Mice
Experiments were performed with female Balb/c mice aged 10-12 weeks, which were delivered from the central animal facility of the University of Düsseldorf, where mive were bred under specified pathogen-free conditions. During infection experiments, mice were housed in plastic cages and received a standard diet (Woehrlin, Bad Salzuflen, Germany) and water ad libitum.
Protective vaccination
Vaccination was performed under identical experimental conditions as described previously [8]. The non-infectious vaccine, consisting of erythrocyte ghosts isolated from P. chabaudi-parasitized erythrocytes, was prepared as detailed previously [7, 8, 37]. These membrane ghosts were previously characterized to contain parasite-synthesized proteins [38, 39]. Approximately 106 ghosts suspended in 100 µl Freund’s complete adjuvant (FCA) were subcutaneously injected at weeks 3 and 1 before infection with P. chabaudi blood-stage malaria. In parallel, only FCA was injected in control mice.
Blood-stage malaria of P. chabaudi
P. chabaudi infections were maintained in outbred mice by weekly passages of infected blood under sterile conditions. The non-clonal line of P. chabaudi [40], resembles P. chabaudi AS in terms of restriction fragment length polymorphism as well as dihydrofolate reductase and cysteine protease sequence identities [41]. Moreover, the used line of P. chabaudi is self-healing as the AS clone, which is under control of genes of the H-2 complex and the non-H-2 background as well as sex and sex hormones of the infected mouse strain [42]. The Balb/c mice were infected with 106 P. chabaudi-infected erythrocytes. Parasitaemia was evaluated in Giemsa-stained smears from tail blood and erythrocytes were counted in a Neubauer chamber as described previously [8]. Both groups of vaccinated and non-vaccinated mice contained 4 ‘control’ mice, which were not sacrificed for liver sampling. All 4 mice in the non-vaccinated group succumbed to infection during crisis. In the vaccinated group, however, only 1 mouse succumbed to infection during crisis, whereas 3 mice survived the infection for at least 3 weeks, in accordance with previous results [8].
Liver sampling
To analyze hepatic gene expression during the course of P. chabaudi infections, both vaccinated (V) and non-vaccinated mice (N) were concomitantly infected, and groups of 3 mice were sacrificed at different time points of infections: upon infection on day 0 p.i. (groups Vd0 and Nd0), at early prepatency on day 1 p.i. (groups Vd1 and Nd1), at early patency on day 4 p.i. (groups Vd4 and Nd4) when parasitized erythrocytes begin to appear in peripheral blood with parasitaemias varying between 1-5%, at peak parasitaemia on day 8 p.i. (groups Vd8 and Nd8), and towards the end of the crisis phase on day 11 p.i. (groups Vd11 and Nd11) when parasitemia declined to 5-1%. The course of parasitaemia was previously determined in mice sacrificed in the different groups [43], which corresponded to that in living infected mice under identical experimental conditions [8]. Livers were aseptically removed from sacrificed mice, rapidly frozen in liquid nitrogen and stored at -80o C until use.
RNA isolation
Frozen livers were individually ground in a mortar under liquid nitrogen. Total RNA was isolated from ‘pulverized’ aliquots of each individual liver by the standard Trizol protocol (Qiagen, Hilden, Germany), followed by an additional cleaning up with the miRNeasy Kit (Qiagen). The Agilent 2100 Bioanalyzer platform (Agilent Technologies) was then used to check integrity and quality of RNA. The RIN values of all 30 liver RNA samples ranged between 8.7 and 9.1.
Cy3-Labeling of RNA
Each RNA sample (equivalents of 100 ng) were used to produce Cy3-labeled cRNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s protocol. Yields of cRNA and dye-incorporation were determined with the ND-1000 Spectrophotometer (NanoDrop Technologies). The incorporations ranged between 18 and 23 fmol Cy3/ng cRNA.
Hybridization of Agilent Mouse Whole Genome Oligo Microarrays
Agilent’s 8x60K oligo microarrays (design number 028005) were used, which contained 8 arrays per slide. Each array displayed 39,430 Entrez Gene RNAs. Using the Agilent Gene Expression Hybridization Kit, hybridization was performed according to the Agilent processing protocol (Agilent technologies). Specifically, 600 ng Cy3-labelled fragmented cRNA was hybridized overnight at 65o C using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature and then with the preheated Agilent Gene Expression Wash Buffer 2 at 37o C for 1 min.
Scanning and analyses of microarrays
Microarrays were scanned with the Agilent’s Microarray Scanner System (Agilent Technologies). Microarray image files were processed with the Agilent Feature Extraction Software determining feature intensities (including background substraction), rejecting outliers and calculating statistical confidences of the array spots. All the 30 microarrays were normalized by the quantile method. The expression variance was stabilized through the log2 transform. In-home functions developed in Matlab (MathWorks) were used to construct the heat map of the most highly variable transcripts, the hierarchical clustering dendrograms (calculated using the unweighted pair group method with arithmetic mean and Euclidean distance measure), and the Principal Component Analysis (PCA). The microarray data have been deposited at the NCBI’s Gene Expression Omnibus (GEO) database with accession number GSE129133.
Microarray-based analyses of genes involved in erythropoiesis
The used Agilent’s 8x60K microarrays contain probes for the following genes: Acyp1 (Acylphosphatase 1 erythrocyte isozyme), Add2 (Adducin2), Ahsp (α hemoglobin stabilizing protein), Ank1 (Ankyrin1), Cld13 (Claudin13), Epb4.1 (Erythrocyte membrane protein band 4.1), Ebp4.2 (Erythrocyte membrane protein 4.2), Ebp4.9 (Erythrocyte membrane protein 4.9), Epo (Erythropoietin), Epor (Erythropoietin receptor), Ermap (Erythroblast membrane associated protein), Gata1 (GATA-binding factor 1), Gfi1b (Growth factor independent 1B transcriptional repressor), Gypa (Glycophorin a), Kel (Kell blood group antigen), Klf1 (Krueppel-like factor 1), Rhag (Rh-associated glycoprotein), Rhd (Rh blood group D antigen), Slc4a1 (Solute carrier family 4 member 1 = protein band 3), Spta1 (Spectrin α erythrocytic 1), Sptb (Spectrin β erythrocytic), Tal1 (T-cell acute lymphocytic leukemia protein 1), and Tmod1 (Tropomodulin 1). The expression profiles of these 23 genes were determined from the normalized microarrays prepared from the individual livers of both vaccinated and non-vaccinated mice during infections with P. chabaudi on days 0, 1, 4, 8, and 11 p.i.. Gene expression levels were measured as light intensities by the scanned microarrays, normalized and log2 transformed, and were given as means ± SD as a dispersion metric in all figures. T-test was used to determine statistical significance of differences of gene expression levels between vaccinated and non-vaccinated mice both at a given day p.i. and during the intervals between the different sampling days p.i.. The number of '*’ marks in the figures that appear over interval lines between sampling points or over the sampling points are the number of zeros after the decimal point of the p-values for the statistical significance of the difference in instant of the two series and of the difference between two intervals, respectively.
Quantitative real-time PCR of erythroid genes
High Capacity cDNA Reverse Transcription Kit (Life Technologies) and TaqMan mRNA assays (Life Technologies) were used to perform reverse transcription of mRNAs coding for the following proteins: RHD (assay ID: Mm00456910_m1), ERMAP (Mm_00469273_m1), GATA1 (Mm01352636_m1), SLC4A1 (Mm00441492_m1), CLDN13 (Mm00491038_s1), ADD2 (Mm00478923_m1), ACYP1 (Mm00481325_m1), EPB4.2 (Mm00469111_m1), EPB4.9 (Mm00469121_m1), EPOR (Mm01202755_m1), and EPO (Mm00833882_m1). The TaqMan® gene expression master mix (Life Technologies) was used for PCR reactions according to the instructions given by the manufacturer on a 7900HT real-time PCR System, as previously described [35]. Raw Ct values were calculated using the SDS software v.2.4 with GAPDH for normalization, and the comparative Ct method (2-ΔΔCt) was used to calculate fold change of expression [44]. Statistical significance of corresponding data sets between vaccinated and non-vaccinated mice were analyzed with the two-tailed unpaired heteroskedastic Student´s T-test (*=p-value<0.05).