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

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