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Roles of PRDM1 in human NK-cell differentiation and activation

ABSTRACT: Key regulatory roles of PRDM1 in human NK-cell differentiation and activation

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Van-An Duong

LAB HEAD: Sheng Pan

PROVIDER: PXD068794 | Pride | 2026-01-19

REPOSITORIES: Pride

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			Action	DRS
	20180301_DDA_DE30_IgG_LA_Feb27.pep.md5	Other
	20180301_DDA_DE30_IgG_LA_Feb27.pep.xml	Pepxml
	20180301_DDA_DE30_IgG_LA_Feb27.raw	Raw
	20180301_DDA_DE30_PRDM1_LA_Feb27.pep.xml	Pepxml
	20180301_DDA_DE30_PRDM1_LA_Feb27.raw	Raw

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Publications

Key regulatory roles of PRDM1 in human NK-cell differentiation and activation.

Liu Xuxiang X Shi Yunfei Y Zhang Jibin J Shetty Kunal K Chew Krystie K Küçük Can C Gong Qiang Q Esmeray Esra E Li Haiqing H Chen Ru R Pan Sheng S Dąbrowska Katarzyna K Moore Roger E RE Garcia-Mansfield Krystine K Pirrotte Patrick P Wang Jinhui J Li Yuping Y Dong Gehong G Lee Logan L McKeithan Timothy W TW Iqbal Javeed J Chan Wing C WC

Leukemia 20251209 1

PRDM1, encoding a transcription factor (TF), regulates plasma cell and CD8<sup>+</sup> T-cell terminal differentiation and T<sub>h</sub>2 lineage specification, while its role in human NK-cell differentiation and homeostasis is largely unknown. Here, we employed a multi-omics approach to dissect the transcriptional control of PRDM1 on human NK-cells. PRDM1 is important in NK-cell terminal differentiation based on gene expression profiling and its targeting of key regulators in the process. PRDM1 ...[more]

PMID: 41366532

Similar Datasets

Key regulatory roles of PRDM1 in human NK-cell differentiation and activation

Project description:PRDM1, encoding a transcription factor (TF), regulates plasma cell and CD8+ T-cell terminal differentiation and Th2 lineage specification, while its role in human NK-cell differentiation and homeostasis is largely unknown. Here, we employed a multi-omics approach to dissect the transcriptional control of PRDM1 on human NK-cells. We also employed the APEX2 proximity-based biotinylation method, which enables efficient biotin-labeling of proteins within ~20 nm radius. NK-cells expressing APEX2-tagged PRDM1 were cultured with feeders for 7 or 28 days for the analysis of proximity-labeled proteins. Of the 30 PRDM1-associated cofactors identified by RIME, 12 (40%) were also detected in the APEX2 assay. Consistent with the RIME assay, RUNX3, RUNX1, and CBF-β were also biotinylated by PRDM1- APEX2. A lot more cofactors were identified in the APEX2 experiment, including HDAC1/2, histone deacetylases present in multiple corepressor complexes, similar to a previous study in mouse plasmablasts.

2026-01-19 | PXD069044 | Pride

Proteomic characterization of CD56posCD57 NK cell subsets

Project description:NK cells are lymphocytes that provide a first defense against viral infections and cancer. They act (i) cytotoxic by killing virus-infected and tumorigenic cells and (ii) immune regulatory by releasing cytokines and chemokines. These innate immune cells are commonly further classified as CD56bright and CD56dim NK cells. Former studies confirmed immune regulatory CD56bright NK cells as progenitors of cytotoxic CD56dim NK cells. CD57 was previously described as T cell marker for senescence and terminal differentiation. Recent studies detected CD57+ and CD57- NK cells among the CD56dim NK cell population and suggested a fully mature developmental status for CD57+ NK cells. The recent NK cell maturation model includes CD34+ hematopoietic stem cells (HSC), which develop into CD56bright NK cells, later into CD56dimCD57- and finally into terminally maturated CD56dimCD57+ (1) (2) (3). The molecular mechanisms of human NK cell differentiation and maturation remain unknown to this date. We performed for the first time a proteomic analysis of these distinct developmental stages of human primary NK cells, isolated from overall 10 healthy human blood donors. CD56bright NK cells versusCD56dim and CD56dimCD57- versus CD56dimCD57+ NK cells were analyzed by using quantitative peptide sequencing, which revealed individual protein signatures (3400 proteins) of these different NK cell developmental stages. Notably, our data support the current NK cell differentiation model by highlighting both strong distinctions between CD56dim/bright NK cells and close relationships between CD57+/- NK cells on the proteomic level. Among the most prominent and conserved regulated proteins, we detected myosin IIa, Calvasculin and Calcyclin with very similar expression patterns. We investigated their sub-cellular localization and observed specific recruitment- and accumulation-events at the NK cell immunological synapse (NKIS) after NK activation.

2013-01-23 | PRD000666 | Pride

Divergent roles for STAT4 in shaping effector differentiation of ILC1 and NK cells during gut inflammation II

Project description:Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1) require the transcription factor STAT4 to elicit rapid effector responses and protect against pathogens. Herein, by combining genetic and transcriptomic approaches, we revealed that STAT4 played an unexpected divergent role in regulating effector differentiation of murine ILC1 and NK cells, during intestinal inflammation. Stat4 deletion in Ncr1-expressing cells led to an increased generation of cytotoxic ILC1 in the inflamed large intestine. By contrast, Stat4-deficient NK cells showed impaired terminal differentiation, characterized by lower levels of IRF-8 and KLRG1. STAT4 expression in NCR+ innate lymphocytes restrained gut inflammation and controlled both systemic IFN-g levels and the number of type 2 adaptive T cells in the large intestine. Collectively our data shed light on shared and distinctive mechanisms of transcriptional regulation driven by STAT4 in NK cells and ILC1 required for protection during intestinal inflammation.

2023-09-28 | GSE210977 | GEO

Divergent roles for STAT4 in shaping effector differentiation of ILC1 and NK cells during gut inflammation I

2023-09-28 | GSE210483 | GEO

Transcriptomic and epigentic analysis of human peripheral blood NK cell subsets revealing role of Bcl11b in differentiation

Project description:Transcriptomic analysis of seven human peripheral blood NK cell subsets and three T cell subsets purified from healthy cytomeglovirus seropositive donors. Epigenetic analysis including identification of open chromatin and active enhancer elements confirms key regulatory factors defining an NK cell differentiation axis. Chromatin-immunoprecipitation sequencing reveals contribution of key transcription factors associated with NK cell differentiation including Bcl11b.

| EGAS00001005025 | EGA

Effect of resting or activated human regulatory T cells (Tregs) on human natural killer (NK) cell differentiation in vitro.

Project description:Activated but not resting Tregs affect NK cell differentiation. We used microarray analysis to study differences of gene expression of NK cell differentiation in the presence of resting or activated Tregs.

2016-06-08 | GSE55091 | GEO

RNA-Seq of FACS-sorted ex vivo NK cells from control (Cre neg, GFPNK/NK), STAT5BNK/NK, N642HNK/NK and diseased N642HNK/NK mice

Project description:Somatic STAT5B gain-of-function mutations have been frequently found in patients with T- and NK-cell neoplasms. STAT5BN642H represents the most frequently occuring STAT5B mutation. To investigate the molecular mechanism of STAT5BN642H-driven NK-cell leukemia, we performed RNA-Seq of liver derived FACS-sorted diseased N642HNK/NK and aged non-diseased control (Cre neg, GFPNK/NK), STAT5BNK/NK, N642HNK/NK NK cells.

2024-05-01 | E-MTAB-13797 | biostudies-arrayexpress

The transcription factor ETS1 is a master regulator of human NK cell differentiation [ChIP-seq]

Project description:Natural killer (NK) cells are innate lymphoid cells that play a critical role in the direct immune defense against tumor cells and pathogens, and additionally have important immune regulatory functions by cytokine secretion. Whereas NK cell biology has been extensively studied in mouse models, transcriptional control of human NK cell differentiation is poorly understood. In this study, we generated ETS1-deficient human embryonic stem cell (hESC) clones using the CRISPR/Cas9 technology. In a complementary approach, we generated ETS1 loss-of-function cord blood hematopoietic stem cells (HSCs) by retroviral transduction of the dominant-negative ETS1 p27 isoform. We show that the transcription factor ETS1 is required for human NK cell differentiation. Transcriptome and ChIP analysis reveal that ETS1 directly regulates expression of several NK cell-linked transcription factors. Also, expression of genes involved in cytokine secretion and cytotoxic activity is ETS1-dependent, whereby these effector functions are decreased in residual NK cells developing from ETS1 loss-of-function cord blood hematopoietic stem cells. Our data show that ETS1 is a critical regulator of human NK cell development and function, and provide important insights in the underlying molecular mechanisms.

2020-10-15 | GSE124103 | GEO

The transcription factor ETS1 is a master regulator of human NK cell differentiation [RNA-seq]

2020-10-15 | GSE105021 | GEO

Transcriptome analysis of Bcl11b-deficient murine NK cells

Project description:Epigenetic landscapes can provide insight into regulation of gene expression and cellular diversity. Here, we examined the transcriptional and epigenetic profiles of seven human blood NK cell populations, including adaptive NK cells. The BCL11B gene, encoding a transcription factor (TF) essential for T cell development and function, was the most extensively regulated, with expression increasing throughout NK cell differentiation. Several Bcl11b-regulated genes associated with T cell-signaling were specifically expressed in adaptive NK cell subsets. Regulatory networks revealed reciprocal regulation at distinct stages of NK cell differentiation, with Bcl11b repressing RUNX2 and ZBTB16 in canonical and adaptive NK cells, respectively. A critical role for Bcl11b in driving NK cell differentiation was corroborated in BCL11B mutated patients and by ectopic Bcl11b expression. Moreover, Bcl11b was required for adaptive NK cell responses in a murine CMV model, supporting expansion of these cells. Together, we define the TF regulatory circuitry of human NK cells and uncover a critical role for Bcl11b in promoting NK cell differentiation and function.

2021-05-28 | GSE162472 | GEO

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