Simultaneous Host and Parasite Expression Profiling Identifies Tissue-specific Transcriptional Programs Associated with  Susceptibility or Resistance to Cerebral Malaria

Fiona E Lovegrove^[1,†], Lourdes Peña-Castillo^[2,†], Naveed Mohammad^[2], W Conrad Liles^[1,4], Timothy R Hughes^[2,3,4] and Kevin C Kain^[1,4,*]

• Abstract

The development and outcome of cerebral malaria (CM) reflects a complex interplay between parasite-expressed virulence factors and host response to infection. To simultaneously analyze transcriptional programs in both parasite and host over the course of infection, we created microarrays to concurrently detect transcripts in the genomes of both Plasmodium berghei and mouse.

Analysis of RNA from brain, lung, liver, and spleen of mice infected with P. berghei ANKA showed that parasite gene expression is readily detected in whole organ RNA. Comparison of CM-susceptible (C57BL/6) and CM-resistant (BALB/c) mice showed that both host and parasite display distinct organ-specific transcriptional signatures in susceptible versus resistant animals. 

Host genes whose expression differs between CM-resistant and CM-susceptible mice, at either baseline or induced by infection, tend to relate to humoral and immune response, complement activation, or cell-cell interactions, suggesting differences in immune function that may directly underlie protection from or susceptibility to CM. 

P. berghei, in contrast, displayed differential expression of genes related to apparent biosynthestic activities, with the majority of transcriptional activity observed in the lung. 

These data show that analysis of host and parasite gene expression profiles by hybridizing infected host samples to a single microarray is feasible, and can facilitate dissection of complex host-pathogen interactions.

• Manuscript

• Full paper
• Figure 1 (pdf) (eps)
• Microarray probe specificity
• Figure 2 (pdf) (eps)
• Overview of mouse and malaria gene expression in all organs
• Figure 3 (pdf) (eps)
• Differentially expressed mouse genes
• Figure 4 (pdf) (eps)
• A network of mouse genes differentially expressed at day 0 in liver
• Figure 5 (pdf) (eps)
• Differentially expressed malaria genes
• Figure 6 (pdf) (eps)
• Gene groups previously implicated in host response to malaria with significant enrichment of genes selected by the linear model
• All Figures in a Single File (pdf) (ps)

• Supplementary Material

• Additional file 1: Significant PPI Networks
• Additional file 2: Significant Pathways
• Additional file 3: Correlation between RT-PCR and microarray intensity data
• Additional file 4:  Figure 1 Supplementary (pdf) (ps) 
• Gene groups previously implicated in host response to malaria without significant enrichment of genes selected by the linear model
• Additional file 5: Figure 2 Supplementary (pdf) (eps)
• PbA gene groups potentially involved in malaria pathogenesis
• PCR Primers

• Microarray Experiment Information

• Experiment design
• Samples used, extract preparation and labelling
• Hybridization procedures and parameters
• Data extraction, normalization and statistical analysis
• Array design
• Probe description
• The annotation table contains probe sequences, columns listing the closest ENSEMBL, Refseq; GenBank description, GO-BP annotations, Domain (most significant), Protein annotations.

• Data:
• Raw data (GPR Files output by GenePix 3.0)
• Normalized Data per probe (log2 scale) (tab-delimited text file)
• Normalized Data per probe for Slide 003 (log2 scale) (tab-delimited text file)
• Normalized Data (averaged per gene, log2 scale)
• P-values Day 0
• P-values Responding Infection

• Figure Data

• Figure 1 (text data) (Excel file): 
• Cumulative distribution of normalized log2 intensites for probe specificity hybridization test.
• Figure 2-B (text data): 
• Median-subtracted normalized log2 intensity of top 2159 highly-expressed malaria genes
• Figure 2-A (text data): 
• Median-subtracted normalized log2 intensity of top 2268 highly-expressed mouse genes
• Figure 3 (text data) (Excel file): 
• -log10 of pvalues, normalized log2 ratios, median-subtracted normalized log2 intensity of differentially expressed mouse genes (baseline and over the infection).
• Figure 5 (text data) (Excel file): 
• normalized log2 ratios, median-subtracted normalized log2 intensity of differentially expressed malaria genes (over the infection).