Table 1.
Summary of gene expression datasets investigating the human immunological response to malaria infection
| GEO series | Title of dataset | Publication | Design | Infection/antigenic Stimulation | Species | Tissue | Age | Participant origin | Expression profiling | Subjects (samples)a | Controls | Platform name | Platform technology |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GSE2900 | Host response malaria | Griffiths et al. (2005) | Comparison of GEP in febrile children with convalescent samples 2 weeks post discharge | Field | P. falciparum | Whole blood: PAX gene | Children 2–126 months | Kenya | Array | 22 (28) | Subject paired samples: diagnosis and post treatment | LC-36 | Spotted DNA/cDNA |
| GSE5418 | Gene expression analysis in malaria infection | Ockenhouse et al. (2006) | Comparison of GEP in early, pre-symptomatic blood-stage infection post CHMI with symptomatic malaria-experienced adults with naturally acquired malaria | CHMI and Field | P. falciparum | PBMC | Adults; 19–49 years | USA and Cameroon | Array | 37 (74) | 22 un-infected malaria-naïve American adults | Affymetrix human genome U133A array | In situ oligonucleotide |
| GSE15221 | Malaria primes the innate immune response due to IFNγ induced enhancement of Toll-like receptor expression and function | Franklin et al. (2009) and Sharma et al. (2011) and Hirako et al. (2018) | Comparison GEP at malaria diagnosis and 28 days post treatment | Field | P. falciparum | PBMC | Adults 30 ± 10 years | Brazil; Porto Velho | Array | 21 (42) | Subject paired samples: diagnosis and post treatment | Illumina human-6 v2.0 | Oligonucleotide beads |
| GSE26876 | Time kinetics of gene expression in NK92 cells after P. falciparum-iRBC encounter | De 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 0 | In vitro—iRBC | P. falciparum | NK92 cell line | N/A | N/A | Array | N/A (12) | Paired samples: pre and post exposure | Affymetrix human gene 1.0 ST array | In situ oligonucleotide |
| GSE33811 | Paired whole blood human transcription profiles from children with severe malaria and mild malaria | Krupka et al. (2012) | Comparison of GEP in severe malaria and subsequent mild malaria in same subjects 1 month later | Field | P. falciparum | Whole blood: tri-reagent BD | Children: 8–45 months | Malawi | Array | 5 (10) | Subject paired samples: severe and mild malaria | Affymetrix Human Gene 1.0 ST Array | In situ oligonucleotide |
| GSE34404 | The genomic architecture of host whole blood transcriptional response to malaria infection | Idaghdour et al. (2012) | Comparison of GEP in mild malaria with age matched un-infected controls | Field | P. falciparum | Whole blood: Tempus | Children; median age 3.7 years | Benin | Array | 94 subjects (94) and 64 controls (64) | Uninfected age matched | Illumina HumanHT-12 V4.0 expression bead chip | Oligonucleotide beads |
| GSE55843 | Loss and dysfunction of Vdelta2 + gamma delta-low T cells is associated with clinical tolerance to malaria | Jagannathan et al. (2014) | Comparison of GEP of Vδ2 + T cells from children with ‘high’ and ‘low’ episodes of malaria in the preceding year | In vitro—iRBC | P. falciparum | Vδ2 + T cells | Children: 4–5 years | Uganda | Array | 78 (156) | N/A | Agilent-039494 SurePrint G3 Human GE v2 8 × 60K Microarray 03938 | In situ oligonucleotide |
| GSE53292 | Transcriptomic analysis of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected host cell | Jaijyan et al. (2015) | Comparison of GEP of uninfected HepG2 with those infected with wild-type and knock out sporozoites | In vitro—sporozoites | P. falciparum | HepG2 cells | N/A | N/A | High throughput sequencing | NK | NK | Illumina Genome Analyzer IIx (Homo sapiens) | High-throughput sequencing |
| GSE50957 | Molecular hallmarks of experimentally acquired immunity to malaria [Pilot Study] | Tran et al. (2016) and Vallejo et al. (2018) | Comparison of GEP pre and post infection | CHMI | P. falciparum | Whole blood: PAX gene | Adults: 19–22 years | USA | High throughput sequencing | 5 (10) | Subject paired samples: Pre and post infection | Illumina HiSeq 2000 (Homo sapiens) | High-throughput sequencing |
| GSE52166 | Molecular hallmarks of naturally acquired immunity to malaria | Tran et al. (2016) | Comparison of GEP pre and post infection | Field | P. falciparum | Whole blood: Tempus | Adults and Children 13.5–23.3 years | Malawi | High throughput sequencing | 8 (16) | Paired same subject pre infection | Illumina HiSeq 2000 (Homo sapiens) | High-throughput sequencing |
| GSE64338 | Expression 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 later | Field | P. falciparum | Whole blood: Tri-Reagent BD | Adults | Rwandan | Array | 19 (38) | Subject paired samples: diagnosis and post treatment | [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array | In situ oligonucleotide |
| GSE64493 | FCRL5 delineates functionally impaired memory B cells associated with malaria exposure | Sullivan (2015) | Comparison of GEP between classical and atypical memory B cells in Uganda children | Field | P. falciparum | PBMC | Children 8–10 years | Uganda | Array | 12 | NK | Agilent-039494 SurePrint G3 Human GE v2 8 × 60K Microarray 039381 | In situ oligonucleotide |
| GSE67184 | Transcription profiling of malaria-naïve and semi-immune colombian volunteers in a Plasmodium vivax sporozoite challenge | Rojas-Penas (2015), Vallejo (2018) and Gardinassi (2018) | Comparison of GEP changes between malaria naïve and semi-immune adults pre-infection and at diagnosis | CHMI | P. vivax | Whole blood: Tempus | Adults | Columbia | High throughput sequencing | 12 (24) | Subject paired samples: pre-infection and diagnosis | Illumina HiSeq 2500 (Homo sapiens) | High-throughput sequencing |
| GSE67469 | Transcription profiling of malaria-naïve and semi-immune colombian volunteers in a Plasmodium vivax sporozoite challenge | Rojas-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 4 | CHMI | P. vivax | Whole blood: Tempus | Adults | Columbia | RT-qPCR | 16 (85) | Subject paired samples: Pre infection and multiple time-points post infection | Fluidigm 96×96 nanofluidic arrays for 96 genes: blood informative transcripts | RT-PCR |
| GSE7586 | Genome wide analysis of placental malaria | Muehlenbachs (2007) | Comparison of GEP in women with placental malaria and those without | Field | P. falciparum | Placenta | Adults | Tanzania | Array | 20 (20) | NK | [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array | In situ oligonucleotide |
| GSE77122 | Involvement of β-defensin 130 (DEFB130) in the macrophage microbicidal mechanisms for killing Plasmodium falciparum | Terkawi (2017) | Human monocyte-derived macrophages were co-cultured with P. falciparum iRBCs, saponin-treated iRBCs, or non-infected RBCs | In vitro—iRBC | P. falciparum | Macrophages | NK | NK | Array | NK (8) | NK | Agilent-028004 SurePrint G3 Human GE 8 × 60K Microarray | In situ oligonucleotide |
| GSE93664 | Comparison of the transcriptomic profile of P. falciparum reactive polyfunctional and IFNγ monofunctional human CD4 T cells | Burel (2017) | Comparison of GEP in monofunctional and polyfunctional IFN producing T cells collected 21 days post CHMI infection | CHMI + in vitro—iRBC | P. falciparum | IFN producing T cells | 18–42 years | Australia | Array | 8 (2) | NK | [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array | In situ oligonucleotide |
| GSE100562 | RNA-sequencing analysis of response to P. falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso | Quin (2017) | Comparison of GEP in onocytes and CD14− cells in P. falciparum infected and uninfected malaria-exposed Fulani and Mossi sympatric ethnic groups | Field | P. falciparum | Monocytes (CD14+) and lymphocytes (CD14−) | 15–24 years | Burkino Faso | High throughput sequencing | 23 (23) | NK | Illumina HiSeq 2500 (Homo sapiens) | High-throughput sequencing |
| GSE1124 | Whole blood transcriptome of childhood malaria | Boldt (2019) | Comparison of GEP of children with asymptomatic parasitemia, uncomplicated malaria, malaria with severe anaemia and cerebral malaria | Field | P. falciparum | Whole blood: PAX gene | 0.5–6 years | Gabon | Array | NK | Healthy control children | [HG-U133A] Affymetrix Human Genome U133A Array | In situ oligonucleotide |
| GSE114076 | Differential gene expression profile of human neutrophils cultured with Plasmodium falciparum-parasitized erythrocytes | Terkawi (2018) | Comparison of GEP in neutrophils incubated with iRBC or non-infected RBC | In vitro—iRBC | P. falciparum | Neutrophils | NK | NK | Array | 1 (8) | Culture with non-infected RBC | Agilent-072363 SurePrint G3 Human GE v3 8 × 60K Microarray | In situ oligonucleotide |
| GSE97158 | Transcriptional responses induced by controlled human malaria infection (CHMI) | Rothan (2018) | Comparison of GEP in whole blood pre and post sporozoite CHMI in malaria exposed adults | CHMI | P. falciparum | Whole blood: PAX gene | Adults | Tanzania | High throughput sequencing | 10 (40) | Subject paired samples: pre and post CHMI | Illumina HiSeq 2000 (Homo sapiens) | High-throughput sequencing |
| GSE65928 | Malaria-associated atypical memory B cells exhibit markedly reduced B cell receptor signaling and effector function | Portugal (2015) | Comaprison of GEP of naïve B cells, classical and atypical memory B cells in immune adults | Field | P. falciparum | B cells | Adults: 18–37 years | Mali | Array | 20 (20) | US healthy adults | [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version] | In situ oligonucleotide |
| GSE72058 | Activated neutrophils are associated with pediatric cerebral malaria vasculopathy in Malawian children | Feintuch (2016) | Comparison of GEP in cerebral malaria between children with malaria retinopathy and those without | Field | P. falciparum | Whole blood: Tri-Reagent BD | Children 6 month–12 years | Mali | Array | 98 (98) | NK | [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] | In situ oligonucleotide |
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
aSamples analysed for publication