Defining the role of NF-ĸB p105/p50 in human macrophage through the transcriptomic analysis of NFKB1 deletion in THP-1 cells
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PROVIDER: PRJNA680317 | ENA |
REPOSITORIES: ENA
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Project description:Effect of LPS stimulation on WT vs NFKB1-/- human macrophage induced THP-1 cell line
2021-11-03 | GSE162015 | GEO
Project description:We report the application of ChIP-Seq for high-throughput profiling of NFKB1/p50 binding dynamics. The binding profiles were performed under three conditions/models. We first examine the p50 binding in HEK293T cells during G1 and S phase. HEK293T cells were synchronized with double thymidine block method. Before and after release to S phase, ChIP was performed, and chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that these NFKB1/p50 binding peaks in G1 phase dramatically reduced at S phase. Then, we further examine the p50 binding in HEK293T/TopBP1 cells in response to tamoxifen treatment. These cells have stable expression of TopBP1 activation domain fusion with estrogen receptor. After treatment, chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that these NFKB1/p50 binding peaks in vehicle control sample dramatically reduced after tamoxifen treatment. Final, we compare the genome wide binding behavior of wild type p50 and mutant p50 2KR (K354R and K356R). HEK293T cells was transfected with plasmids expression HA-tagged wild type or mutation p50. Chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that both wild type and p50 2KR mutant share similar binding profile. However, in general, p50 mutant has less binding affinity to NFKB binding sites. This study provides a preliminary but solid basis to our understanding of NFKB1/p50 binding dynamics.
2020-08-13 | GSE129618 | GEO
Project description:Phosphorylation of the NF-ĸB p50 subunit is known to regulate target gene expression. The role of p50 S80 phosphorylation in regulating LPS-induced transcription by utilising wild type (WT) and NFKB1S80A THP-1 cells is investigated.
2020-09-19 | GSE120212 | GEO
Project description:Background: Ozone (O3) is the predominant oxidant air pollutant associated with respiratory inflammation, lung dysfunction, and worsening preexisting airway diseases. We previously determined that lack of NF-kB signlaing pathway suppressed lung injury and inflammation caused by O3 in mice. The current study was to determine transcriptome mechanisms orchestrated by NF-kB during the development of pulmonary O3 injury. Methods: To investigate the role of NF-kB1 pathway in lung gene expression changes, Nfkb1-deficient (Nfkb1-/-) and wild-type (Nfkb1+/+) mice were exposed to air or 0.3-ppm O3. Total RNAs were isolated from lung homogenates and cDNA microarray analyses were performed to elucidate NF-kB1-directed transcriptomics in basal lungs (air-exposed) as well as in the lung exposed to O3 (48 hr). Results: In air-exposed Nfkb1-/- lungs, leukocyte extravasation/adhesion and antigen presentation genes were overexpressed while immunity genes were suppressed, supporting the dual role of Nf-kB1 homodimer as a transcriptional repressor as well as transcriptional activator and the phenotype of Nfkb1-/- mice (defective response to infection and specific antibody production). After O3 exposure. Nfkb1-/- mice showed suppressed expression of lung cell cycle genes and enhanced expression of DNA damage checkpoint regulation pathway genes, compared to Nfkb1+/+ mice. Conclusion: Overall, deficiency of NF-kB1 in mouse lungs altered transcriptomes to protect lungs from O3-induced inflammation, cell proliferation, and DNA damages.
2021-09-29 | GSE166398 | GEO
Project description:Effect of NF-kappa B (NF-kB) p50 (Nfkb1) deletion on ozone-induced pulmonary transcriptome changes in mice
| PRJNA700686 | ENA
Project description:Genome-wide maps of NFKB1/p50 binding dynamics
| PRJNA531961 | ENA
Project description:Skeletal muscle atrophy is a debilitating condition associated with weakness, fatigue, and reduced functional capacity. Nuclear factor-kappaB (NF-κB) transcription factors play a critical role in atrophy. Knockout of genes encoding p50 or the NF-κB co-transactivator, Bcl-3, abolish disuse atrophy and thus they are NF-κB factors required for disuse atrophy. We do not know however, the genes targeted by NF-κB that produce the atrophied phenotype. Here we identify the genes required to produce disuse atrophy using gene expression profiling in wild type compared to Nfkb1 (gene encodes p50) and Bcl-3 deficient mice. There were 185 and 240 genes upregulated in wild type mice due to unloading, that were not upregulated in Nfkb1-/- and Bcl-3-/- mice, respectively, and so these genes were considered direct or indirect targets of p50 and Bcl-3. All of the p50 gene targets were contained in the Bcl-3 gene target list. Most genes were involved with protein degradation, signaling, translation, transcription, and transport. To identify direct targets of p50 and Bcl-3 we performed chromatin immunoprecipitation of selected genes previously shown to have roles in atrophy. Trim63 (MuRF1), Fbxo32 (MAFbx), Ubc, Ctsl, Runx1, Tnfrsf12a (Tweak receptor), and Cxcl10 (IP-10) showed increased Bcl-3 binding to κB sites in unloaded muscle and thus were direct targets of Bcl-3. p50 binding to the same sites on these genes either did not change or increased, supporting the idea of p50:Bcl-3 binding complexes. p65 binding to κB sites showed decreased or no binding to these genes with unloading. Fbxo9, Psma6, Psmc4, Psmg4, Foxo3, Ankrd1 (CARP), and Eif4ebp1 did not show changes in p65, p50, or Bcl-3 binding to κB sites, and so were considered indirect targets of p50 and Bcl-3. This work represents the first study to use a global approach to identify genes required to produce the atrophied phenotype with disuse. 24 mice were used based on 4 mice per group, 3 mouse genotypes (wild type, Nfkb1-/-, Bcl3-/-) and 2 conditions (weight-bearing and unloaded).
2011-01-10 | E-GEOD-23497 | biostudies-arrayexpress
Project description:Pro-inflammatory cytokines were shown to promote growth and survival of cancerous cells. TNF induced RelA:p50 NF-κB dimer via the canonical pathway is thought to link inflammation with cancer. Integrating biochemical and computational studies we identify that deficiency of non-canonical signal transducer p100 triggers a positive autoregulatory loop, which instead perpetuates an alternate RelB:p50 containing NF-κB activity upon TNF treatment. TNF stimulated RelB:p50 dimer is sufficient for mediating NF-κB target gene-expressions and suppressing apoptotic cellular death independent of principal NF-κB subunit RelA. We further demonstrate that activating mutations in non-canonical NF-κB module deplete multiple myeloma cells of p100, thereby, provoking autoregulatory RelB:p50 activation. Finally, autoregulatory control reinforces protracted pro-survival NF-κB response, albeit comprising of RelB:p50, upon TNF priming that protects myeloma cells with dysfunctional p100 from subsequent apoptotic insults. In sum, we present evidence for positive autoregulation mediated through the NF-κB system and its potential involvement in human neoplasm.
2017-06-12 | GSE68615 | GEO
Project description:Skeletal muscle atrophy is a debilitating condition associated with weakness, fatigue, and reduced functional capacity. Nuclear factor-kappaB (NF-κB) transcription factors play a critical role in atrophy. Knockout of genes encoding p50 or the NF-κB co-transactivator, Bcl-3, abolish disuse atrophy and thus they are NF-κB factors required for disuse atrophy. We do not know however, the genes targeted by NF-κB that produce the atrophied phenotype. Here we identify the genes required to produce disuse atrophy using gene expression profiling in wild type compared to Nfkb1 (gene encodes p50) and Bcl-3 deficient mice. There were 185 and 240 genes upregulated in wild type mice due to unloading, that were not upregulated in Nfkb1-/- and Bcl-3-/- mice, respectively, and so these genes were considered direct or indirect targets of p50 and Bcl-3. All of the p50 gene targets were contained in the Bcl-3 gene target list. Most genes were involved with protein degradation, signaling, translation, transcription, and transport. To identify direct targets of p50 and Bcl-3 we performed chromatin immunoprecipitation of selected genes previously shown to have roles in atrophy. Trim63 (MuRF1), Fbxo32 (MAFbx), Ubc, Ctsl, Runx1, Tnfrsf12a (Tweak receptor), and Cxcl10 (IP-10) showed increased Bcl-3 binding to κB sites in unloaded muscle and thus were direct targets of Bcl-3. p50 binding to the same sites on these genes either did not change or increased, supporting the idea of p50:Bcl-3 binding complexes. p65 binding to κB sites showed decreased or no binding to these genes with unloading. Fbxo9, Psma6, Psmc4, Psmg4, Foxo3, Ankrd1 (CARP), and Eif4ebp1 did not show changes in p65, p50, or Bcl-3 binding to κB sites, and so were considered indirect targets of p50 and Bcl-3. This work represents the first study to use a global approach to identify genes required to produce the atrophied phenotype with disuse.
2011-01-10 | GSE23497 | GEO
Project description:In future high-throughput transcriptomic studies, we propose that the use of cell lines nullizygous for important target genes of environmental chemicals will greatly facilitate the interpretation of gene expression profiles. To provide support for this concept, we generated transcript profiles of known or putative NF-kB activators in wild-type and NFKB1-null HeLa cells. Both cell lines were treated with interleukin 1 (IL1beta), tumor necrosis alpha (TNFalpha) or one of two chemicals identified in high throughput assays for NF-kB activity (chlorhexidine diacetate and carbocyanine). The profiles were generated using TempO-Seq targeted sequencing of ~3000 human genes. Almost all of the genes regulated by IL1beta and TNFalpha in wild-type cells were no longer altered in the NFKB1-null cells and approximately half of the genes regulated by Chlorhexidine diacetate and carbocyanine were dependent on NFKB1 for expression changes. These studies demonstrate that many of the changes in gene expression after exposure to the putative NF-kB activators were NFKB1-dependent.
2021-07-01 | GSE153616 | GEO