouploaded genes mapped to the entity in question. Inparallel, an independent pathway over-representationanalysis was also performed using the GeneSpring pro-gram. Human pathway databases, including IntegratingNetwork Objects with Hierachies (INOH), Reactome,Kyoto Encyclopedia Genes and Genomes (KEGG), Bio-carta, National Cancer Institute (NCI) and NetPath,were imported into the software for pathway analysis ofstatistically significant genes.Real-time quantitative RT-PCR assaysTotal RNA was isolated using the RNeasy Mini kit (Qia-gen) as described. The cDNA was synthesized frommRNA with poly(dT) primers and Superscript IIILee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 3 of 9reverse transcriptase (Invitrogen). Transcript expressionwas monitored using a Power SYBR® Green PCR mastermix kit (Applied Biosystems) with corresponding pri-mers. The fluorescence signals were measured using the7500 real-time PCR system (Applied Biosystems). Thespecificity of the SYBR® Green PCR signal was con-firmed by melting curve analysis. The threshold cycle(CT) was defined as the fractional cycle number atwhich the fluorescence reached 10 times the standarddeviation of the base-line (from cycle 2 to 10). The ratiochange in target gene relative to the b-actin controlgene was determined by the 2-ΔΔCT method as describedelsewhere [11].Microarray data accession numberMicroarray data has been deposited in the Gene Expres-sion Omnibus (GEO) database [12] with the accessionnumber: GSE24533.ResultsWe used the Affymetrix GeneChip Human Gene 1.0 STarray to compare the global gene expression profiles ofhuman primary type I-like alveolar epithelial cells fromthree independent donors (n = 3) after infection withpdmH1N1, seasonal H1N1 viruses or mock controlinfection at 8 h post-infection. Changes were observedin 602 transcripts from 434 individual host genes (p <0.05 in one-way ANOVA test).In a preliminary analysis, the gene expression datafrom each epithelial cell donor was analyzed separatelyto define the donor-to-donor variation after influenzainfection. We used a ± 1.5-fold change in gene expres-sion as the cut-off value and genes were classified intothose that were ≥ 1.5-fold up-regulated (+) or down-regulated (-) relative to mock-infected cells and thosewith no change in expression (fold change between -1.5and +1.5).Overall, 93.2% and 74.6% of genes were concordantlyexpressed in the alveolar epithelial cells from the threedonors after infection with pdmH1N1 and seasonalH1N1 virus respectively. The expression of those geneswith discordant results among donors was further ana-lyzed. In 36 of 41 instances (87.8%) after pdmH1N1infection and all instances after seasonal H1N1 infec-tion, the apparently discordant genes had the sametrend of expression, being either up- or down-regulatedin all donors and the differences only reflected whetherthe cut-off of ≥ 1.5-fold change in gene expression com-pared to mock-infected cells was met. The remainingfive genes showed a contradictory regulation in cellsfrom different donors infected with pdmH1N1 virus.These included C20orf94 (chromosome 20 open readingframe 94), IPP (intracistemal A particle-promoted poly-peptide), MRPL30 (mitochondrial ribosomal proteinL30), RTN4IP1 (reticulon 4 interacting Protein 1) andSNORD44 (small nucleolar RNA, C/D box 44).Given the high overall concordance in gene expressionprofiles found among the three donors in our analysis,the fold change of gene expression levels in response toeither the pdmH1N1 or seasonal H1N1 respectively,compared to mock infection, was averaged across thethree donors for subsequent analysis. We filtered theaverage gene-expression data using a cut-off value of1.5-fold up- or down-regulation in the pdmH1N1- andseasonal H1N1-infected cells compared to mockinfected cells. Compared to mock infected cells, 88genes were up or down-regulated in response to seaso-nal H1N1 infection while 18 genes were affected inpdmH1N1 infected cells, all of them being up-regulated(Figure 1A and Additional File 1: Summary of geneexpression in response to influenza A virus infection).Sixteen of the 18 genes induced by the pdmH1N1were similarly regulated in response to seasonal H1N1infection with respect to both trend and extent of geneexpression (Figure 1B). Only two genes, basic leucinezipper transcription factor, ATF-like 2 (BATF2) andsolute carrier family 15, member 3 (SLC15A3) were dif-ferentially expressed in response to pdmH1N1 infectiononly. On the other hand, there were 72 genes (68 geneswere down-regulated and 4 genes up-regulated) affectedin response to seasonal H1N1 but not in response topdmH1N1 infection when compared with the mockinfected cells (Figure 1B).In order to compare the viral replication efficiency ofthe two viruses, the expression level of viral M gene wasdetermined using real-time PCR (Figure 2). Althoughthere was a trend to higher M gene copy numbers incells infected with seasonal H1N1 virus, the differenceswere not statistically significant and comparable infec-tious viral titres were detected in the cell supernatant byviral titration. Genes of particular interest indentified inthe microarray analysis were verified using real timequantitative PCR (Figures 2 and 3).In order to investigate whether the trend towards highervirus replication with seasonal H1N1 virus was responsiblefor the difference in the gene expression we carried out anexperiment using MOI = 6. The M gene expression of thetwo viruses was similar, but the differential expression ofZBTB3, ZNF175, ZNF383, ZNF587 and ZNF8 genes withexpression in seasonal H1N1 infected cells being lowerthan pdmH1N1 infected cells was maintained.Over-representation analysis using InnateDBTo determine the biological relevance of the host geneexpression elicited by the two viruses and in particularto identify any differences observed between theseviruses, we compared the over-represented GO termsand biological pathways associated with the pdmH1N1-Lee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 4 of 9regulated genes to those associated with the genesaltered in response to seasonal H1N1. We used theInnateDB analysis environment, and verified the resultsof GO and pathway analyses using GeneSpring.We observed that host responses induced by bothviruses were associated with ontological entities relatedto innate immunity and responses to virus infections.However, the genes expressed only in response to seaso-nal influenza virus were associated with DNA bindingand transcription-related functions (Figure 4).Pathway analysis returned a similar result, with genesregulated in response to both viruses belonging to clas-sical innate immune response pathways, while genesregulated in response to seasonal H1N1 infection onlyFigure 1 Summary of genes expressed in response to pdmH1N1 and seasonal H1N1 infection. (A) Genes that are significantly regulated(p < 0.05 and fold change ≥1.5) in response to pdmH1N1 and seasonal H1N1 compared with mock infection at 8h post-infection are shown.(B) Venn-diagram showing the genes that are differentially expressed in response to pdmH1N1 or seasonal H1N1 only and those that are co-regulated by both viruses.Figure 2 Validation of microarray data by real-time PCR. Expression of viral M gene and five ZNF genes were assessed after 8 h infection bypdmH1N1 and seasonal H1N1 viruses compared to mock. Data shown was from three individual donors denoted as donor 1, 2 and 3.Lee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 5 of 9demonstrating functions related to transcription andmRNA transport (Figure 5).Comparison of the differentially expressed gene lists toInterferome [13,14], an IFN-regulated gene database,revealed that of the 16 genes up-regulated in response toboth seasonal and pandemic H1N1 infection, 15 of these(93.75%) are related to the IFN response. A transcriptionfactor over-representation analysis was also performed usingInnateDB in order to identify transcription factors involvedin the regulation of seasonal-, pandemic- and shared-response genes. Of the 13 transcription factors regulatinggenes affected by both seasonal and pandemic viruses, four(IRF1, IRF2, IRF7, IRF8) are known IFN response factors.We also used InnateDB to compare the interactionsbetween genes differentially expressed in response toeither virus. Only a single difference was observed, withthe seasonal H1N1 response network distinguished bythe presence of the interacting DNA damage response-related genes DNA-damage-inducible transcript 4(DDIT4) and RAP1 interacting factor (RIF1), both ofwhich were down-regulated in response to seasonalH1N1 but unchanged in response to pdmH1N1.DiscussionComparable IFN responses to pdmH1N1 and seasonalH1N1 infectionIn this study, we found that 16 out of 18 genes (88.9%)induced by the pdmH1N1 virus were also similarly regu-lated in response to seasonal H1N1 infection, and therewas no significant difference in expression level betweenthe two viruses.Among these 16 genes, 15 were either IFNs or IFN-sti-mulated genes and we found comparable up-regulation ofthe type III IFNs, IL28A, IL28B and IL29 following seaso-nal H1N1 or pdmH1N1 infection. Although type I andtype III IFNs bind to distinct receptors, they elicit similarintracellular signals and gene expression profiles [15].Figure 3 Validation of IFN gene expression by real-time PCR.Expression of type I (IFNb) and type III (IL29) IFNs were assessed byreal-time PCR in pdmH1N1-, seasonal H1N1- and mock infected cellsat 8 h post-infection. The gene expression level averaged from thethree individual donors is shown.Figure 4 Significantly enriched GO terms in response to seasonal and pandemic H1N1 infection. MF = molecular function, BP =biological process, CC = cellular component. Only GO terms to which at least two differentially expressed genes were mapped are included.Lee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 6 of 9IL28A, IL28B and IL29 are recognized type III IFNs whichsignal through a receptor complex consisting of IL10R2and IFNlR1. Upon binding of IFNs, corresponding recep-tor subunits dimerize to form the receptor complex andactivate the JAK-STAT signalling pathway, which thenresults in downstream induction of genes such as ISGF3, atrimetric transcription factor complex of signal transducerand activator of transcription 1 and 2 (STAT1, STAT2)and IFN regulatory factor 9 (IRF9). Downstream genesregulated by this mechanism include genes reported tohave anti-viral activity such as IFN-stimulated gene 15(ISG15) and myxovirus (influenza virus) resistance 1(MX1) [16]. In this study, we found that IFN-related genesincluding IL28A, IL28B, IL29, IRF9, ISG15 and MX1 weresignificantly up-regulated in response to both pdmH1N1and seasonal H1N1 infections and to a similar degree, sug-gesting that similar host anti-viral mechanisms are trig-gered in response to both H1N1 viruses.In the microarray data, we were unable to detect theexpression of type I IFNs, such as IFNb, in response toeither pdmH1N1 or seasonal H1N1 infection. However,we confirmed by real-time PCR the expression of IFNbin response to both viruses, though present, it was nota-bly lower when compared with type III IFN, IL29(Figure 3). Similar patterns of expression of both IFNgenes were seen in pdmH1N1 and seasonal H1N1 infec-tion. This is in agreement with our previous finding thatthere was very low induction of type I IFNs in responseto pdmH1N1 or seasonal H1N1 in alveolar epithelialcells and bronchial epithelial cells at 6 h post-infection[3], which is probably related to the potent activity ofviral immune evasion genes such as NS1. Our resultsindicate that type III IFNs are likely to be particularlyimportant in host defence in both pdmH1N1 and seaso-nal H1N1, possibly even more so than type I IFNs.Lack of host translational control by small nucleolar RNAin response to pdmH1N1 infectionWhen we examined genes expressed in response to sea-sonal H1N1 influenza virus but not pdmH1N1 virus, wenoted a number of genes with roles in transcriptional ortranslation control, including DNA binding and mRNAtransport. These genes were down-regulated in response toinfection with seasonal H1N1 influenza virus relative topdmH1N1. Several of these down-regulated genes aresmall nucleolar RNAs. Previous studies have suggested thathost translational machinery is suppressed by the down-regulation of small nucleolar RNAs, such as SNORA4, incells following influenza A infection [17]. Here we observethat SNORA4 is significantly down-regulated in responseto seasonal H1N1 infection but not in pdmH1N1 infectedcells, suggesting that seasonal H1N1 virus may be moreefficient at suppressing host translational mechanisms,allowing for efficient translation of viral mRNA [18-20].We also identified six small nucleolar RNAs that maypotentially act through a similar mechanism while thefunctions of individual candidates in influenza pathogenesiswill require further investigation.Lack of the control of transcriptional suppression by zincfinger proteins in pdmH1N1 infected cellsWe found that nine of the genes down-regulatedin response to seasonal H1N1 influenza virus (but notpdmH1N1) encode zinc finger proteins, includingZNF175. ZNF175 contains 13 zinc fingers and a KRABdomain, for a motif known to be associated withFigure 5 Significantly enriched pathways in response to seasonal and pandemic H1N1 infection. Only pathways to which at least twodifferentially expressed genes were mapped are included.Lee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 7 of 9transcriptional suppression [21]. Previous data have sug-gested that zinc finger proteins are up-regulated inresponse to HIV infection and that they inhibit productionof new virus through suppression of the HIV long terminalrepeat (LTR) promoter activity [21]. Further work demon-strated that this suppression occurs via direct binding totwo distinct regulatory regions: the negative regulatory ele-ment and the Ets element [22]. To date, no correlationbetween zinc finger proteins and influenza virus has beenreported, however, we showed in this study that there wasa significant down-regulation of multiple zinc finger pro-teins in response to seasonal H1N1 infection comparedwith pdmH1N1. Further study will be important to inves-tigate if there is an antiviral role of these zinc finger pro-teins against influenza infection.Comparison with Transcriptomic Data from ExperimentalAnimal InfectionRecently, a microarray analysis was reported characteriz-ing host immune responses in ferret lung followinginfection with the pdmH1N1 (A/California/07/2009)and seasonal H1N1 (A/Brisbane/59/2007) [23]. In con-cordance with our study, they observed that IFNresponses were triggered early after infection by bothH1N1 viruses. However, in contrast to our data, theyreport that the range and magnitude of ISGs induced byseasonal H1N1 was more limited compared topdmH1N1. However, these results are confounded bythe fact that seasonal influenza replicated less efficientlyin the ferret lung compared to pdmH1N1 and clearlylower levels of infection will be associated with lowerinduction of host responses. Thus, data from animal stu-dies cannot differentiate whether the observed effectswere due to intrinsic differences in host responsesinduced by the viruses or whether they reflect the viralreplication competence in particular tissues in theexperimental animal model used. Our data arises from asingle-cycle synchronous infection of cells with anequivalent virus dose and is therefore more relevant toinvestigate the host responses that are driven by intrin-sic differences between the two H1N1 viruses. It is alsonoteworthy that although seasonal influenza H1N1replicated less efficiently than pdmH1N1 in ferret lungin vivo, the two viruses replicate comparably in humantype I alveolar epithelial cells and in ex vivo lung cul-tures [3]. Arguably, the ex vivo lung data showing com-parable viral tropism and replication competence withseasonal H1N1 and pdmH1N1 reflects more closely theepidemiology of the pandemic where pdmH1N1 diseaseseverity was in fact comparable or milder than that sea-sonal influenza. If the differences in disease severityobserved following experimental infection of ferrets wasa true reflection of human disease, it would be expectedthat pdmH1N1 would be markedly more severe inhumans than it appears to be. These observations infact highlight the relevance of using primary and ex vivohuman cell culture data to complement data fromexperimental animals.ConclusionsIn this study, we compared the host response to seasonaland pandemic H1N1 influenza virus in a relevant humanrespiratory cell model, the primary human type I-likeepithelial cells that are a primary target in the lung thatmay lead to primary viral pneumonia [24,25], includinginfection with the recently identified pdmH1N1 virus [3,8].We conclude that both seasonal H1N1 and pdmH1N1trigger similar host IFN-related antiviral responses. TypeIII IFNs, were more prominently induced by bothviruses when compared with type I IFNs. This highlightsthe significance of type III IFN signalling in the patho-genesis of both pdmH1N1 and seasonal H1N1 viruses.In agreement with our other recent findings, weobserved that the cytokine and overall host responseprofile triggered by both viruses were similar [3,26] andthat pdmH1N1 does not produce the cytokine dysregu-lation as seen in H5N1 infection. The differencebetween the pandemic and seasonal H1N1 viruses lay intheir ability to potentially alter host transcriptional andtranslational responses. Down-regulation of zinc fingerproteins and small nucleolar RNAs - possible viral tran-scriptional suppressors and eukaryotic translation initia-tion factors, respectively - may facilitate the efficientreplication of seasonal H1N1 influenza virus in the host.Lacking suppression via these mechanisms suggestspdmH1N1 virus may be relatively less adapted for repli-cation in human type I-like alveolar epithelial cells.We demonstrate differences in regulation of ten zincfinger proteins and seven small nucleolar RNAs in hostresponses to pdmH1N1 and seasonal H1N1 influenzavirus. The role of these proteins in influenza pathogen-esis merits further investigation.Additional materialAdditional file 1: Summary of gene expression in response toinfluenza A virus infection. Fold change of gene expression inresponse to pdmH1N1 and seasonal H1N1 at 8 h post-infection time inhuman type I-like alveolar epithelial cells that showed significantdifference (p < 0.05, with Benjamini-Hochberg multiple testing correctionand fold change ≥ 1.5) in expression level compared to mock infectedcells were shown. The “-” and no sign before the number indicates thedown- and up-regulation of the gene respectively in influenza A infectedcells compared to mock. HGNC Gene Symbol is HUGO GeneNomenclature Committee approved gene symbol. *Ratio [pdmH1N1]/[seasonal H1N1] indicates the fold change of gene expression inresponse to pdmH1N1 compared to seasonal H1N1 infection at 8 hpost-infection time.Lee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 8 of 9AcknowledgementsWe thank WW Gai and Genome Research Centre, The University of HongKong for their technical support in this study. This work was supported bygrants of National Institutes of Health (NIAID contract no.HHSN266200700005C), Canadian Institutes of Health Research (reference no:TPA-90195), Research Fund for Control of Infectious Disease (Ref: LAB-15,RFCID commissioned study on human swine influenza virus and RFCIDgrant, reference no. 06060552), and funding from the Area of ExcellenceScheme of the University Grants Committee, Hong Kong SAR Government(AoE/M-12/06). We acknowledge support from the Canadian Institutes forHealth Research to REWH. REWH held a Canada Research Chair.Author details1Department of Microbiology, The University of Hong Kong, Hong KongSAR, PR China. 2Department of Pathology, The University of Hong Kong,Hong Kong SAR, PR China. 3British Columbia Centre for Disease Control,Vancouver, British Columbia, Canada. 4Department of Cardiothoracic Surgery,Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, PR China. 5Departmentof Cardiothoracic Surgery, Queen Mary Hospital, Pokfulam, Hong Kong SAR,PR China. 6Centre for Microbial Diseases and Immunity Research, Universityof British Columbia, Vancouver, British Columbia, Canada. 7The University ofHong Kong-Pasteur Research Centre, Hong Kong SAR, PR China.Authors’ contributionsSMYL, RWYC, MCWC and JSMP conceived and designed the experiments.RWYC, MCWC and SSRK generated the type I-like alveolar epithelial cells andperformed the virus infection experiments in bio-safety level 3 facility. SMYL,JLG, RWYC, MCWC, TKWC, YG, REWH, JSMP analyzed the data. CKL, ADLSand REWH contributed cells, reagents and analysis tools for this study. SMYL,JLG, JSMP wrote the paper and all authors contributed to critical revision ofthe manuscript.Competing interestsThe authors declare that they have no competing interests.Received: 7 June 2010 Accepted: 28 October 2010Published: 28 October 2010References1. Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom S, Garten RJ,Gubareva LV, Xu X, Bridges CB, Uyeki TM: Emergence of a novel swine-origin influenza A (H1N1) virus in humans. The New England Journal ofMedicine 2009, 360(25):2605-2615.2. Woo PC: Swine influenza: then and now. Hong Kong Medical Journal 2009,15(3):166-167.3. Chan MC, Chan RW, Yu WC, Ho CC, Yuen KM, Fong JH, Tang LL, Lai WW,Lo AC, Chui WH, et al: Tropism and innate host responses of the 2009pandemic H1N1 influenza virus in ex vivo and in vitro cultures ofhuman conjunctiva and respiratory tract. The American Journal ofPathology 2010, 176(4):1828-1840.4. 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Journal of Infectious Diseases 2010, 201(3):346-353.doi:10.1186/1465-9921-11-147Cite this article as: Lee et al.: Systems-level comparison of hostresponses induced by pandemic and seasonal influenza A H1N1 virusesin primary human type I-like alveolar epithelial cells in vitro. RespiratoryResearch 2010 11:147.Lee et al. Respiratory Research 2010, 11:147http://respiratory-research.com/content/11/1/147Page 9 of 9

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