Human - murine concordance of molecular signatures in nerve-sparing murine partial bladder outlet obstruction (NeMO)
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ABSTRACT:
PROVIDER: PRJNA861847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20584065.fastq.gz | Fastqsanger.gz | |||
| SRR20584066.fastq.gz | Fastqsanger.gz | |||
| SRR20584067.fastq.gz | Fastqsanger.gz | |||
| SRR20584068.fastq.gz | Fastqsanger.gz | |||
| SRR20584069.fastq.gz | Fastqsanger.gz |
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Project description:Recently, we described a nerve-sparing mid-urethra model of partial outlet obstruction (NeMO) that has high consistency and minimal mortalities, unlike the traditional model of obstruction proximal to the bladder neck. To uncover pathogenic pathways in PBO, we performed NeMO and examined the transcriptional responses in the bladder. NeMO increased bladder mass, relative bladder mass, hyperactivity and decreased voiding efficiency. In NeMO vs. sham bladders, there were 831 differentially expressed genes, which correlated significantly with physiologic parameters. Of the 796 genes mapped to human orthologues, upregulated genes were enriched for functions related to extracellular matrix, and cytokine activation, and downregulated genes were enriched for functions relating to muscle contraction and metabolism. To identify candidate drug targets for the treatment of PBO, we analysed the conserved transcriptional response to PBO in human and mouse. Gene sets related to cytokine activation, including the TNF pathway, were consistently upregulated in both human and mouse bladders affected by obstruction, revealing a potential therapeutic target. Accordingly, we depleted macrophages, which are an important source of TNF, with clodronate (CL). In NeMO, CL significantly decreased hyperactive voiding, residual volumes and improved voiding efficiency (p<0.05). Moreover, the expression levels of cytokines/chemokines correlated with several bladder functional parameters. Thus, genes that control progression of pathology in bladder obstruction are consistently dysregulated in NeMO and human bladders affected by PBO, supporting the use of the nerve-sparing mouse obstruction model for therapeutic exploration.
2022-07-27 | GSE209625 | GEO
Project description:This study investigates the impact of NEMO knockout on healing from traumatic tibial injury within a murine muscle satellite cell model. NEMO KO mice were profiled via RNA-seq at 0, 2, 4, 7 days post cold shock injury (DPI). The largest transcriptional response was observed at 2 DPI within the WT model, but NEMO knockouts exhibited delayed myogenesis and muscle regenerative defects. Furthermore, it was observed that new fiber formation is defected upon transplantation of mutant derived MuSCs. mRNA profiling further suggested that loss of NF-kB signaling in MuSC’s in response to NEMO KO alters their ECM and cytokine secretome production. Additional profiling was performed at 2DPI via ATAC-seq within WT and NEMO mouse satellite cells, with observed changes in chromatin remodeling suggesting bidirectional MuSC-transcriptional regulator communication in skeletal muscle regeneration.
2024-04-01 | GSE262348 | GEO
Project description:In response to DNA double strand breaks (DSBs), the ATM kinase activates NF-κB factors to stimulate gene expression changes that promote survival and allow time for cells to repair damage. In cell lines, ATM can activate NF-κB transcription factors via two independent, convergent mechanisms. One is ATM-mediated phosphorylation of nuclear NF-κB essential modulator (Nemo) protein, which leads to monoubiquitylation and export of Nemo to the cytoplasm where it engages the IκB kinase (IKK) complex to activate NF-κB. Another is DSB-triggered migration of ATM into the cytoplasm where it promotes monoubiquitylation of Nemo and resulting IKK-mediated activation of NF-κB. ATM has many other functions in the DSB response beyond activation of NF-κB, and Nemo activates NF-κB downstream of diverse stimuli, including developmental or proinflammatory stimuli such as lipopolysaccharides (LPS). To elucidate the in vivo role of DSB-induced, ATM-dependent changes in expression of NF-κB-responsive genes, we generated mice expressing phosphomutant Nemo protein lacking consensus SQ sites for phosphorylation by ATM or related kinases. We demonstrate that these mice are viable/healthy, fertile, and exhibit overall normal B and T lymphocyte development. Moreover, treatment of their B lineage cells with LPS induces normal NF-κB-regulated gene expression changes. Furthermore, in marked contrast to results from a pre-B cell line, primary B lineage cells expressing phosphomutant Nemo treated with the genotoxic drug etoposide induce normal ATM- and Nemo-dependent changes in expression of NF-κB-regulated genes. Our data demonstrate that ATM-dependent phosphorylation of Nemo SQ motifs in vivo is dispensable for DSB-signaled changes in expression of NF-κB-regulated genes.
2024-08-08 | GSE264315 | GEO
Project description:Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstream NF-kappaB transcription factor and subsequent gene activation. The position of NEMO within this pathway makes it an attractive target from which to search for new proteins that link NF-kappaB signaling to additional pathways and upstream effectors. In this work, we have used protein microarrays to identify novel NEMO interactors. A total of 112 protein interactors were identified, with the most statistically significant hit being the canonical NEMO interactor IKKbeta, with IKKalpha also being identified. Of the novel interactors, more than 30% were kinases, while at least 25% were involved in signal transduction. Binding of NEMO to several interactors, including CALB1, CDK2, SAG, SENP2 and SYT1, was confirmed using GST pulldown assays and coimmunoprecipitation, validating the initial screening approach. Overexpression of CALB1, CDK2 and SAG was found to stimulate transcriptional activation by NF-kappaB, while SYT1 overexpression repressed TNFalpha-dependent NF-kappaB transcriptional activation in human embryonic kidney cells. Corresponding with this finding, RNA silencing of CDK2, SAG and SENP2 reduced NF-kappaB transcriptional activation, supporting a positive role for these proteins in the NF-kappaB pathway. The identification of a host of new NEMO interactors opens up new research opportunities to improve understanding of this essential cell signaling pathway. For microarray screening, Invitrogen Protoarray v4.0 protein microarrays were used. Human NEMO expressed as a C-terminal GST fusion was purified from E. coli lysates and labelled with biotin. NEMO or biotinylated GST were applied to the microarrays and binding partners detected using streptavidin-Alexa Fluor 647. Significant interactors on both arrays were detected using Invitrogen Protoarray Prospector software and a Z-score cutoff of 3.0. Following subtraction of interactors present on the GST control array, a final set of significant NEMO interactors was derived. Full experimental details are supplied in Fenner, B. J., Scannell, M. & Prehn, J. H. M. (2010). Expanding the substantial interactome of NEMO using protein microarrays. PLoS ONE (in press).
2010-06-19 | E-GEOD-19841 | biostudies-arrayexpress
Project description:Host defense and inflammation are regulated by the NF-kB essential modulator (NEMO), a scaffolding protein with a broad immune cell and tissue expression profile. Hypomorphic mutations in inhibitor of nuclear factor kappa B kinase regulatory subunit gamma (IKBKG) encoding NEMO typically present with immunodeficiency. Here we characterized a novel pediatric autoinflammatory syndrome in 3 unrelated male patients with distinct X-linked IKBKG germ-line mutations that led to overexpression of a NEMO protein isoform lacking the domain encoded by exon 5 (NEMO-Dex5). This isoform failed to associate with TANK binding kinase 1 (TBK1), and dermal fibroblasts from affected patients activated NF-kB in response to TNF, but not TLR3 or RIG-I-like-receptor (RLR) stimulation when isoform levels were high. By contrast, T cells, monocytes and macrophages that expressed NEMO-Dex5 exhibited increased NF-kB activation and IFN production, and blood cells from these patients expressed a strong interferon and NF-kB transcriptional signature. Immune cells and TNF-stimulated dermal fibroblasts upregulated the inducible IKK protein (IKKi) that was stabilized by NEMO-Dex5, promoting type I IFN induction and antiviral responses. These data reveal how IKBKG mutations that lead to alternative splicing of skipping exon 5 cause a clinical phenotype we name NEMO Deleted exon 5 Autoinflammatory Syndrome (NDAS), distinct from the immunodeficiency syndrome resulting from loss-of-function IKBKG mutations.
2023-05-17 | GSE196243 | GEO
Project description:Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstream NF-kappaB transcription factor and subsequent gene activation. The position of NEMO within this pathway makes it an attractive target from which to search for new proteins that link NF-kappaB signaling to additional pathways and upstream effectors. In this work, we have used protein microarrays to identify novel NEMO interactors. A total of 112 protein interactors were identified, with the most statistically significant hit being the canonical NEMO interactor IKKbeta, with IKKalpha also being identified. Of the novel interactors, more than 30% were kinases, while at least 25% were involved in signal transduction. Binding of NEMO to several interactors, including CALB1, CDK2, SAG, SENP2 and SYT1, was confirmed using GST pulldown assays and coimmunoprecipitation, validating the initial screening approach. Overexpression of CALB1, CDK2 and SAG was found to stimulate transcriptional activation by NF-kappaB, while SYT1 overexpression repressed TNFalpha-dependent NF-kappaB transcriptional activation in human embryonic kidney cells. Corresponding with this finding, RNA silencing of CDK2, SAG and SENP2 reduced NF-kappaB transcriptional activation, supporting a positive role for these proteins in the NF-kappaB pathway. The identification of a host of new NEMO interactors opens up new research opportunities to improve understanding of this essential cell signaling pathway.
2010-01-20 | GSE19841 | GEO
Project description:We previously demonstrated that IKKα binds to and phosphorylates ATM thus potentiating the non-homologous end joining DNA damage repair pathway in cancer cells. Hence, inhibiting IKKα enhances the efficacy of DNA damage-based anticancer therapy. Whether additional elements contribute to this resistance-related mechanism remains unknown. We here show that NEMO physically interacts with the ATM-IKKα complex before damage. Upon exposure to damaging agents, NEMO is dispensable for ATM activation, but it is required to drive active ATM and IKKα to the sites of damage thus enabling DNA damage resolution. Recognition of damaged DNA by this IKKα/NEMO/ATM complex is partially mediated by direct interaction of NEMO to histones but highly dependent on PARP1 activity. Finally, we detected increased ATR activity in NEMO-deficient cells, and that ATR inhibition potentiates the effect of chemotherapy upon NEMO or IKKα depletion. Bioinformatic analysis of public CRC datasets support the functional impact of the IKKα/NEMO/ATM pathway in patient prognosis, which could be therapeutically exploited.
2024-02-11 | PXD043552 | Pride
Project description:Many immune responses depend upon activation of NF-κB, a key transcription factor in the elicitation of a cytokine response. Here we show that N4BP1 inhibits TLR-dependent activation of NF-κB by interacting with the NF-κB signaling essential modulator (NEMO, also known as IκB kinase γ) to attenuate NEMO-NEMO dimerization or oligomerization. The UBA-like (ubiquitin associated-like) and CUE-like (ubiquitin conjugation to ER degradation) domains in N4BP1 mediate the interaction with the NEMO COZI domain. Both in vitro and in mice, N4bp1 deficiency specifically enhances TRIF-independent (TLR2, TLR7, or TLR9-mediated), but not TRIF-dependent (TLR3 or TLR4-mediated), NF-κB activation leading to increased production of proinflammatory cytokines. In response to TLR4 or TLR3 activation, TRIF causes activation of caspase-8, which cleaves N4BP1 distal to residues D424 and D490 and abolishes its inhibitory effect. N4bp1-/- mice also exhibit diminished numbers of T cells in the peripheral blood. Our work identifies N4BP1 as an inhibitory checkpoint protein that must be overcome to activate NF-κB, and a TRIF-initiated caspase-8-dependent mechanism by which this is accomplished.
2021-02-08 | GSE165916 | GEO
Project description:The canonical NF-κB pathway is active in 70% of all pancreatic cancer cases and NF-κB Essential Modulator (NEMO) is essential for the activation of this pathway. In our study, we used KC mice, which express the oncogenic KRAS and develop precancerous lesions termed Pancreatic Intraepithelial Neoplasias (PanINs), and KNeC mice, which express the oncogenic KRAS and have NEMO deleted in their pancreatic cells. These mice were injected with cerulein to promote the development of pancreatitis (cerulein dosage= 50μg/kg). Cerulein was injected at 8 hourly intervals for 2 days in total. The first injection day was when mice reached their sixth week of age and the second injection day was 3 days after the first injection day. Both KC and KNeC mice developed PanINs. At the age of 10 months, pancreata of KC and KNeC mice were analyzed. Using laser capture microdissection, PanINs from both groups were excised and their transcriptome was analyzed though RNA-seq.
2024-03-13 | E-MTAB-12433 | biostudies-arrayexpress
Project description:Death receptor-mediated hepatocyte apoptosis is implicated in a wide range of liver diseases including viral hepatitis, alcoholic hepatitis, ischemia/reperfusion injury, fulminant hepatic failure, cholestatic liver injury and cancer. Deletion of NF-ĸB essential modulator in hepatocytes (NemoΔhepa) causes the spontaneous development of hepatocellular carcinoma preceded by steatohepatitis in mice and thus serves as an excellent model for the progression from chronic hepatitis to liver cancer. In the present study we aimed to dissect the death-receptor mediated pathways that contribute to liver injury in NemoΔhepa mice. Therefore, we generated NemoΔhepa/TRAIL-/- and NemoΔhepa/TNFR1-/- animals and analyzed the progression of liver injury. NemoΔhepa/TRAIL-/- displayed a similar phenotype to NemoΔhepa mice characteristic of high apoptosis, infiltration of immune cells, hepatocyte proliferation and steatohepatitis. These pathophysiological features were significantly ameliorated in NemoΔhepa/TNFR1-/- livers. Hepatocyte apoptosis was increased in NemoΔhepa and NemoΔhepa/TRAIL-/- mice while NemoΔhepa/TNFR1-/- animals showed reduced cell death concomitant with a strong reduction in pJNK levels. Cell cycle parameters were significantly less activated in NemoΔhepa/TNFR1-/- livers. Additionally, markers of liver fibrosis and indicators of tumour progression were significantly decreased in these animals. The present data demonstrate that the death receptor TNFR1 but not TRAIL is important in determining progression of liver injury in hepatocyte-specific Nemo knockout mice. Expression profiling of livers from wild type, NEMO, NEMO-TRIAL, and NEMO-TNFR null mice
2014-09-03 | E-GEOD-33161 | biostudies-arrayexpress