Biology subjects

Scheidereit, C.

Publications and source records attributed to Scheidereit, C..

7 recordsLinked to original sources

bioRxiv2023

A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1

The activation of IKK/ NF-{kappa}B by genotoxic stress is a crucial process in the DNA damage response. Due to the anti-apoptotic impact of NF-{kappa}B it can affect cell fate decisions upon DNA damage and therefore interfere with tumour therapy-induced cell death. Here, we developed a dynamical model describing IKK/ NF-{kappa}B signalling that faithfully reproduces quantitative time course data and enabled a detailed analysis of pathway regulation. The approach elucidates a pathway topology with two hubs, where the first integrates signals from two DNA damage sensors and the second forms a coherent feedforward loop. The analyses reveal a critical role of the sensor protein PARP-1 in the pathway regulation. Introducing a method for calculating the impact of individual components on pathway activity in a time-resolved manner we show how irradiation dose influences pathway activation. Our results give a mechanistic understanding relevant for the interpretation of experimental and clinical studies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/538686v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@5ba82borg.highwire.dtl.DTLVardef@17dc530org.highwire.dtl.DTLVardef@1cf6fborg.highwire.dtl.DTLVardef@19ae207_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2022

A new type of transcriptional reprogramming by an IRF4 mutation in lymphoma

SUMMARY PARAGRAPHDisease-causing mutations in genes encoding transcription factors (TFs) are a recurrent finding in hematopoietic malignancies and might involve key regulators of lineage adherence and cellular differentiation1-3. Such mutations can affect TF-interactions with their cognate DNA-binding motifs4, 5. Whether and how TF-mutations impact upon the nature of binding to TF composite elements (CE) and influence their interaction with other TFs is unclear. Here, we report a new mechanism of TF alteration in human lymphomas with perturbed B cell identity. It is caused by a recurrent somatic missense mutation c.295T>C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cell-differentiation and -activation6, 7. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF composite elements (CEs). Furthermore, IRF4-C99R thoroughly modifies IRF4 function, by blocking IRF4-dependent plasma cell induction, and up-regulating disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single arginine mutation creates a complex switch of TF specificity and gene regulation. These data open the possibility of designing specific inhibitors to block the neomorphic, disease-causing DNA-binding activities of a mutant transcription factor.

cancer biology↗

bioRxiv2022

Autophagy limits inflammatory gene expression through targeting of nuclear p65/RelA by LC3 and p62 for lysosomal degradation

The interplay between NF-{kappa}B signaling and autophagy regulates inflammatory signaling in different cellular contexts and in response to different stimuli. The impairment of this crosstalk may play a role in chronic inflammation and in tumorigenesis. However, the molecular mechanism by which these two pathways interact to regulate the inflammatory response remains elusive. By using biochemical analysis and imaging techniques, we characterized the interaction of the endogenous autophagic marker LC3 and NF-{kappa}B/p65 in response to different stress conditions. Following irradiation or TNF stimulation, nuclear accumulation of LC3 strongly co-localized with p65, suggesting that nuclear p65 is targeted for autophagic degradation. Mechanistically, we showed that the nuclear p65-LC3 interaction is mediated by ubiquitination of the same p65, which is recognized by the cargo receptor p62, resulting in its cytoplasmic export and lysosomal proteolysis. Accordingly, autophagy inhibition by depletion of the essential autophagy gene ATG16L1 selectively stabilizes nuclear p65, in turn enhancing NF-{kappa}B gene expression of pro-inflammatory cytokine. Our results revealed a novel molecular mechanism that modulates the NF-{kappa}B inflammatory response through nuclear sequestration of the NF-{kappa}B/p65 subunit by autophagy proteins. These findings are of importance for developing novel therapeutic strategies against chronic inflammatory diseases displaying defective autophagy and constitutive NF-{kappa}B activity.

molecular biology↗

bioRxiv2021

TSG101 Associates with PARP1 and is Essential for PARylation and DNA Damage-induced NF-κB Activation

In a genome-wide screening for components of the dsDNA-break-induced IKK-NF-{kappa}B pathway we identified scores of regulators, including tumor susceptibility protein TSG101. TSG101 is essential for DNA damage-induced formation of cellular poly(ADP-ribose) (PAR). TSG101 directly binds to PARP1 and is required for PARP1 activation. This function of TSG101 is independent of its role in the ESCRT-I endosomal sorting complex. In the absence of TSG101, the PAR-dependent formation of a nuclear PARP1-IKK{gamma} signalosome, which triggers IKK activation, is impaired. According to its requirement for PARP1 and NF-{kappa}B activation, TSG101 deficient cells are defective in DNA repair and apoptosis protection. Loss of TSG101 results in PARP1 trapping at damage sites and mimics the effect of pharmacological PARP-inhibition. We also show that loss of TSG101 in connection with inactivated tumor suppressors BRCA1/2 in breast cancer cells is lethal. Our results imply TSG101 as a therapeutic target to achieve synthetic lethality in cancer treatment.

molecular biology↗

bioRxiv2019

A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA

The I{kappa}B kinase (IKK) - NF-{kappa}B pathway is activated as part of the DNA damage response and controls both resistance to apoptosis and inflammation. How these different functions are achieved remained unknown. We demonstrate here that DNA double strand breaks elicit two subsequent phases of NF-{kappa}B activation in vivo and in vitro, which are mechanistically and functionally distinct. RNA-sequencing reveals that the first phase controls anti-apoptotic gene expression, while the second drives expression of senescence-associated secretory phenotype (SASP) genes. The first, rapidly activated phase is driven by the ATM-PARP1-TRAF6-IKK cascade, which triggers proteasomal destruction of I{kappa}B and is terminated through I{kappa}B (NFKBIA) re-expression. The second phase is activated days later in senescent cells but is independent of IKK and the proteasome. An altered phosphorylation status of p65, in part driven by GSK3{beta}, results in transcriptional silencing of NFKBIA and IKK-independent, constitutive activation of NF-{kappa}B in senescence. Collectively, our study reveals a novel physiological mechanism of NF-{kappa}B activation with important implications for genotoxic cancer treatment.

cell biology↗

bioRxiv2019

Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors

Although human endogenous retroviruses (HERVs) represent a substantial proportion of the human genome and some HERVs have been suggested to be involved in neurological disorders, little is known about their biological function and pathophysiological relevance. HERV-K(HML-2) comprises evolutionarily young proviruses transcribed in the brain. We report that RNA derived from an HERV-K(HML-2) env gene region binds to the human RNA-sensing Toll-like receptor (TLR) 8, activates human TLR8, as well as murine Tlr7, and causes neurodegeneration through TLR8 and Tlr7 in neurons and microglia. HERV-K(HML-2) RNA introduced extracellularly into the cerebrospinal fluid (CSF) of either C57BL/6 wild-type mice or APPPS1 mice, a mouse model for Alzheimers disease (AD), resulted in neurodegeneration. Tlr7-deficient mice were protected against neurodegenerative effects, but were re-sensitized towards HERV-K(HML-2) RNA when neurons ectopically expressed murine Tlr7 or human TLR8. Accordingly, transcriptome datasets of human brain samples from AD patients revealed a specific correlation of upregulated HERV-K(HML-2) and TLR8 RNA expression. HERV-K(HML-2) RNA was detectable more frequently in CSF from AD individuals compared to controls. Our data establish HERV-K(HML-2) RNA as an endogenous ligand for human TLR8 and murine Tlr7 and imply a functional contribution of specific human endogenous retroviral transcripts to neurodegenerative processes such as AD.

neuroscience↗

bioRxiv2019

A quantitative modular modeling approach reveals the consequences of different A20 feedback implementations for the NF-kB signaling dynamics

Signaling pathways involve complex molecular interactions and are controlled by non-linear regulatory mechanisms. If details of regulatory mechanisms are not fully elucidated, they can be implemented by different, equally reasonable mathematical representations in computational models. The study presented here focusses on NF-{kappa}B signaling, which is regulated by negative feedbacks via I{kappa}B and A20. A20 inhibits NF-{kappa}B activation indirectly through interference with proteins that transduce the signal from the TNF receptor complex to activate the I{kappa}B kinase (IKK) complex. We focus on the question how different implementations of the A20 feedback impact the dynamics of NF-{kappa}B. To this end, we develop a modular modeling approach that allows combining previously published A20 modules with a common pathway core module. The resulting models are based on a comprehensive experimental data set and therefore show quantitatively comparable NF-{kappa}B dynamics. Based on defined measures for the initial and long-term behavior we analyze the effects of a wide range of changes in the A20 feedback strength, the I{kappa}B feedback strength and the TNF stimulation strength on NF-{kappa}B dynamics. This shows similarities between the models but also model-specific differences. In particular, the A20 feedback strength and the TNF stimulation strength affect initial and long-term NF-{kappa}B concentrations differently in the analyzed models. We validated our model predictions experimentally by varying TNF concentrations applied to HeLa cells. These time course data indicate that only one of the A20 feedback models appropriately describes the impact of A20 on the NF-{kappa}B dynamics.\n\nAuthor summaryModels are abstractions of reality and simplify a complex biological process to its essential components and regulations while preserving its particular spatial-temporal characteristics. Modelling of biological processes is based on assumptions, in part to implement the necessary simplifications but also to cope with missing knowledge and experimental information. In consequence, biological processes have been implemented by different, equally reasonable mathematical representations in computational models. We here focus on the NF-{kappa}B signaling pathway and develop a modular modeling approach to investigate how different implementations of a negative feedback regulation impact the dynamical behavior of a computational model. Our analysis shows similarities of the models with different implementations but also reveals implementation-specific differences. The identified differences are used to design and perform informative experiments that elucidate unknown details of the regulatory feedback mechanism.

systems biology↗