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Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [single-cell RNA-seq]

ABSTRACT: Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [single-cell RNA-seq]

PROVIDER: PRJNA793274 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17386270.fastq.gz	Fastqsanger.gz
	SRR17386271.fastq.gz	Fastqsanger.gz
	SRR17386272.fastq.gz	Fastqsanger.gz
	SRR17386273.fastq.gz	Fastqsanger.gz
	SRR17386274.fastq.gz	Fastqsanger.gz

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Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [RNA-seq]

Project description:Lymphoid tissue inducer (LTi) cells, known to be critical for the generation of secondary lymphoid tissues, are the founding member of innate lymphoid cells (ILCs). However, how the development and functions of this ILC subset are regulated is far from clear. In this study, we discovered a striking role of the transcription factor TCF-1 in the development of Peyer’s patches (PPs) but not lymph nodes (LNs). Despite TCF-1 is critical for ILC development at multiple stages, we found normal development of LTi cells in TCF-1-deficient mice indicating that dysfunction of these LTi cells led to the deficiency in Peyer’s patches formation. Through bulk and single cell RNA-Seq, we found differential gene expression patterns between LTi cells from the PPs, LNs and the small intestine laminal propria (siLP), and an important role of TCF-1 in regulating the expression of lymphotoxin (LT) specifically in PP LTi cells. Mechanistically, TCF-1 may regulate Lta indirectly through promoting the expression of GATA3, a critical transcription factor in regulating LTi functions. LTβR agonist injection during the embryonic stage partially rescued the formation of PPs in the TCF-1-deficient mice. Thus, a dose effect of LT expression in LTi cells regulated by TCF-1 contributes to a differential regulation of organogenesis of distinct secondary lymphoid structures.

2023-08-22 | GSE190299 | GEO

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [Chic-seq]

2023-08-22 | GSE190301 | GEO

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [DNase-seq]

2023-08-22 | GSE190300 | GEO

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [single-cell RNA-seq]

2023-08-22 | GSE192825 | GEO

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues

Project description:Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues

| PRJNA786605 | ENA

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [Chic-seq]

Project description:Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [Chic-seq]

| PRJNA786607 | ENA

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [DNase-seq]

Project description:Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [DNase-seq]

| PRJNA786608 | ENA

Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [RNA-seq]

Project description:Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [RNA-seq]

| PRJNA786609 | ENA

Transcription factor TCF-1 regulates the functions, but not the development, of lymphoid tissue inducer subsets in different tissues.

Project description:Lymphoid tissue inducer (LTi) cells, a subset of innate lymphoid cells (ILCs), play an essential role in the formation of secondary lymphoid tissues. However, the regulation of the development and functions of this ILC subset is still elusive. In this study, we report that the transcription factor T cell factor 1 (TCF-1), just as GATA3, is indispensable for the development of non-LTi ILC subsets. While LTi cells are still present in TCF-1-deficient mice, the organogenesis of Peyer's patches (PPs), but not of lymph nodes, is impaired in these mice. LTi cells from different tissues have distinct gene expression patterns, and TCF-1 regulates the expression of lymphotoxin specifically in PP LTi cells. Mechanistically, TCF-1 may directly and/or indirectly regulate Lta, including through promoting the expression of GATA3. Thus, the TCF-1-GATA3 axis, which plays an important role during T cell development, also critically regulates the development of non-LTi cells and tissue-specific functions of LTi cells.

| S-EPMC10504686 | biostudies-literature

Bcl6 is a subset defining transcription factor of Lymphoid Tissue inducer-like ILC3

Project description:Innate lymphoid cells (ILC) are tissue-resident effector cells with important roles in tissue homeostasis, protective immunity and inflammatory disease. Current nomenclature divides ILC into subsets based on the expression of master transcription factors and effector cytokine programs. In mucosal barrier tissues, group 3 ILC (ILC3) have been defined by the expression of the master transcription factor RORgt. However, ILC3 can be further subdivided into two major subsets – natural cytotoxicity receptor-expressing (NCR+) ILC3 and lymphoid tissue inducer (LTi)-like ILC3 which share type 3 effector modules but also exhibit significant ontological, transcriptional, phenotypic and functional heterogeneity. In particular, LTi-like ILC3 exhibit effector functions not typically associated with other RORgt-expressing lymphocytes, provoking the hypothesis that other master transcription factors may contribute to LTi-like ILC3 biology. Here we identify Bcl6 as an LTi-like ILC3 associated transcription factor in both mice and humans. Deletion of Bcl6 led to dysregulation of the LTi-like ILC3 transcriptional program and changes to subset-specific phenotypic markers and effector functions. Strikingly, loss of Bcl6 enhanced expression of the type 3 effector cytokines IL-17A and IL-17F in LTi-like ILC3, which was found to be in part dependent upon the commensal microbiota. Together these findings implicate Bcl6 as an ILC3 subset-defining transcription factor and part of a network that confers phenotype and function on LTi-like ILC3. Our study further provides a missing link to redefine analogous immune modules in innate and adaptive lymphocyte responses.

2023-10-31 | GSE228852 | GEO

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