SummaryUbiquitination and deubiquitination are crucial for assembly and disassembly of signaling complexes. LUBAC-generated linear (M1) ubiquitin is important for signaling via various immune receptors. We show here that the deubiquitinases CYLD and A20, but not OTULIN, are recruited to the TNFR1- and NOD2-associated signaling complexes (TNF-RSC and NOD2-SC), at which they cooperate to limit gene activation. Whereas CYLD recruitment depends on its interaction with LUBAC, but not on LUBAC’s M1-chain-forming capacity, A20 recruitment requires this activity. Intriguingly, CYLD and A20 exert opposing effects on M1 chain stability in the TNF-RSC and NOD2-SC. While CYLD cleaves M1 chains, and thereby sensitizes cells to TNF-induced death, A20 binding to them prevents their removal and, consequently, inhibits cell death. Thus, CYLD and A20 cooperatively restrict gene activation and regulate cell death via their respective activities on M1 chains. Hence, the interplay between LUBAC, M1-ubiquitin, CYLD, and A20 is central for physiological signaling through innate immune receptors.

The development of plasma biomarkers has proven to be more challenging than initially anticipated. Many studies have reported lists of candidate proteins rather than validated candidate markers with an assigned performance to a specific clinical objective. Biomarker research necessitates a clear rational framework with requirements on a multitude of levels. On the technological front, the platform needs to be effective to detect low abundant plasma proteins and be able to measure them in a high throughput manner over a large amount of samples reproducibly. At a conceptual level, the choice of the technological platform and available samples should be part of an overall clinical study design that depends on a joint effort between basic and clinical research. Solutions to these needs are likely to facilitate more feasible studies. Targeted proteomic workflows based on SRM mass spectrometry show the potential of fast verification of biomarker candidates in plasma and thereby closing the gap between discovery and validation in the biomarker development pipeline. Biological samples need to be carefully chosen based on well-established guidelines either for candidate discovery in the form of disease models with optimal fidelity to human disease or for candidate evaluation as well-designed and annotated clinical cohort groups. Most importantly, they should be representative of the target population and directly address the investigated clinical question. A conceptual structure of a biomarker study can be provided in the form of several sequential phases, each having clear objectives and predefined goals. Furthermore, guidelines for reporting the outcome of biomarker studies are critical to adequately assess the quality of the research, interpretation and generalization of the results. By being attentive to and applying these considerations, biomarker research should become more efficient and lead to directly translatable biomarker candidates into clinical evaluation.

LUBAC modulates signalling by various immune receptors. In TNF signalling, linear (also known as M1) ubiquitin enables full gene-activation and prevents cell death. However, the mechanisms underlying cell-death prevention remain ill-defined. We show that LUBAC activity enables TBK1 and IKKε recruitment to and activation at the TNFR1-signalling complex (TNFR1-SC). Whilst exerting only limited effects on TNF-induced gene-activation, TBK1/IKKε are essential to prevent TNF-induced cell death. Mechanistically, TBK1/IKKε phosphorylate RIPK1 in the TNFR1-SC, thereby preventing RIPK1-kinase-activity-dependent cell death. This activity is essential in vivo , as it prevents TNF-induced lethal shock. Strikingly, NEMO/IKKγ, which mostly, but not exclusively, binds to the TNFR1-SC via M1-ubiquitin, mediates recruitment of the adaptors TANK and NAP1/AZI2 which are constitutively associated with TBK1/IKKε and TBK1, respectively. We here discover a previously unrecognised TBK1/IKKε-mediated cell-death checkpoint and uncover an essential survival function for NEMO by enabling recruitment and activation of these noncanonical IKKs to prevent TNF-induced cell death.