Schematic representation of the sampling process.

<p>Schematic representation of the sampling process.</p

<i>IFITM3</i> rs12252 genotypic and allelic frequencies among the four groups of patients and its association with hospitalization, assuming a dominant model.

<p><i>IFITM3</i> rs12252 genotypic and allelic frequencies among the four groups of patients and its association with hospitalization, assuming a dominant model.</p

Percentage of C allele carriers (CC or CT genotypes) in the different samples.

General population data are from the European 1000 genomes (Data from [11] were also included).</p

Patients characterization regarding age and gender variables.

<p>Patients characterization regarding age and gender variables.</p

Sample characterization.

<p>Sample characterization.</p

Correlations between CD25^bright/CD4⁺ aTreg frequencies and immunoblot band numbers.

<p>A–C: Bands recognized in immunoblots of HEp2-cytoplasmic proteins by SLE patients, unaffected relatives and unrelated control subjects. D–F: Bands recognized in immunoblots of HEp2-nuclear proteins. Regression lines represent linear regression.</p

Systematic gating for CD25^bright aTregs.

<p>A. First, in order to specify the upper limit of CD25 staining in conventional T-cells for each sample, the ninety-ninth percentile of PE/Cy5 fluorescence intensity within CD4⁻CD45RO⁻ cells (a population containing no Tregs) was determined as gate A. CD4⁺CD25^bright aTregs in the same sample were then quantified as those CD4⁺ cells that exceeded this value at least three-fold (gate B). B–D. The CD25^bright gate (B) contains high proportions of Foxp3+ cells in samples from SLE patients, unaffected relatives and healthy control subjects. As exemplified by an active SLE patient (panel B), an unaffected relative (panel C) and a healthy control subject (panel D), the CD25^bright gate B defined as 3xMFI(gate A) regularly contained 70–90% Foxp3+ cells within CD4+ lymphocytes when additional samples were stained for the same markers as previously but now in combination with intracellular Foxp3 staining.</p

Coreferentialities with CD25^bright/CD4⁺ frequencies.

*<p>Significance according to permutation test (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033992#s4" target="_blank">methods</a>). Effects of bystander coreferentiality were checked for all significant tests (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033992#s4" target="_blank">methods</a>), but rates of simulated bystander data reaching the respective test significance never exceeded 5%.</p

Correlations between aTreg frequencies (CD25^bright/CD4⁺) and quantified SLE-associated specific autoreactive IgG.

<p>A–C: IgG anti-dsDNA. D–F: IgG anti-Sm. Regression lines represent linear regression.</p

Group-wise coreferentialities between CD25^bright/CD4+ aTreg frequencies and <i>IL2RA</i> genetic-effects model scores.

<p>A: SLE patients, B: unaffected relatives, C: unrelated controls. Reactivities to cytoplasmic bands are indicated by filled circles, anti-nuclear reactivities by triangles and anti-brain reactivities by crosses.</p