Common gene expression profile in response to the mucus layer contact.

<p>Genes showing increased expression in both <i>E. histolytica</i> HM1:IMSS and Rahman during contact with the human colon.</p><p>FC: Fold Change; BF: Bonferroni adjusted p value≤0.05.</p

Classification of modulated transcripts into functional categories.

<p>Proteins were annotated according to Pathema and NCBI databases web sites.</p

Schematic of <i>Entamoeba histolytica</i> activities leading to mucus layer depletion and invasion of the human colon.

<p>During its vegetative life style (A), <i>E. histolytica</i> exploits lipids (from lipid-rich food particles, bacteria, and shed epithelial cells) and carbohydrates (undigested glycan-rich food particles provided by the bolus or shed mucus fragment) present in the colonic environment. (B) When dietary polysaccharides are scarce, we hypothesize that <i>E. histolytica</i> turns to host mucus by first deploying a set of polysaccharide hydrolases that depletes the protective oligosaccharide side chains of mucin which can be then targeted by cysteine proteases leading to the depletion of the protective mucus barrier and allowing subsequent invasion of the mucosa. This adaptive foraging could reflect the coevolved functional versatility of <i>E. histolytica</i> glycobiome and the structural diversity of host mucus glycans involved in the interaction.</p

Human colon explants incubated with <i>E. histolytica</i> HM1:IMSS or Rahman trophozoites.

<p>Longitudinal tissue sections of colon explants incubated during 1 or 7<i>E. histolytica</i> HM1:IMSS or Rahman trophozoites. The upper panel (A) corresponds to the alcian blue staining of the mucus in the top followed by staining of the tissue where the epithelial cells and the crypts of Liberkün (counterstain in red with Safranin) are visible. The lower panel (B) corresponds to immunohistochemistry revealing the presence of trophozoites in the top by immunostaining for the Gal/GalNAc lectin and the tissue by counterstaining with Hematoxylin/Eosin (bleu). Note the presence of Rahman trophozoites on top of the mucus layer even after 7 h of incubation and the massive destruction of the mucosa in the presence of HM1:IMSS. Scale bar = 50 µm.</p

Transcriptomic landscape describing the virulent and non-virulent signatures of <i>E. histolytica</i>.

<p>The scheme summarizes the transcriptomic map of <i>E. histolytica</i> highlighting two categories of genes: those permanently expressed in each strain and those overexpressed when amoebas are in contact with human colon explants. The signature of HM1:IMSS is on the left and the Rahman non-virulent signature is on the right. Central in the scheme are the genes common to the two strains and only upregulated when the parasites are in contact with the mucus. The adhesion-cell surface molecules are depicted in green; proteases in black; carbohydrates metabolism in red; lipid metabolism in purple. Only the most striking differences were highlight in this figure, others categories are described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003824#ppat-1003824-t002" target="_blank">tables 2</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003824#ppat-1003824-t003" target="_blank">3</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003824#ppat-1003824-t004" target="_blank">4</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003824#ppat-1003824-t005" target="_blank">5</a>, and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003824#ppat-1003824-t006" target="_blank">6</a>.</p

Summary of the microarray data.

<p>The transcriptomic modulations obtained in the 4 comparisons. In total, 614 transcripts with a fold change greater than two were significantly modulated (Bonferroni adjusted p-value<0.05).</p

The <i>E. histolytica</i> HM1: IMSS ubiquitous gene expression profile.

<p>Genes showing increased expression in <i>E. histolytica</i> HM1:IMSS compared to Rahman both in culture and during contact with the human colon.</p><p>FC: Fold Change; BF: Bonferroni adjusted p value≤0.05.</p

Experimental design and strategy for microarray data analysis.

<p>A. Scheme representing the four experimental conditions and transcriptome comparisons. B. Cross-comparative analysis accomplished to identify strain-specific and common responses under the two conditions tested. The transcriptome data were processed as indicated in order to identify gene expression profiles associated with the strain and the colon explant contact. A/B designates the pool of genes overexpressed in condition A compared to condition B. + means that the common overexpressed genes of the comparisons are kept, whereas - indicates genes that were discarded. Note that the profiles obtained by this strategy are composed of genes with increase transcript levels in a particular strain versus the other.</p

Results of the Principal Component Analysis.

<p>The figure represents the projection of the 48 arrays on the first three Principal Components. The sum of these principal three axes corresponds to 64.5% of the total variance. The representation corresponds to: The Rahman strain in contact with mucus (Red), Rahman strain in axenic culture (Blue), HMI:IMSS strain in contact with mucus (Green), and HMI:IMSS strain in axenic culture (Purple).</p

Enzymes overexpressed and involved in carbohydrate metabolism specific to the virulent HM1:IMSS strain.

<p>Genes involved in glycan metabolism with significant and specific overexpression in HM1:IMSS are shown in green. The genes were chosen according to a Bonferroni adjusted p value≤0.05 and without fold change cutoff (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003824#ppat.1003824.s011" target="_blank">Table S9</a>).</p