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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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE162015 | GEO | 2021/11/03
REPOSITORIES: GEO
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Project description:Defining the role of NF-ĸB p105/p50 in human macrophage through the transcriptomic analysis of NFKB1 deletion in THP-1 cells
| PRJNA680317 | ENA
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: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: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:Genome-wide maps of NFKB1/p50 binding dynamics
| PRJNA531961 | ENA
Project description:Effect of NF-kappa B (NF-kB) p50 (Nfkb1) deletion on ozone-induced pulmonary transcriptome changes in mice
| PRJNA700686 | ENA
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
Project description:M1 and M2 macrophage phenotypes, which mediate proinflammatory and antiinflammatory functions, respectively, represent the extremes of immunoregulatory plasticity in the macrophage population. This plasticity can also result in intermediate macrophage states that support a balance between these opposing functions. In sepsis, M1 macrophages can compensate for hyperinflammation by acquiring an M2-like immunosuppressed status that increases the risk of secondary infection and death. The M1 to M2 macrophage reprogramming that develops during LPS tolerance resembles the pathological antiinflammatory response to sepsis. Here, we determined that p21 regulates macrophage reprogramming by shifting the balance between active p65-p50 and inhibitory p50-p50 NF-?B pathways. p21 deficiency reduced the DNA-binding affinity of the p50-p50 homodimer in LPS-primed and -rechallenged macrophages, impairing their ability to attenuate IFN-? production and acquire an M2-like hyporesponsive status. High p21 levels in sepsis patients correlated with low IFN-? expression, and p21 knockdown in human monocytes corroborated its role in IFN-? regulation. The data demonstrate that p21 adjusts the equilibrium between p65-p50 and p50-p50 NF-?B pathways to mediate macrophage plasticity in LPS tolerance. Identifying p21-related pathways involved in monocyte reprogramming may lead to potential targets for sepsis treatment.
| S-EPMC4966310 | biostudies-literature
Project description:Flexor tendon injuries heal with excessive scar tissue that limits range of motion and increases incidence of re-rupture. The molecular mechanisms that govern tendon healing are not well defined. Both the canonical nuclear factor kappa B (NF-κB) and mitogen activated protein kinase (MAPK) pathways have been implicated in tendon healing. The gene NFKB1 (proteins p105/p50) is involved in both NF-κB and MAPK signaling cascades. In the present study, we tested the hypothesis that global NFKB1 deletion would increase activation of both NF-κB and MAPK through loss of signaling repressors, resulting in increased matrix deposition and altered biomechanical properties. As hypothesized, NFKB1 deletion increased activation of both NF-κB and MAPK signaling. While gliding function was not affected, NFKB1 deletion resulted in tendons that were significantly stiffer and trending towards increased strength by four weeks post-repair. NFKB1 deletion resulted in increased collagen deposition, increase macrophage recruitment, and increased presence of myofibroblasts. Furthermore, NFKB1 deletion increased expression of matrix-related genes (Col1a1, Col3a1), macrophage-associated genes (Adgre1, Ccl2), myofibroblast markers (Acta2), and general inflammation (Tnf). Taken together, these data suggest that increased activation of NF-κB and MAPK via NFKB1 deletion enhance macrophage and myofibroblast content at the repair, driving increased collagen deposition and biomechanical properties.
| S-EPMC6662789 | biostudies-literature
Project description:Investigsting the role of NF-ĸB p50 S80 phosphorylation in regulating LPS-induced transcription in THP-1 cells
| PRJNA492130 | ENA