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Next generation sequencing analysis of DN1 transcriptomes from Wild type, gl/gl and transgenic CD2-Ostm1 gl/gl mice

ABSTRACT: The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR. Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype.

ORGANISM(S): Mus musculus

PROVIDER: GSE72184 | GEO | 2016/09/01

SECONDARY ACCESSION(S): PRJNA293281

REPOSITORIES: GEO

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Next generation sequencing analysis of DN1 transcriptomes from Wild type, gl/gl and transgenic CD2-Ostm1 gl/gl mice

Project description:The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRTâ??PCR validation was performed using SYBR Green assays Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR. Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype. DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were compared by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000.

2016-09-01 | E-GEOD-72184 | biostudies-arrayexpress

Mus musculus

Project description:Next generation sequencing analysis of DN1 transcriptomes from Wild type, gl/gl and transgenic CD2-Ostm1 gl/gl mice

| PRJNA293281 | ENA

Acetivibrio cellulolyticus CD2

Project description:Acetivibrio cellulolyticus CD2 genome sequencing project.

| PRJNA45843 | ENA

Analysis of CD2 interactome in primary murine CD4+ T cells

Project description:CD2 is a receptor expressed on T cells and when engaged, it promotes T cell activation. However the mechanisms and molecular partners of CD2 that mediate T cell activation remain unclear. Here we used AP-MS to determine the interactome of CD2 prior and upon its engagement. For this purpose, we used a knockin mouse expressing an endogenous One Step Tag (OST) version of the CD2 molecule. Affinity purification of the OST tagged protein was performed using Streptactin beads, from T cells left non-stimulated, or stimulated for 1min or 5min with anti-CD2 antibodies. Each AP-MS purification was associated with a corresponding control (purification from WT CD4+ T cells, cultured and stimulated in the same conditions). The number of replicate biological experiments was n=3 for all conditions.

2022-07-12 | PXD029750 | Pride

Stenotrophomonas sp. CD2 isolate:soil

Project description:Stenotrophomonas sp. CD2 isolate:soil Genome sequencing

| PRJNA856778 | ENA

Polymorphism in estrogen receptor binding site causes CD2-dependent sex bias in T cell autoimmune diseases

Project description:Complex autoimmune diseases are sexually dimorphic. An interplay between predisposing genetics and sex-related factors likely determines the sex discrepancy in the immune response, but conclusive evidence regarding the underlying molecular mechanisms is lacking. Using forward genetics, we positionally identified a polymorphic estrogen receptor binding site that regulates CD2 expression, leading to female-specific differences in mouse models of T cell-dependent autoimmunity. Female mice with reduced CD2 levels displayed a diminished T cell activation and autoimmune T cell response. Mechanistically, CD2 affected LAG-3 expression. Our findings help to explain the sexual dimorphism in human autoimmunity, as CD2 associated with rheumatoid arthritis and its regulation through 17-β-estradiol was conserved in human T cells. Hormonal regulation of CD2 has implications for CD2-targeted therapy. Indeed, anti-CD2 treatment more potently affected female mice. In conclusion, our results demonstrate the relevance of sex-genotype interactions and deliver strong evidence for CD2 as a sex-sensitive predisposing factor in autoimmunity.

2021-07-15 | PXD024126 | Pride

CD8 in vitro CD2-costimulation

Project description:Purified primary human CD8 T cells were stimulated in vitro in parallel using a magnetic bead conjugated to either anti-CD3/28 or anti-CD2/3/28 antibodies. Cells were cultured for 6 days in complete RPMI1640 and 10ng/ml IL2 and were harvested on day 6 and RNA was isolated for further labelling and hybridisation.

2015-08-12 | E-MTAB-3470 | biostudies-arrayexpress

Differential gene expression in peripheral blood CD2+ leukocytes from PATH particpants

2009-05-26 | GSE7894 | GEO

Transcription profiling of human peripheral blood CD2+ leukocytes from PATH particpants

Project description:Gene expression profiling was carried out on peripheral blood CD2+ leukocytes from 29 children with asthma. The primary research question is whether gene expression differs in individuals from high socioeconomic status environments vs low socioeconomic status environments. Experiment Overall Design: Gene expression profiling was carried out on peripheral blood CD2+ leukocytes from 29 children with asthma. The primary research question is whether gene expression differs in individuals from high socioeconomic status environments vs low socioeconomic status environments.

2009-06-01 | E-GEOD-7894 | biostudies-arrayexpress

Phosphoproteomic analysis of CD2 signaling reveals an AMPK-dependent targeted granule secretion in human cytotoxic T cells

Project description:The in-depth analysis of co-stimulatory signaling enhancing the activity of cytotoxic T cells represents a major approach towards the development of immunotherapies. Here we describe that CD2 co-stimulation plays a critical role in the functioning of human cytotoxic T cells (CTLs). We found that CD2 promotes the formation of functional immune synapses by orchestrating the polarization of lytic granules towards the synaptic interface. To broadly explore the CD2 signaling network, we undertook an analysis of protein phosphorylation in CD2-stimulated CTLs, which revealed 549 unique CD2-regulated phosphorylation events in 373 proteins. CD2 stimulation elicited an intricated network of signaling events participating in the regulation of T cell metabolism, vesicular trafficking, autophagy, cell polarity and cytoskeleton organization. We further show that a functionally critical node of this network is the AMP-activated protein kinase (AMPK), which regulates granule polarization at the CTL synapse. Polarized trafficking of granules is driven by the concerted action of TAK1/LKB1/CamKK2 kinases, which locally activate AMPK enriched on CTL lysosome membranes, illustrating a novel functional cross-talk between vesicular compartments in CTLs. Our results thus establish CD2 signaling as key for regulating targeted granule secretion in CTLs and reveal an AMPK-dependent mechanism to explain how AMPK-activating drugs boost anti-tumour CTL activity.

2020-04-28 | PXD013840 | Pride

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