Gene Expression Profiling Specifies Chemokine, Mitochondrial and Lipid Metabolism Signatures in Leprosy

<div><p>Herein, we performed microarray experiments in Schwann cells infected with live <i>M. leprae</i> and identified novel differentially expressed genes (DEG) in <i>M. leprae</i> infected cells. Also, we selected candidate genes associated or implicated with leprosy in genetic studies and biological experiments. Forty-seven genes were selected for validation in two independent types of samples by multiplex qPCR. First, an <i>in vitro</i> model using THP-1 cells was infected with live <i>Mycobacterium leprae</i> and <i>M. bovis</i> bacillus Calmette-Guérin (BCG). In a second situation, mRNA obtained from nerve biopsies from patients with leprosy or other peripheral neuropathies was tested. We detected DEGs that discriminate <i>M. bovis</i> BCG from <i>M. leprae</i> infection. Specific signatures of susceptible responses after <i>M. leprae</i> infection when compared to BCG lead to repression of genes, including <i>CCL2</i>, <i>CCL3</i>, <i>IL8</i> and <i>SOD2</i>. The same 47-gene set was screened in nerve biopsies, which corroborated the down-regulation of <i>CCL2</i> and <i>CCL3</i> in leprosy, but also evidenced the down-regulation of genes involved in mitochondrial metabolism, and the up-regulation of genes involved in lipid metabolism and ubiquitination. Finally, a gene expression signature from DEG was identified in patients confirmed of having leprosy. A classification tree was able to ascertain 80% of the cases as leprosy or non-leprous peripheral neuropathy based on the expression of only <i>LDLR</i> and <i>CCL4</i>. A general immune and mitochondrial hypo-responsive state occurs in response to <i>M. leprae</i> infection. Also, the most important genes and pathways have been highlighted providing new tools for early diagnosis and treatment of leprosy.</p></div

Clustering of differentially expressed genes in nerve biopsies of leprosy and non-leprous patients peripheral neuropathy.

<p>The left graph displays a dendrogram representing the 1D clusterization of genes and the 2D map corresponding to the levels of standardized gene expression profiles (z-score), while the graph on the right displays the three significant clusters (pink, blue and yellow). Red dotted lines in the dendrogram (up-left) indicate weak unions, discouraged by the Bayesian clustering analysis. Values represented in the dendrogram branches correspond to log-odds of the union of corresponding branches. Gray lines in the graphs on the right indicate gene z-scores on leprosy and non-leprous samples, while black solid and dotted lines represent the mean and CI95% of the mean for all genes belonging to each cluster, respectively. Solid pink, blue and yellow lines indicate the mean of all genes in all samples belonging to the leprosy and non-leprous groups.</p

Gene expression from nerve biopsies from leprosy and non-leprous patients with peripheral neuropathy.

<p>Among the 47-gene set only genes that showed at least a suggestive result (n = 15) are presented. Two-tailed levels of significance less than or equal to 0.01 (**), 0.05 (*) and 0.1 (^.) were considered as “highly significant”, “significant”, and “suggestive”, respectively. A total of 50 samples non-leprous patients (white columns) and 35 samples from leprosy samples (black columns).</p

Discrimination between leprosy and non-leprous patients with peripheral neuropathy by combination of LDLR and CCL4 expression.

<p>Graph of a trained classification tree, where rounded rectangles represent internal nodes and hexagons represent terminal nodes. Percentages in each node represent the proportion of specified observations in each group.</p