Naive IgDCD27, IgDCD27, and switched IgDCD27 B cells were sorted from the blood samples of donors 1 and 2

Total RNA from each cell fraction was reverse transcribed and V6 or V3.15 μ or γ transcripts were amplified by PCR, using a seminested strategy (see Materials and methods). The PCR products were labeled by a run-off reaction with specific fluorescent V-FR3 primers, and subjected to electrophoresis on an automated sequencer. The resulting size distribution of the peaks directly reflects the size distribution of H-CDR3 for the given transcripts. Peaks identified by an asterisk were further sequenced to evaluate intrapeak clonal diversity.<p><b>Copyright information:</b></p><p>Taken from "Somatic diversification in the absence of antigen-driven responses is the hallmark of the IgMIgDCD27 B cell repertoire in infants"</p><p></p><p>The Journal of Experimental Medicine 2008;205(6):1331-1342.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2413031.</p><p></p

Serial splenic cryosections were double-labeled either with anti-IgD (green) and anti-CD27 (red) antibodies (A–D) or with anti-IgD (green) and anti-CD1c (red) antibodies (E–H), and then examined under a confocal microscope

CD27 cells (B and D) were present in the MZ corresponding to the outer zone of the IgD-positive ring surrounding the GC (A and C). Boxes with dotted lines in A and B indicate the zone magnified in C and D. A higher level of CD1c expression was observed in the MZ (F), resulting in a yellow appearance in the merged images (G and H), caused by the coexpression of IgD and CD1c at similar intensities. H shows higher magnification of the zone delimited by the box with dotted lines in G. Co, corona. Bars, 50 μm.<p><b>Copyright information:</b></p><p>Taken from "Somatic diversification in the absence of antigen-driven responses is the hallmark of the IgMIgDCD27 B cell repertoire in infants"</p><p></p><p>The Journal of Experimental Medicine 2008;205(6):1331-1342.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2413031.</p><p></p

image_2.tiff

Objective<p>Autoimmune lymphoproliferative syndrome (ALPS) with FAS mutation (ALPS-FAS) is a nonmalignant, noninfectious, lymphoproliferative disease with autoimmunity. Given the central role of natural regulatory T cells (nTregs) in the control of lymphoproliferation and autoimmunity, we assessed nTreg-suppressive function in 16 patients with ALPS-FAS.</p>Results<p>The proportion of CD25^highCD127^low Tregs was lower in ALPS-FAS patients than in healthy controls. This subset was correlated with a reduced CD25 expression in CD3⁺CD4⁺ T cells from ALPS patients and thus an abnormally low proportion of CD25^highFOXP3⁺ Helios⁺ T cells. The ALPS patients also displayed a high proportion of naïve Treg (FOXP3^lowCD45RA⁺) and an unusual subpopulation (CD4⁺CD127^lowCD15s⁺CD45RA⁺). Despite this abnormal phenotype, the CD25^highCD127^low Tregs’ suppressive function was unaffected. Furthermore, conventional T cells from FAS-mutated patients showed normal levels of sensitivity to Treg suppression.</p>Conclusion<p>An abnormal Treg phenotype is observed in circulating lymphocytes of ALPS patients. However, these Tregs displayed a normal suppressive function on T effector proliferation in vitro. This is suggesting that lymphoproliferation observed in ALPS patients does not result from Tregs functional defect or T effector cells insensitivity to Tregs suppression.</p

Relative AID and expression levels were determined for various splenic B cell subsets from different donors

AID and B sequences were amplified by real-time quantitative PCR from cDNA from IgDCD27, IgDCD27 (naive), and IgDCD27 cells purified by two consecutive cell sortings. The results shown were obtained from two independent PCRs (except for D6), each performed in triplicate. The relative expression of AID or in each subset was calculated by the comparative method, normalizing to 1 the expression of AID in the IgDCD27 fraction and of in the naive subset of the 8-mo-old donor (D3). PCRs with a threshold cycle (Ct) >35 were considered NS.<p><b>Copyright information:</b></p><p>Taken from "Somatic diversification in the absence of antigen-driven responses is the hallmark of the IgMIgDCD27 B cell repertoire in infants"</p><p></p><p>The Journal of Experimental Medicine 2008;205(6):1331-1342.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2413031.</p><p></p

(A) Two different marker combinations were used to isolate splenic GC (CD19CD24CD38) and transitional B cells (CD19CD38CD24) or naive IgDCD27, IgDCD27 and switched IgDCD27 B cells

(B) Spectratyping was performed on V3.15 and V6 μ and/or γ transcripts from each cell fraction, as described in the legend of . Peaks identified by an asterisk were further sequenced to evaluate intrapeak clonal diversity.<p><b>Copyright information:</b></p><p>Taken from "Somatic diversification in the absence of antigen-driven responses is the hallmark of the IgMIgDCD27 B cell repertoire in infants"</p><p></p><p>The Journal of Experimental Medicine 2008;205(6):1331-1342.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2413031.</p><p></p

image_1.tiff

Objective<p>Autoimmune lymphoproliferative syndrome (ALPS) with FAS mutation (ALPS-FAS) is a nonmalignant, noninfectious, lymphoproliferative disease with autoimmunity. Given the central role of natural regulatory T cells (nTregs) in the control of lymphoproliferation and autoimmunity, we assessed nTreg-suppressive function in 16 patients with ALPS-FAS.</p>Results<p>The proportion of CD25^highCD127^low Tregs was lower in ALPS-FAS patients than in healthy controls. This subset was correlated with a reduced CD25 expression in CD3⁺CD4⁺ T cells from ALPS patients and thus an abnormally low proportion of CD25^highFOXP3⁺ Helios⁺ T cells. The ALPS patients also displayed a high proportion of naïve Treg (FOXP3^lowCD45RA⁺) and an unusual subpopulation (CD4⁺CD127^lowCD15s⁺CD45RA⁺). Despite this abnormal phenotype, the CD25^highCD127^low Tregs’ suppressive function was unaffected. Furthermore, conventional T cells from FAS-mutated patients showed normal levels of sensitivity to Treg suppression.</p>Conclusion<p>An abnormal Treg phenotype is observed in circulating lymphocytes of ALPS patients. However, these Tregs displayed a normal suppressive function on T effector proliferation in vitro. This is suggesting that lymphoproliferation observed in ALPS patients does not result from Tregs functional defect or T effector cells insensitivity to Tregs suppression.</p

Additional file 1: of Next generation phenotyping using narrative reports in a rare disease clinical data warehouse

Extracted phenotypical concepts per cohort. For each cohort, we list the top50 concepts ranked by Frequency and TF-IDF. The first column is the UMLS code of the phenotypical concepts, the second column is the French preferred terms, the third column is the English preferred terms, the fourth column is the frequencies score (FREQ), the fifth column is the TF-IDF score, the sixth column is the rank of the concept sorted by the frequency score, the seventh column is the rank of the concept sorted by the TF-IDF score and the eighth column is the expert evaluation (1: relevant concept, 0: none relevant concept). (XLS 93 kb

Inherited MST1 Deficiency Underlies Susceptibility to EV-HPV Infections

<div><p>Epidermodysplasia verruciformis (EV) is characterized by persistent cutaneous lesions caused by a specific group of related human papillomavirus genotypes (EV-HPVs) in otherwise healthy individuals. Autosomal recessive (AR) EVER1 and EVER2 deficiencies account for two thirds of known cases of EV. AR RHOH deficiency has recently been described in two siblings with EV-HPV infections as well as other infectious and tumoral manifestations. We report here the whole-exome based discovery of AR MST1 deficiency in a 19-year-old patient with a T-cell deficiency associated with EV-HPV, bacterial and fungal infections. MST1 deficiency has recently been described in seven patients from three unrelated kindreds with profound T-cell deficiency and various viral and bacterial infections. The patient was also homozygous for a rare <em>ERCC3</em> variation. Our findings broaden the clinical range of infections seen in MST1 deficiency and provide a new genetic etiology of susceptibility to EV-HPV infections. Together with the recent discovery of RHOH deficiency, they suggest that T cells are involved in the control of EV-HPVs, at least in some individuals.</p> </div

Immunophenotyping of the patient.

A<p>Normal ranges were obtained from internal laboratory controls (N = 10) unless specified otherwise.</p>B<p>normal ranges from the work of Lugada <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Lugada1" target="_blank">[47]</a>.</p>C<p>normal ranges taken from the work of Nehme <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Nehme1" target="_blank">[30]</a>.</p>D<p>normal ranges taken from the work of Shearer <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Shearer1" target="_blank">[48]</a>.</p>E<p>normal ranges taken from the work of Bisset <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Bisset1" target="_blank">[49]</a>.</p>F<p>normal ranges taken from the work of Eidenscheck <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Eidenschenk1" target="_blank">[50]</a>.</p

Homozygous <i>MST1</i> nonsense mutation in one patient with EV-HPV, bacterial and fungal infections.

<p>(A) Pedigree of the family with EV-HPV, bacterial and fungal infections. Generations are designated by a Roman numeral (I, II). P1 is represented by a black symbol. The symbol *indicates the individuals genotyped with the Affymetrix Genome-wide SNP 6.0 array. The Familial segregation of the mutation R115X is shown on the pedigree. (B) Automated sequencing profile, showing the R115X <i>MST1</i> mutation in gDNA extracted from EBV-B cells from the patient and comparison with the sequence obtained from a healthy control. The C→T mutation leads to the replacement at residue 115 of an Arg (R) residue by a STOP codon (X). (C) Schematic representation of the structure of the MST1 protein adapted from the work of Nehme <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Nehme1" target="_blank">[30]</a>. R115X is situated in the kinase domain, close to the previously reported R117X mutation described by Nehme <i>et al.,</i> indicated by a black arrow. The second mutation (1103delT X369) described by Nehme <i>et al.,</i> 1103delT X369, and the mutation described by Abdollahpour <i>et al.</i> (W250X) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044010#pone.0044010-Abdollahpour1" target="_blank">[31]</a> are also indicated by black arrows.</p