Comparison of whole blood and spleen transcriptional signatures over the course of an experimental malaria infection

Abstract

Although the spleen is broadly accepted as the major lymphoid organ involved in generating immune responses to the erythrocytic stages of the malaria parasite, Plasmodium, human splenic tissue is not readily available in most cases. As a result, most studies of malaria in humans rely on peripheral blood to assess cellular immune responses to malaria. The suitability of peripheral blood as a proxy for splenic immune responses is however unknown. Here, we have simultaneously analysed the transcriptomes of whole blood and spleen over 12 days of erythrocytic stage Plasmodium chabaudi infection in C57BL/6 mice. Using both unsupervised and directed approaches, we compared gene expression between blood and spleen over the course of infection. Taking advantage of publicly available datasets, we used machine learning approaches to infer cell proportions and cell-specific gene expression signatures from our whole tissue transcriptome data. Our findings demonstrate that spleen and blood are quite dissimilar, sharing only a small amount of transcriptional information between them, with transcriptional differences in both cellular composition and transcriptional activity. These results suggest that while blood transcriptome data may be useful in defining surrogate markers of protection and pathology, they should not be used to predict specific immune responses occurring in lymphoid organs.

Transcriptome analysis of blood and spleen in virulent and avirulent mouse malaria infection

“…Time-series gene expression analysis is most helpful in identifying genes with transient expression changes and in investigation of gene regulation profiles during an infection. In our previous studies, we showed that pathology signatures can be picked up from blood transcriptome and they are quite distinct in the avirulent P. chabaudi AS or virulent P. chabaudi CB infection 8 ; further analysing the blood and spleen transcriptome from the avirulent P. chabaudi AS infection, we identified only a small set of immune genes shared between them 14 . Here we report a new dataset of spleen transcriptome from the virulent P. chabaudi CB infection, which were collected from the same mice as the published blood transcriptome 8 .…”

“…1 . These methods are expanded versions of descriptions in our related studies 8 , 14 . Female C57BL/6 mice aged between 6–8 weeks were injected intraperitoneally with 10 5 infected red blood cells of P. chabaudi AS or CB strain.…”

“…Therefore, it is very important to understand whether the immune responses detected in the blood serve as a reliable proxy for immune responses occurring in the spleen; if so, to what extent and at which stage of infection are they most closely related. To date, few studies have performed transcriptomic analyses of the blood in the mouse model 9 and only one study carried out by us attempted to investigate the similarities between blood and spleen transcriptome 14 .…”

“…Here we report a new dataset of spleen transcriptome from the virulent P. chabaudi CB infection, which were collected from the same mice as the published blood transcriptome 8 . Our datasets, including the published PcAS/PcCB blood 8 , PcAS spleen 14 and this new PcCB spleen transcriptome, offer a unique possibility to identify the complete set of activated or suppressed genes during an acute blood stage infection, to infer their rates of change and their causal effects. Further, it would be of high interest to investigate whether the interaction between blood and spleen differ in these two infections or whether more subtle relationship can be unearthed using more elaborate time modeling methods.…”

“…Gene expression data were deposited at the Gene Expression Omnibus database (GEO) under the following accession numbers: GSE93631 19 (AS and CB blood) and GSE123391 20 (AS spleen) which were published previously 8 , 14 ; GSE145781 21 (CB spleen) and GSE145634 22 (the raw data of parasite RNA experiment) which were new datasets.…”