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RNA-seq and methyl-seq of A20 mouse cells using a novel TETact activation of CD4

ABSTRACT: Stably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of CRISPR dCas9-based activation systems. To counter this, we created an improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). To evaluate the specificity of our TETact system, we conducted RNA-seq on A20 cells containing the TETact-v3 system targeting the CD4 promoter, along with non-targeting control TETact-v3 cells as well as wildtype A20. A20 is a BALB/C B cell lymphoma cell line that does not normally express CD4. Non-transduced A20 showed a very similar gene expression profile with the control TETact-v3 cells. Importantly, comparing of TETact-v3 cells targeting CD4 promoter to with cells expressing non-targeting sgRNA revealed CD4 as the sole significantly upregulated gene. Expression of the other genes in the CD4-targeting samples correlated strongly with the control sample. Together these experiments reveal the exquisite specificity of the TETact system. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE212345 | GEO | 2022/09/07

REPOSITORIES: GEO

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RNA-seq of A20 mouse cells using a novel TETact activation of CD4

Project description:Stably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of CRISPR dCas9-based activation systems. To counter this, we created an improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). To evaluate the specificity of our TETact system, we conducted RNA-seq on A20 cells containing the TETact-v3 system targeting the CD4 promoter, along with non-targeting control TETact-v3 cells as well as wildtype A20. A20 is a BALB/C B cell lymphoma cell line that does not normally express CD4. Non-transduced A20 showed a very similar gene expression profile with the control TETact-v3 cells. Importantly, comparing of TETact-v3 cells targeting CD4 promoter to with cells expressing non-targeting sgRNA revealed CD4 as the sole significantly upregulated gene. Expression of the other genes in the CD4-targeting samples correlated strongly with the control sample. Together these experiments reveal the exquisite specificity of the TETact system.

2022-09-07 | GSE203162 | GEO

Whole genome enzymatic methyl-seq of A20 mouse cells using a novel TETact activation of CD4

2022-09-07 | GSE211754 | GEO

Mouse WT vs. A20 KO BMDM differential proteomics

Project description:A20 is a negative regulator of NF-κB signaling, crucial to control inflammatory responses and ensure tissue homeostasis. A20 is thought to restrict NF-κB activation both by its ubiquitin-editing activity as by non-enzymatic activities. Besides its role in NF-κB signaling, A20 also acts as a protective factor inhibiting apoptosis and necroptosis. Because of the ability of A20 to both ubiquitinate and deubiquitinate substrates and its involvement in many cellular processes, we hypothesized that deletion of A20 might generally impact on protein levels, thereby disrupting cellular processes. We performed a differential proteomics study of bone marrow derived macrophages (BMDMs) from control and myeloid-specific A20 knockout mice, both in untreated conditions and after LPS and TNF treatment, and demonstrate proteome-wide changes in protein expression upon A20 deletion. Several inflammatory proteins are up-regulated in the absence of A20, even without an inflammatory stimulus. Depending on the treatment and the time, more proteins are regulated. Together these changes may affect multiple signaling pathways disturbing tissue homeostasis and inducing (autoimmune) inflammation, as suggested by genetic studies in patients.

2018-05-15 | PXD008726 | Pride

A20 contribution to NF-κB regulation, Ripoptosome formation and TNF-induced cell death [mouse]

Project description:A20 is known key regulator of NF-κB activity and inflammatory response, but its role in the control of cell death receptor signaling is not completely understood. Although A20 is widely accepted anti-apoptotic protein, we demonstrate that elevated expression of A20 in both, human and murine keratinocytes results in sensitisation to TNF-induced cell death. We prove that the Ripoptosome formation in A20 overexpressing cells is prerequisite for the TNF-induced cell death execution. We demonstrate that both canonical and non-canonical NF-κB signaling pathways are regulated upon increase of A20 expression. A20 dependent alteration of cIAPs and TRAF1 expressions are involved in the multiple level control of cell death in keratinocytes with elevated A20 expression.

2020-02-20 | GSE128248 | GEO

A20 contribution to NF-κB regulation, Ripoptosome formation and TNF-induced cell death [human]

2020-02-20 | GSE128247 | GEO

Effect of A20 deletion in a retroviral mouse model of AML

Project description:We show that AML patients who experience induction failure have elevated expression of the NF-kB target gene TNFAIP3/A20 and impaired necroptotic cell death, leading to a worse prognosis with chemotherapy. A20High AML samples display resistance to anthracyclines, while A20Low AML samples show sensitivity. Loss of A20 in AML cells restores sensitivity to anthracycline treatment by inducing necroptosis. Moreover, our studies revealed that A20 plays a critical role in AML development as deletion or knockdown of A20 effectively suppresses leukemic cells by mediating spontaneous necroptosis. A20 prevents necroptosis in AML by targeting the necroptosis effector RIPK1, and anthracycline-induced necroptosis is abrogated in A20High AML cells. These findings suggest that NF-kB-driven A20 overexpression plays a role in failed chemotherapy induction and highlights the potential of targeting an alternative cell death pathway in AML. The data contained here provide a platform in which to examine the effects of A20 loss in a retroviral mouse model of AML.

2024-09-03 | GSE250372 | GEO

A20 IN MARGINAL ZONE LYMPHOMAS

Project description:Unique and shared cytogenetic abnormalities have been documented for marginal zone lymphomas (MZLs) arising at different sites. Recently, homozygous deletions of the chromosomal band 6q23, involving the tumor necrosis factor alpha-induced protein 3 (TNFAIP3, A20) gene, a negative regulator of NF-kappa B, were described in ocular adnexal MZL, suggesting a role for A20 as a tumor suppressor in this disease entity. Here, we investigated inactivation of A20 by DNA mutations or deletions in a panel of extranodal (EMZL), nodal (NMZL) and splenic (SMZL) MZLs. Inactivating mutations encoding truncated A20 proteins were identified in 6/32 (18.8%) MZLs, including 3/11 (27.3%) EMZLs, 2/9 (22.2%) NMZLs, and 1/12 (8.3%) SMZLs. Two additional unmutated non-splenic MZLs also showed mono- or biallelic A20 deletions by FISH and/or array-CGH. Thus, A20 loss by both somatic mutations and/or deletions represents a common genetic aberration across all MZL subtypes, which may contribute to lymphomagenesis by inducing constitutive NF-kappa B activation. Keywords: Genome variation profiling by SNP array 27 MZL samples. No technical replications.

2009-04-01 | E-GEOD-13989 | biostudies-arrayexpress

RNA sequencing of CRISPR/Cas9-generated A20 DUB-inative and A20 knock-out U937 cells to elucidate the role of human A20 DUB-domain

Project description:Objectives: Genetic variations in TNFAIP3 (A20) de-ubiquitinase (DUB) domain increase the risk of systemic lupus erythematosus (SLE) and rheumatoid arthritis. A20 is a negative regulator of NF-κB but the role of its DUB domain and related genetic variants remain unclear. We aimed to study the functional effects of A20 DUB-domain alterations in immune cells and understand its link to SLE pathogenesis. Methods: CRISPR/Cas9 was used to generate human U937 monocytes with A20 DUB-inactivating C103A knock-in mutation. Whole genome RNA-sequencing was used to identify differentially expressed genes between WT and C103A knock-in cells. Functional studies were performed in A20 C103A U937 cells and in immune cells from A20 C103A mice and genotyped healthy individuals with A20 DUB polymorphism rs2230926. Neutrophil extracellular trap (NET) formation was adressed ex vivo in neutrophils from A20 C103A mice and SLE-patients with rs2230926. Results: Genetic disruption of A20 DUB domain in human and murine myeoloid cells did not give rise to enhanced NF-κB signaling. Instead, cells with C103A mutation or rs2230926 polymorphism presented an upregulated expression of PADI4, an enzyme regulating protein citrullination and NET formation, two key mechanisms in autoimmune pathology. A20 C103A cells exhibited enhanced protein citrullination and extracellular trap formation, which could be suppressed by selective PAD4 inhibition. Moreover, SLE-patients with rs2230926 showed increased NETs and increased frequency of autoantibodies to citrullinated epitopes. Conclusions: We propose that genetic alterations disrupting the A20 DUB domain mediate increased susceptibility to SLE through the upregulation of PADI4 with resultant protein citrullination and extracellular trap formation.

2019-07-10 | GSE116780 | GEO

A20 governs fibrosis susceptibility in bleomycin-induced mouse scleroderma model

Project description:In addition to autoimmune and inflammatory diseases, variants of the TNFAIP3 gene encoding A20 are also associated with systemic sclerosis (SSc). However, it remains unclear how genetic factors contribute to fibrosis in SSc, and which cell types drive disease due to SSc-specific genetic alterations. We characterized the expression and function of A20, and its negative transcriptional regulator DREAM, in patient with SSc. We found that levels of A20 were significantly reduced in SSc skin and lung biopsies, while DREAM was elevated and showed anti-correlation with A20. Mice haploinsufficient for A20, or harboring fibroblasts-specific A20 deletion, recapitulated major pathological and genomic features of SSc, whereas DREAM-null mice showed elevated A20 expression and were protected from fibrosis. In fibroblasts, A20 mitigated ex vivo profibrotic responses. An anti-fibrotic small molecule targeting the adiponectin receptors stimulated A20 expression in vitro in wildtype but not A20-deficient fibroblasts, and in bleomycin-treated mice. Thus, A20 has a novel function in negative regulation of fibroblast responses, and together with DREAM, constitutes a critical regulatory network governing the fibrotic process in SSc, suggesting that A20 and DREAM represent novel druggable targets.

2022-02-01 | GSE194380 | GEO

RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

Project description:Purpose: The goals of this study are to compare the transcriptome profiling (RNA-seq) of different A20 expression in HCT116 cells, to find potiential target genes for A20 mediated immnue escape. Results: There were 352 genes altered after A20 was knocked out with the log-fold >2 or <-2 compared to WT cells, and p value<0.01 . And 143 genes changed after rescued the expression of A20 in A20-KO cells compared to A20-KO cells. Among these altered genes, 13 genes were changes consistently. Conclusion:Gain- and loss-A20 functional studies proved that A20 could decrease the ¡°eat-me¡± signal calreticulin (CRT) protein on cell membranes via stabilizing stanniocalcin 1 (STC1). Mechanistically, A20 inhibited the degradation of STC1 protein which could capture the CRT inside cell rather than to translocated to cell membrane.

2023-08-30 | GSE206390 | GEO

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