Table 3.

Gene expression studies informing understanding of naturally acquired immunity to malaria infection

Measure of NAI	Publication	Design	Sample	Species	Subjects for comparison		Key finding	Comment
Prior exposure to malaria	Tran et al. (2016)	Comparison of GEP changes from paired infected and uninfected samples	Whole blood	P. falciparum	Malaria-naïve, symptomatic Dutch CHMI volunteers at diagnosis (n = 5)	Malaria experienced Malian children (> 13 years) and adults infected in the field (n = 8)	Graded activation of pathways of downstream proinflammatory cytokines with highest activation in malaria-naive subjects and significantly reduced activation in malaria experienced Malians
	Ockenhouse et al. (2006)	Comparison of GEP changes in infection-controls samples US malaria naïve subjects	PBMC	P. falciparum	US malaria-naïve CHMI volunteers with early, blood-stage infection (n = 22)	Malaria-experienced Cameroonian adults presenting with naturally acquired febrile malaria (n = 15)	Similar induction of pro-inflammatory cytokines seen between pre-symptomatic and symptomatic individuals regardless of prior malaria exposure
	Rojas-Pena et al. (2015) and Vallejo et al. (2018)	Comparison of GEP changes from paired infected and uninfected samples	Whole blood	P. vivax	Columbian malaria-naïve (MN) CHMI volunteers at diagnosis (n = 7)	Columbian malaria-exposed (ME) CHMI volunteers at diagnosis (n = 9)	Little differentiation seen between MN and ME populations by Rojas-Penas et al. However network co-expression analysis by Vallejo et al. showed the inflammatory response was attenuated in ME volunteers with decreased class II antigen presentation in dendritic cells	No significant difference between groups for pre-patent period or parasitaemia at diagnosis suggesting there may have been no difference in functional immunity between groups
	Jagannathan et al. (2014)	Comparison of GEP between groups	Vδ2+ T cells	P. falciparum	Ugandan children with low prior malaria incidence (n = 4)	Ugandan children with low prior malaria incidence (n = 4)	Comparison of basal gene expression patterns of sorted, un-stimulated Vδ2+ T cells identified 48 differentially expressed genes, many with known roles in immunomodulation. For each of these genes, expression was higher among children with high prior exposure to malaria	Data suggest recurrent malaria infection causes up-regulation of immunoregulatory pathways that dampen the pro-inflammatory immune response to P. falciparum infection and help explain immunological tolerance to the parasite
Symptoms at diagnosis	Tran et al. (2016)	Comparison of GEP changes from paired infected and uninfected samples	Whole blood	P. falciparum	Malaria experienced Malian children (> 13 years) and adults infected in the field and asymptomatic at diagnosis (EA, n = 5)	Malaria experienced Malian children (> 13 years) and adults infected in the field and symptomatic with fever at the time of diagnosis (EF, n = 3)	Only 70 differentially expressed genes (DEGs) were identified between these groups despite the apparent clinical differences	2 of the 5 individuals in the EA group progressed to febrile malaria within 5 days of initial diagnosis by PCR
Disease severity	Krupka et al. (2012)	Comparison of GEP in same subjects at diagnosis with severe and subsequent mild malaria	Whole blood	P. falciparum	Malawian children who, after presenting with severe malaria (all had cerebral malaria), were found to have mild malaria one month later on screening by blood smear (n = 5)		Pathway analysis showed relative up regulation of Type I IFN signaling pathway, regulation of inflammation, regulation of leukocyte proliferation and T cell activation in episodes of mild malaria
	Boldt et al. (2019)	Comparison of GEP between groups	Whole blood	P. falciparum	Healthy uninfected Gabonese children	Gabonese children with asymptomatic parasitaemia, mild malaria, malaria with severe anaemia and cerebral anaemia (0.5–6 years)	GEP of 22 genes significantly differed among groups. Immunoglobulin production, complement regulation and IFN beta signaling were most conspicuous

PBMC peripheral blood mononuclear cells, GEP gene expression profile, CHMI controlled human malaria infection