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Table 1 Summary of gene expression datasets investigating the human immunological response to malaria infection

From: Use of gene expression studies to investigate the human immunological response to malaria infection

GEO seriesTitle of datasetPublicationDesignInfection/antigenic StimulationSpeciesTissueAgeParticipant originExpression profilingSubjects (samples)aControlsPlatform namePlatform technology
GSE2900Host response malariaGriffiths et al. (2005)Comparison of GEP in febrile children with convalescent samples 2 weeks post dischargeFieldP. falciparumWhole blood: PAX geneChildren 2–126 monthsKenyaArray22 (28)Subject paired samples: diagnosis and post treatmentLC-36Spotted DNA/cDNA
GSE5418Gene expression analysis in malaria infectionOckenhouse et al. (2006)Comparison of GEP in early, pre-symptomatic blood-stage infection post CHMI with symptomatic malaria-experienced adults with naturally acquired malariaCHMI and FieldP. falciparumPBMCAdults; 19–49 yearsUSA and CameroonArray37 (74)22 un-infected malaria-naïve American adultsAffymetrix human genome U133A arrayIn situ oligonucleotide
GSE15221Malaria primes the innate immune response due to IFNγ induced enhancement of Toll-like receptor expression and functionFranklin et al. (2009) and Sharma et al. (2011) and Hirako et al. (2018)Comparison GEP at malaria diagnosis and 28 days post treatmentFieldP. falciparumPBMCAdults 30 ± 10 yearsBrazil; Porto VelhoArray21 (42)Subject paired samples: diagnosis and post treatmentIllumina human-6 v2.0Oligonucleotide beads
GSE26876Time kinetics of gene expression in NK92 cells after P. falciparum-iRBC encounterDe Carvalho et al. (2011)Comparison of GEP variation of NK92 cells after 6, 12, and 24 h of co-culture with either infected or uninfected RBC compared to time-point 0In vitro—iRBCP. falciparumNK92 cell lineN/AN/AArrayN/A (12)Paired samples: pre and post exposureAffymetrix human gene 1.0 ST arrayIn situ oligonucleotide
GSE33811Paired whole blood human transcription profiles from children with severe malaria and mild malariaKrupka et al. (2012)Comparison of GEP in severe malaria and subsequent mild malaria in same subjects 1 month laterFieldP. falciparumWhole blood: tri-reagent BDChildren: 8–45 monthsMalawiArray5 (10)Subject paired samples: severe and mild malariaAffymetrix Human Gene 1.0 ST ArrayIn situ oligonucleotide
GSE34404The genomic architecture of host whole blood transcriptional response to malaria infectionIdaghdour et al. (2012)Comparison of GEP in mild malaria with age matched un-infected controlsFieldP. falciparumWhole blood: TempusChildren; median age 3.7 yearsBeninArray94 subjects (94) and 64 controls (64)Uninfected age matchedIllumina HumanHT-12 V4.0 expression bead chipOligonucleotide beads
GSE55843Loss and dysfunction of Vdelta2 + gamma delta-low T cells is associated with clinical tolerance to malariaJagannathan et al. (2014)Comparison of GEP of Vδ2 + T cells from children with ‘high’ and ‘low’ episodes of malaria in the preceding yearIn vitro—iRBCP. falciparumVδ2 + T cellsChildren: 4–5 yearsUgandaArray78 (156)N/AAgilent-039494 SurePrint G3 Human GE v2 8 × 60K Microarray 03938In situ oligonucleotide
GSE53292Transcriptomic analysis of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected host cellJaijyan et al. (2015)Comparison of GEP of uninfected HepG2 with those infected with wild-type and knock out sporozoitesIn vitro—sporozoitesP. falciparumHepG2 cellsN/AN/AHigh throughput sequencingNKNKIllumina Genome Analyzer IIx (Homo sapiens)High-throughput sequencing
GSE50957Molecular hallmarks of experimentally acquired immunity to malaria [Pilot Study]Tran et al. (2016) and Vallejo et al. (2018)Comparison of GEP pre and post infectionCHMIP. falciparumWhole blood: PAX geneAdults: 19–22 yearsUSAHigh throughput sequencing5 (10)Subject paired samples: Pre and post infectionIllumina HiSeq 2000 (Homo sapiens)High-throughput sequencing
GSE52166Molecular hallmarks of naturally acquired immunity to malariaTran et al. (2016)Comparison of GEP pre and post infectionFieldP. falciparumWhole blood: TempusAdults and Children 13.5–23.3 yearsMalawiHigh throughput sequencing8 (16)Paired same subject pre infectionIllumina HiSeq 2000 (Homo sapiens)High-throughput sequencing
GSE64338Expression data from whole blood samples of Rwandan adults with mild malaria with matched sample 30 days later (convalescence)Subramaniam et al. (2015)Comparison of GEP in mild malaria and 30 days laterFieldP. falciparumWhole blood: Tri-Reagent BDAdultsRwandanArray19 (38)Subject paired samples: diagnosis and post treatment[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST ArrayIn situ oligonucleotide
GSE64493FCRL5 delineates functionally impaired memory B cells associated with malaria exposureSullivan (2015)Comparison of GEP between classical and atypical memory B cells in Uganda childrenFieldP. falciparumPBMCChildren 8–10 yearsUgandaArray12NKAgilent-039494 SurePrint G3 Human GE v2 8 × 60K Microarray 039381In situ oligonucleotide
GSE67184Transcription profiling of malaria-naïve and semi-immune colombian volunteers in a Plasmodium vivax sporozoite challengeRojas-Penas (2015), Vallejo (2018) and Gardinassi (2018)Comparison of GEP changes between malaria naïve and semi-immune adults pre-infection and at diagnosisCHMIP. vivaxWhole blood: TempusAdultsColumbiaHigh throughput sequencing12 (24)Subject paired samples: pre-infection and diagnosisIllumina HiSeq 2500 (Homo sapiens)High-throughput sequencing
GSE67469Transcription profiling of malaria-naïve and semi-immune colombian volunteers in a Plasmodium vivax sporozoite challengeRojas-Penas (2015)Comparison of GEP changes between malaria naïve and semi-immune adults over the time-course of malaria infection: pre-infection, day 5, day 7, day 9, diagnosis and month 4CHMIP. vivaxWhole blood: TempusAdultsColumbiaRT-qPCR16 (85)Subject paired samples: Pre infection and multiple time-points post infectionFluidigm 96×96 nanofluidic arrays for 96 genes: blood informative transcriptsRT-PCR
GSE7586Genome wide analysis of placental malariaMuehlenbachs (2007)Comparison of GEP in women with placental malaria and those withoutFieldP. falciparumPlacentaAdultsTanzaniaArray20 (20)NK[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 ArrayIn situ oligonucleotide
GSE77122Involvement of β-defensin 130 (DEFB130) in the macrophage microbicidal mechanisms for killing Plasmodium falciparumTerkawi (2017)Human monocyte-derived macrophages were co-cultured with P. falciparum iRBCs, saponin-treated iRBCs, or non-infected RBCsIn vitro—iRBCP. falciparumMacrophagesNKNKArrayNK (8)NKAgilent-028004 SurePrint G3 Human GE 8 × 60K MicroarrayIn situ oligonucleotide
GSE93664Comparison of the transcriptomic profile of P. falciparum reactive polyfunctional and IFNγ monofunctional human CD4 T cellsBurel (2017)Comparison of GEP in monofunctional and polyfunctional IFN producing T cells collected 21 days post CHMI infectionCHMI + in vitro—iRBCP. falciparumIFN producing T cells18–42 yearsAustraliaArray8 (2)NK[HuGene-2_0-st] Affymetrix Human Gene 2.0 ST ArrayIn situ oligonucleotide
GSE100562RNA-sequencing analysis of response to P. falciparum infection in Fulani and Mossi ethnic groups, Burkina FasoQuin (2017)Comparison of GEP in onocytes and CD14− cells in P. falciparum infected and uninfected malaria-exposed Fulani and Mossi sympatric ethnic groupsFieldP. falciparumMonocytes (CD14+) and lymphocytes (CD14−)15–24 yearsBurkino FasoHigh throughput sequencing23 (23)NKIllumina HiSeq 2500 (Homo sapiens)High-throughput sequencing
GSE1124Whole blood transcriptome of childhood malariaBoldt (2019)Comparison of GEP of children with asymptomatic parasitemia, uncomplicated malaria, malaria with severe anaemia and cerebral malariaFieldP. falciparumWhole blood: PAX gene0.5–6 yearsGabonArrayNKHealthy control children[HG-U133A] Affymetrix Human Genome U133A ArrayIn situ oligonucleotide
GSE114076Differential gene expression profile of human neutrophils cultured with Plasmodium falciparum-parasitized erythrocytesTerkawi (2018)Comparison of GEP in neutrophils incubated with iRBC or non-infected RBCIn vitro—iRBCP. falciparumNeutrophilsNKNKArray1 (8)Culture with non-infected RBCAgilent-072363 SurePrint G3 Human GE v3 8 × 60K MicroarrayIn situ oligonucleotide
GSE97158Transcriptional responses induced by controlled human malaria infection (CHMI)Rothan (2018)Comparison of GEP in whole blood pre and post sporozoite CHMI in malaria exposed adultsCHMIP. falciparumWhole blood: PAX geneAdultsTanzaniaHigh throughput sequencing10 (40)Subject paired samples: pre and post CHMIIllumina HiSeq 2000 (Homo sapiens)High-throughput sequencing
GSE65928Malaria-associated atypical memory B cells exhibit markedly reduced B cell receptor signaling and effector functionPortugal (2015)Comaprison of GEP of naïve B cells, classical and atypical memory B cells in immune adultsFieldP. falciparumB cellsAdults: 18–37 yearsMaliArray20 (20)US healthy adults[HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]In situ oligonucleotide
GSE72058Activated neutrophils are associated with pediatric cerebral malaria vasculopathy in Malawian childrenFeintuch (2016)Comparison of GEP in cerebral malaria between children with malaria retinopathy and those withoutFieldP. falciparumWhole blood: Tri-Reagent BDChildren 6 month–12 yearsMaliArray98 (98)NK[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]In situ oligonucleotide
  1. PBMC peripheral blood mononuclear cells, GEP gene expression profile, CHMI controlled human malaria infection, iRBCs infected red blood cells, N/A not applicable, NK not known
  2. aSamples analysed for publication