XML4NGS : A XML-based description of a Next-Generation sequencing project allowing the generation of a ’Makefile’-driven workflow.

<p>[in french] Poster presented at JOBIM2013 https://colloque.inra.fr/jobim2013/layout/set/print/Soumission2/Liste-des-soumissions-retenues-pour-une-presentation-sous-forme-d-affiche</p> <p>XML4NGS is a schema describing a NGS experiment in XML. It provides a XSLT<br>stylesheet transforming the XML into a Makefile-driven workflow allowing a parallel analysis<br>(alignment, calling, annotation ... ) on a cluster.</p> <p> </p> <p> </p

DataSheet_1_Human gut microbiota-reactive DP8α regulatory T cells, signature and related emerging functions.pdf

In mice, microbiota-induced Tregs both maintain intestinal homeostasis and provide resistance to immuno-pathologies in the adult. Identifying their human functional counterpart therefore represents an important goal. We discovered, in the human colonic lamina propria and blood, a FoxP3-negative IL-10-secreting Treg subset, which co-expresses CD4 and CD8α (hence named DP8α) and displays a TCR-reactivity against Faecalibacterium prausnitzii, indicating a role for this symbiotic bacterium in their induction. Moreover, supporting their role in intestinal homeostasis, we previously reported both their drastic decrease in IBD patients and their protective role in vivo against intestinal inflammation, in mice. Here, we aimed at identifying the genomic, phenotypic and functional signatures of these microbiota-induced Tregs, towards delineating their physiological role(s) and clinical potential. Human F. prausnitzii-reactive DP8α Treg clones were derived from both the colonic lamina propria and blood. RNA-sequencing, flow cytometry and functional assays were performed to characterize their response upon activation and compare them to donor- and tissue-matched FoxP3+ Treg clones. DP8α Tregs exhibited a unique mixed Tr1-like/cytotoxic CD4+ T cell-profile and shared the RORγt and MAF master genes with mouse gut microbiota-induced FoxP3+ Tregs. We revealed their potent cytotoxic, chemotactic and IgA-promoting abilities, which were confirmed using in vitro assays. Therefore, besides their induction by a Clostridium bacterium, DP8α Tregs also partake master genes with mouse microbiota-induced Tregs. The present identification of their complete signature and novel functional properties, should be key in delineating the in vivo roles and therapeutic applications of these unique human microbiota-induced Tregs through their study in pathological contexts, particularly in inflammatory bowel diseases.</p

Heat map and cluster dendograms of gene clusters differentially expressed according to oocyte nuclear maturity.

<p>Hierarchical clustering of cumulus cell samples (columns) and the 132 most significant probes (rows). Upregulated genes are marked in red, downregulated genes are marked in green. CC_GV (blue), cumulus cells from immature oocyte at germinal vesicle stage; CC_MII (pink), cumulus cells from mature oocyte.</p

Downregulated functions in CC_B+ compared to CC_B-.

<p>CC_B+, cumulus cells from mature oocyte yielding a blastocyst at day 5/6 of <i>in vitro</i> culture once fertilised;</p><p>CC_B-, cumulus cells from mature oocyte which stopped developing at the embryo stage at day 5/6 of <i>in vitro</i> culture once fertilised.</p

Heat map and cluster dendograms of gene clusters differentially expressed according to oocyte developmental competence.

<p>Hierarchical clustering of cumulus cell samples (columns) and the 354 most significant probes (rows). Upregulated genes are marked in red, downregulated genes are marked in green. CC_B- (blue), cumulus cells from mature oocyte which arrested at the embryo stage at day 5/6 of <i>in vitro</i> culture once fertilised; CC_B+ (red), cumulus cells from mature oocyte yielding a blastocyst at day 5/6 of <i>in vitro</i> culture once fertilised.</p

Distribution of patients included in study.

<p>Patients were separated into two main groups: microarray and qPCR. The variability group was composed of patients who had one CC_B+ and at least one CC_B-. The pregnancy group was composed of CC_B+ transferred from patients included in the variability group. CC_B+, cumulus cells from a mature oocyte yielding a blastocyst at day 5/6 of <i>in vitro</i> culture once fertilised; CC_B-, cumulus cells from mature oocyte which stopped developing at the embryo stage at day 5/6 of <i>in vitro</i> culture once fertilised; CC_GV, cumulus cells from immature oocyte at germinal vesicle stage; P+, pregnancy; P-, no pregnancy.</p

Relative expression level obtained by qPCR of 9 genes differentially expressed according to oocyte developmental competence.

<p>Results were expressed as means ± SEM of relative expression to the reference gene RPL19. CC_B+, cumulus cells from mature oocyte yielding a blastocyst at day 5/6 of <i>in vitro</i> culture once fertilised; CC_B-, cumulus cells from mature oocyte which stopped developing at the embryo stage at day 5/6 of <i>in vitro</i> culture once fertilised; *, significant difference (p<0.05).</p

Test of hypotheses for Mixed Model Analysis of Variance, impact of developmental competence, patient variability and experience (<i>i.e.</i> qPCR series) on the level of gene expression.

<p><i>y_ijkn</i> gene expression level in <i>n</i>th cumulus cells for a gene according to the <i>i</i>th phenotype from <i>j</i>th patient after <i>k</i>th qPCR series; <i>μ</i> gene expression level mean; P<i>i</i> fixed effect of <i>i</i>th phenotype (<i>i</i> =  CC_B+ cumulus cells from mature oocyte yielding a blastocyst at day 5/6 of <i>in vitro</i> culture once fertilised and <i>i</i> =  CC_B- cumulus cells from mature oocyte which stopped developing at the embryo stage at day 5/6 of <i>in vitro</i> culture once fertilised); A<i>j</i> random effect of the <i>j</i>th patient (<i>j</i> = 1 to 29); Q<i>k</i> random effect of <i>k</i>th qPCR series (<i>k</i> = 1 to 7); (PA)<i>ij</i> first-order interaction between variables phenotype and patient;</p>*<p>Statistical significance of model factors for the levels of expression of the four genes (p<0.05).</p

Dataset of transcriptome of cumulus cells used for meta-analysis.

<p>CCs, cumulus cells; GV, germinal vesicle stage; MII, metaphase II.</p

Upregulated functions in CC_B+ compared to CC_B-.

<p>CC_B+, cumulus cells from mature oocyte yielding a blastocyst at day 5/6 of <i>in vitro</i> culture once fertilised;</p><p>CC_B-, cumulus cells from mature oocyte which stopped developing at the embryo stage at day 5/6 of <i>in vitro</i> culture once fertilised.</p