A
            <scp>TNF</scp>
            ‐p100 pathway subverts noncanonical
            <scp>NF</scp>
            ‐κB signaling in inflamed secondary lymphoid organs

Mukherjee, Tapas; Chatterjee, B. B.; Dhar, Atika; Bais, Sachendra S.; Chawla, M. L.; Roy, Payel; George, Anna; Bal, Vineeta; Rath, Satyajit; Basak, Soumen

doi:10.15252/embj.201796919

Cited by 26 publications

(23 citation statements)

References 43 publications

(80 reference statements)

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“…Notably, we chose a low TNF concentration which would induce a distinct pro‐inflammatory response rather than cell death (Janes et al, ; Vlantis et al, ). This treatment led to the significant up‐ or down‐regulation of 15 proteins in the organoid sample group, including upregulation of typical marker proteins such as Nfkb2 (Mukherjee et al, ; Figure S3A and Table S1).…”

Section: Resultsmentioning

confidence: 99%

Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

Hausmann

Russo

Grossmann

et al. 2020

Cellular Microbiology

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Intestinal epithelial organoids established from gut tissue have become a widely used research tool. However, it remains unclear how environmental cues, divergent microbiota composition and other sources of variation before, during and after establishment confound organoid properties, and how these properties relate to the original tissue. While environmental influences cannot be easily addressed in human organoids, mice offer a controlled assay-system. Here, we probed the effect of donor microbiota differences, previously identified as a confounding factor in murine in vivo studies, on organoids. We analysed the proteomes and transcriptomes of primary organoid cultures established from two colonised and one germ-free mouse colony of C57BL/6J genetic background, and compared them to their tissue of origin and commonly used cell lines. While an imprint of microbiota-exposure was observed on the proteome of epithelial samples, the long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts and closely mimicked expression patterns in the gut epithelium. This included the inflammasome components ASC, Naip1-6, Nlrc4 and Caspase-1, which were highly expressed in all organoids compared to the reference cell line m-IC c12 or mouse embryonic fibroblasts. Taken together, these results reveal that the donor microbiota has little effect on the organoid phenotype and suggest that organoids represent a more suitable culture model than immortalised cell lines, in particular for studies of intestinal epithelial inflammasomes.

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Section: Resultsmentioning

confidence: 99%

Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

Hausmann

Russo

Grossmann

et al. 2020

Cellular Microbiology

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“…Caco-2 cells were treated with DMSO or TPEN as described above for 4 and 8 h. Nuclear extracts were prepared and processed for EMSA as described previously (21). Briefly, nuclear extracts (NE) were prepared after treating Caco-2 cells with 0.5 µM TPEN for indicated periods and normalized for protein concentration.…”

Section: Electrophoresis Mobility Shift Assays (Emsa)mentioning

confidence: 99%

Zinc Chelation Specifically Inhibits Early Stages of Dengue Virus Replication by Activation of NF-κB and Induction of Antiviral Response in Epithelial Cells

et al. 2019

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Zinc is an essential micronutrient which regulates diverse physiological functions and has been shown to play a crucial role in viral infections. Zinc has a necessary role in the replication of many viruses, however, antiviral action of zinc has also been demonstrated in in vitro infection models most likely through induction of host antiviral responses. Therefore, depending on the host machinery that the virus employs at different stages of infection, zinc may either facilitate, or inhibit virus infection. In this study, we show that zinc plays divergent roles in rotavirus and dengue virus infections in epithelial cells. Dengue virus infection did not perturb the epithelial barrier functions despite the release of virus from the basolateral surface whereas rotavirus infection led to disruption of epithelial junctions. In rotavirus infection, zinc supplementation post-infection did not block barrier disruption suggesting that zinc does not affect rotavirus life-cycle or protects epithelial barriers post-infection suggesting the involvement of cellular pathways in the beneficial effect of zinc supplementation in enteric infections. Zinc depletion by N,N,N',N'-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN) inhibited dengue virus and Japanese encephalitis virus (JEV) infection but had no effect on rotavirus. Time-of-addition experiments suggested that zinc chelation affected both early and late stages of dengue virus infectious cycle and zinc chelation abrogated dengue virus RNA replication. We show that transient zinc chelation induces ER stress and antiviral response by activating NF-kappaB leading to induction of interferon signaling. These results suggest that modulation of zinc homeostasis during virus infection could be a component of host antiviral response and altering zinc homeostasis may act as a potent antiviral strategy against flaviviruses.

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“…1C), amplification of the transcriptionally active RelB:p52 protein dimer, as predicted by the computational simulation, is not observed experimentally [ Fig. 1C (26)]. Similarly, in B cells, nfkb2 mRNA is induced by canonical pathway activity, but amplification of RelB:p52 is not seen (18).…”

Section: A Computational Model Of Nfκb Predicts Amplification Of Noncmentioning

confidence: 73%

“…Similarly, in B cells, nfkb2 mRNA is induced by canonical pathway activity, but amplification of RelB:p52 is not seen (18). Indeed, such amplification would be deleterious to developmental processes in the context of chronic inflammation (18,22,26). To establish why the computationally identified potential for substantial crosstalk is not realized, and examine the discrepancy between mRNA induction and protein dimer formation, mechanistically more detailed mathematical models of NIK-mediated reactions were constructed ( Fig.…”

Section: A Computational Model Of Nfκb Predicts Amplification Of Noncmentioning

confidence: 99%

Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB

Mitchell

Hoffmann

2019

Proc. Natl. Acad. Sci. U.S.A.

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Signaling pathways often share molecular components, tying the activity of one pathway to the functioning of another. In the NFκB signaling system, distinct kinases mediate inflammatory and developmental signaling via RelA and RelB, respectively. Although the substrates of the developmental, so-called noncanonical, pathway are induced by inflammatory/canonical signaling, crosstalk is limited. Through dynamical systems modeling, we identified the underlying regulatory mechanism. We found that as the substrate of the noncanonical kinase NIK, the nfkb2 gene product p100, transitions from a monomer to a multimeric complex, it may compete with and inhibit p100 processing to the active p52. Although multimeric complexes of p100 (IκBδ) are known to inhibit preexisting RelA:p50 through sequestration, here we report that p100 complexes can inhibit the enzymatic formation of RelB:p52. We show that the dose-response systems properties of this complex substrate competition motif are poorly accounted for by standard Michaelis-Menten kinetics, but require more detailed mass action formulations. In sum, although tonic inflammatory signaling is required for adequate expression of the noncanonical pathway precursors, the substrate complex competition motif identified here can prevent amplification of the active RelB:p52 dimer in elevated inflammatory conditions to ensure reliable RelB-dependent developmental signaling independent of inflammatory context.NFκB canonical pathway | NFκB noncanonical pathway | inflammation | crosstalk | immune development

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A TNF ‐p100 pathway subverts noncanonical NF ‐κB signaling in inflamed secondary lymphoid organs

Cited by 26 publications

References 43 publications

Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

Zinc Chelation Specifically Inhibits Early Stages of Dengue Virus Replication by Activation of NF-κB and Induction of Antiviral Response in Epithelial Cells

Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB

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