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Transcriptomic analyis of follicular and marginal zone B cells after inducible Tsc1 deletion

ABSTRACT: Transcriptomic analyis of follicular and marginal zone B cells after inducible Tsc1 deletion

PROVIDER: PRJNA746962 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15150364.fastq.gz	Fastqsanger.gz
	SRR15150365.fastq.gz	Fastqsanger.gz
	SRR15150366.fastq.gz	Fastqsanger.gz
	SRR15150367.fastq.gz	Fastqsanger.gz
	SRR15150368.fastq.gz	Fastqsanger.gz

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Transcriptomic analyis of follicular and marginal zone B cells after inducible Tsc1 deletion

Project description:Observations that ongoing mTORC1 activity drives plasma cell poise in MZ B cells we rationed that enforcing mTORC1 activity on mature follicular B cells by inducible B cell specific Tsc1 deletion would confer plasma cell differention poise on follicular B cells. We therefore performed RNA-seq on follicular and marginal zone B cells from Tsc1F.hCD20-TamCre mice after 4 weeks tamoxifen treatment to examine transcriptional markers of plasma cell differentiation poise.

2021-07-22 | GSE180173 | GEO

Transcriptomic analyis follicular and marginal zone B ells after in vivo Notch2 blockade.

Project description:Transcriptomic analyis follicular and marginal zone B ells after in vivo Notch2 blockade.

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Transcriptomic analyis follicular and marginal zone B ells after in vivo Notch2 blockade.

Project description:Marginal zone B cells which make rapid mitosis-independent plasma cell responses are dependent on Notch2 signaling for their generation and maintenance. In order to determine the effect of ongoing Notch signaling on the maintenance of the MZ transcriptome, we performed RNA-seq on MZ and follicular B cells after 12, 24 and 48 hours of in vivo Notch2 antibody blockade

2021-07-22 | GSE180172 | GEO

Dissecting the grey zone between follicular lymphoma and nodal marginal zone lymphoma using morphological and genetic features

Project description:Nodal marginal zone lymphoma is a poorly defined entity in the WHO classification, largely based on criteria by exclusion and the diagnosis often remains subjective. Follicular Lymphoma lacking t(14;18), have similar characteristics which results in a major potential diagnostic overlap which this study aims to dissect. Four subgroups of lymphoma samples (n=56) were analyzed with high-resolution arrayCGH; Nodal marginal zone lymphoma, t(14;18)-negative Follicular Lymphoma, localized t(14:18)-positive Follicular Lymphoma and disseminated t(14;18)-positive Follicular Lymphoma. Gains on chromosomes 7, 8 and 12 were observed in all subgroups. The mean number of aberrations was higher in disseminated t(14;18)-positive Follicular Lymphoma compared to localized t(14:18)-positive Follicular Lymphoma (p<0.01) and the majority of alterations in localized t(14:18)-positive Follicular Lymphoma were also found in disseminated t(14;18)-positive Follicular Lymphoma. Nodal marginal zone lymphoma was marked by 3q gains with amplifications of four genes. A different overall pattern of aberrations was seen in t(14;18)-negative Follicular Lymphoma compared to t(14;18)-positive Follicular Lymphoma. t(14;18)-negative Follicular Lymphoma is marked by specific (focal) gains on chromosome 3 as observed in Nodal marginal zone lymphoma. Our results support the notion that localized t(14:18)-positive Follicular Lymphoma represents an early phase of disseminated t(14;18)-positive Follicular Lymphoma. t(14;18)-negative Follicular Lymphoma bears aberrations that are more alike Nodal marginal zone lymphoma, suggesting a relation between these groups. Four subgroups of follicular lymphoma were analyzed: NMZL (n=14), t-FL (n=12), LOC t+FL (n=16), DIS t+FL (n=14).

2013-07-16 | E-GEOD-40641 | biostudies-arrayexpress

Dissecting the grey zone between follicular lymphoma and nodal marginal zone lymphoma using morphological and genetic features

2013-07-16 | GSE40641 | GEO

RNA-seq analysis of splenic follicular IgD low and IgD high, and marginal zone B cells

Project description:RNA sequencing was performed to determine the uniqueness of splenic follicular IgD low B cells compared to splenic follicular IgD high and marginal zone B cells.

2018-12-03 | GSE111911 | GEO

Transcription profiling of mouse follicular and marginal zone B-cells

Project description:Immature B cells in spleens of mouse and human differentiate into at least two subsets of mature B cells, the follicular (FO) B cells and the marginal zone (MZ) B cells, but functions, maturation and other properties of these cells are largely unknown. To solve these questions, in this study, we performed transcriptome analyses of FO and MZ B cells sorted from spleens of normal unimmunized mice using gene chips. By comparison of gene expression profiles between FO and MZ B cells, we identified 1226 genes that are expressed higher in FO B cells than in MZ B cells. On the other hand, 1734 genes were found to be expressed higher in MZ B cells than in FO B cells. We noticed that some of differentially expressed genes have been reportedly characterized in FO and MZ B cells, suggesting the reliability of the analysis. By using FACS analyses, we confirmed that CD36, CD68, and CD49e are expressed on MZ B-cells but not on FO B-cells. These results revealed new phenotypic and functional properties of FO and MZ B cells, and set a molecular basis for further studying differentiation and functions of these mature B cells. Experiment Overall Design: one follicular B cells replicate and one marginal zone B cells replicate were analyzed.

2008-06-12 | E-GEOD-3599 | biostudies-arrayexpress

Transcriptomic analyis of in-vitro plasma cell generation from follicular and marginal zone B cells with cell cycle inhibition via PD0332991 and rapamycin

Project description:Plasma cell differentiation is thought to be tied to cell division. We observe that marginal zone B cells are able to differentiate to plasma cells without completing a single cell division. In order to characterize the transcriptome of plasma cells derrived from un-divided MZ B cells we performed in vitro plasma cell differentiation cultures in the presence of the CDK4/6 inhibitor PD0332991 or rapamycin using Blimp1-GFP reporter follicular and MZ B cells. We report here that these resulting plasma cells from undivided MZ B cells exhibit normal plasma cell gene expression and function in the absence of mitosis.

2021-07-22 | GSE180170 | GEO

Transcriptomic analyis of donor (B6:SJL.C20) and host follicular and marginal zone B cells after adoptive transfer of follicular B cells into into lymphopenic (Rag2-/-) or replete animals (C57BL6)

Project description:The generation of marginal zone (MZ) B cells is a Notch2 dependent process. We observed that transdifferentiation of follicular (FO) B cells to an MZ-like phenotype is dependent on a lymphopenic environment. We therefore adoptively transftered congenically marked SJL.C20 (CD45.1) mature naive FO B cells into either lymphopenic Rag2-/- or intact C57BL6 (CD45.2) recipient mice and recovered and double sorted intermediate phenotype (MZ-FO) donor B cells at day 4 post transfer from Rag2-/- recipients or both MZ and FO phenotype donor B cells at day 8 post transfer from both recipient groups and performed RNA sequencing.

2022-05-01 | GSE200219 | GEO

IKKα is essential for the development and maintenance of Marginal zone and Follicular B cells

Project description:IKKα kinase is essential for the B cell maturation and secondary lymphoid organ development. In the current study, we evaluated the role of IKKα in the marginal zone and follicular B lymphocyte development by genetically deleting IKKα from the B cell lineage using CD19-Cre mice. The loss of IKKα did not affect the normal development of early B cell progenitors. However, a significant decline was observed in the percentage of immature B lymphocytes, mature marginal zone and follicular B cells along with a severe disruption of splenic marginal and follicular B cell zones. A gene expression analysis performed on the RNA extracted from the newly formed B cells (B220+IgMhi) revealed that IKKα deficiency produces significant changes in the expression of genes involved in MZ and FO B lymphocyte survival, homing and migration. And several among those genes identified belong to G protein family. Specifically, we validated the upregulated expression of regulator of G protein signaling 13 (RGS13), which is a GTPase activating protein (GAP) that negatively regulates G protein signaling and impede B cell migration. Likewise, promigratory B lymphocyte receptor, the sphingosine-1-phosphate receptor 3 (SIPR3) that couple to Gαi showed significantly reduced expression. In addition, an in silico analysis of gene product interactions revealed NF-κB signaling pathways to be a major gene regulating networks perturbed with IKKα deletion. Taken together, this study reveals IKKαNF-κB and G protein signaling axis to be central for the MZ and FO B cells survival, maintenance, homing and migration.

2017-09-14 | GSE102587 | GEO

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