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Transcriptomic analysis of in vitro induced germinal centre-like B cells and plasmablast differentiation

ABSTRACT: Transcriptomic analysis of in vitro induced germinal centre-like B cells and plasmablast differentiation

PROVIDER: PRJNA743057 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15015600.fastq.gz	Fastqsanger.gz
	SRR15015601.fastq.gz	Fastqsanger.gz
	SRR15015602.fastq.gz	Fastqsanger.gz
	SRR15015603.fastq.gz	Fastqsanger.gz
	SRR15015598.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of in vitro induced germinal centre-like B cells and plasmablast differentiation

Project description:To elucidate molecular mechanisms that regulate the terminal differentiation of B cells into plasmablasts, we analysed how the B cell transcriptome changes during an in vitro culture system that mimics the germinal centre response (known as iGB culture). By culturing B cells on feeder cells expressing CD40L and B-cell activating factor BAFF in the presence of interleukin 4 and interleukin 21, this system allows class switch recombination to IgG1-producing cells and formation of CD138+ TACI+ B220low CD19int/low plasmablasts.

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Project description:Antibody-mediated immunity is initiated by B cell interactions with cognate antigen, followed by differentiation into multiple cell subsets, including plasmablast, memory, and germinal center (GC) cells. B cell differentiation trajectories are determined by specific transcription factors, yet very few mechanisms that determine B cell fate at the early stage of the response have been described. Here, we report an epigenetic mechanism that specifically suppresses the plasmablast genetic program and promotes GC B cell fate commitment. Single-cell RNA-seq analysis of antigen-specific B cells revealed activated B cell precursors at the pre-GC stage that express high levels of RNA binding proteins, including YTHDF2, which enhances the decay of methylated transcripts. Ythdf2-deficient B cells exhibited intact proliferation and upregulation of early activation markers in response to antigenic stimulation, whereas differentiation into GC B cells was blocked. Mechanistically, B cells required YTHDF2 to attenuate the plasmablast genetic program during GC seeding, and key transcripts of plasmablast-related genes, including Irf4 and Xbp1, were methylated and bound by YTHDF2. Modulation of YTHDF2-dependent gene expression by YTHDF1 and YTHDF3 was less pronounced, and no functional redundancy of these paralogs in GC seeding was observed. Collectively, this study reveals a novel epigenetic mechanism that specifically directs appropriate B cell fate commitment through post-transcriptional suppression of gene expression.

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YTHDF2 suppresses the plasmablast genetic program and promotes germinal center formation

Project description:YTHDF2 suppresses the plasmablast genetic program and promotes germinal center formation

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Effect of B cell-intrinsic deletion of MLL1 on gene expression of germinal centre B cells during day 13 Trichuris muris infection

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Project description:Selection of B cells subjected to hypermutation in germinal centres (GC) during T-dependent (TD) antibody responses yields memory cells and long-lived plasma cells that produce high affinity antibodies biased to foreign antigens rather than self-antigens. GC also form in T-independent (TI) responses to polysaccharide antigens but failed selection results in GC involution and memory cells are not generated. To date there are no markers that allow phenotypic distinction of T-dependent and T-independent germinal centre B cells. We have now compared the global gene expression of GC B cells purified from mice immunized with either TD or TI antigens and identified eighty genes that are differentially expressed in TD GC. Keywords: T-dependent and T-independent germinal center B cells

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