Fig 2: The patient’s inflammatory plasma protein profile is converted to normal after treatment with the anti-TNF therapeutic Adalimumab Plasma was collected from the patient before and after start of therapy with the anti-TNF therapeutic Adalimumab. Plasma from two healthy controls was used as comparison. The Proteome Profiler Human Cytokine Array was performed according to the manufacturer’s instructions.The concentration of Adalimumab in the patient’s serum is shown (target concentration: > 5 µg/ml).

Fig 3: TNF signaling is altered in patient-derived cells A–DPatient-derived and control fibroblasts were used. (A) FLAG-tagged tandem ubiquitin binding entity (TUBE) assay was performed to pull down linear ubiquitin linkages upon stimulation with 500 ng/ml TNF. (B) The TNFR1-SC was isolated using 500 ng/ml TAP-TNF. (C) Cells were stimulated with 100 ng/ml TNF for the indicated times and analyzed by Western blot. One representative (A–C) of three independent experiments is shown. (D) Cells were stimulated with TNF for 24 h and IL-6 was determined by ELISA. Data are presented as mean ± SD of three individual experiments performed in two technical replicates; *P = 0.014; **P = 0.007; multiple t-test corrected for multiple comparisons using the Holm–Sidak method.EB cells were incubated with 50 µg/ml cycloheximide (CHX) for the indicated times and subjected to analysis by Western blot. One representative (left panel) out of 4 individual experiments analyzed by densitometry (right panel) is shown. Data are presented as mean ± SD. *P = 0.02, unpaired t-test.FPatient-derived and control B cells were cultivated for 24 h and TNF was determined by ELISA. Data are presented as mean ± SD of 3 individual experiments performed in two technical replicates; *P = 0.028; unpaired t-test.GFibroblasts were incubated with 50 µg/ml cycloheximide (CHX) or DMSO and stimulated with TNF as indicated. Viability was measured after 24 h. Data are presented as mean ± SD of 5 individual experiments performed in three technical replicates; ***P = 0.0008, mixed-effects analysis with Tukey’s multiple comparisons test.HIntracellular TNF in CD11b-positive cells from five healthy controls, patient (before anti-TNF treatment), mother, and father was determined by FACS. Source data are available online for this figure.

Fig 4: Expression profile of cytolytic enzyme (granzyme B) and functional cytokines (IFN?, TNF) in CD8+ T cells during decitabine treatment at day 5 post-stimulation(A–C) (A) MFI expression of Granzyme B. Functional cytokines are represented as frequency for (B) IFN?+ and (C) TNF+ expressing T cells. Figure reprinted with permission from Loo Yau et al. (2021).

Fig 5: Signaling output of different innate immune stimuli in patient-derived cells AFibroblasts were stimulated with 1 µg/ml LPS for the indicated times and subjected to analysis by Western blot. One representative out of three independent experiments is shown.BFibroblasts were stimulated with LPS for 24 h. Concentration of IL-6 in the supernatant was determined by ELISA. Data are presented as mean ± SD of three individual experiments performed in two technical replicates; *P = 0.012; multiple t-tests corrected for multiple comparisons using the Holm–Sidak method.CB cells were treated with 100 ng/ml CD40L for the indicated times and subjected to analysis by Western blot. One representative out of three independent experiments is shown.DFibroblasts were incubated with 50 µg/ml cycloheximide (CHX) for the indicated times and subjected to analysis by western blot. One representative (left panel) out of 4 individual experiments analyzed by densitometry (right panel) is shown. Data are presented as mean ± SD. *P = 0.02, unpaired t-test.E, FFibroblasts (E) or B cells (F) were treated with 0.1 µg/ml TNF, 0.1 µg/ml TRAIL, 100 µg/ml poly(I:C), 1 µg/ml LPS or left untreated, and viability was determined after 24 h. Data are presented as mean ± SD of three independent experiments; dots represent individual experiments performed in three technical replicates; ns, non-significant, unpaired t-test.G, HFibroblasts were incubated with 50 µg/ml cycloheximide (CHX) or DMSO and stimulated with the indicated concentrations of TRAIL (G) or poly(I:C) (H). Viability was measured after 24 h. Data are presented as mean ± SD of three individual experiments performed in three technical replicates. Source data are available online for this figure.