Journal: EMBO Reports

Article Title: RIPK1 ablation in T cells results in spontaneous enteropathy and TNF-driven villus atrophy

doi: 10.1038/s44319-025-00441-5

Figure Lengend Snippet: ( A – C ) Representative images of ( A ) aged Ripk1 ΔCD4 mice ( n = 15) and Ripk1 ΔCD4 Casp8 ΔCD4 mice ( n = 16) alongside their respective littermate controls Ripk1 FL/FL mice ( n = 16) and Ripk1 FL/FL Casp8 FL/FL mice ( n = 14), ( B ) their spleen and mLN as well as ( C ) their small intestines (SI). ( D ) Absolute numbers of CD4 + T cells in the spleen of Ripk1 ΔCD4 and Ripk1 ΔCD4 Casp8 ΔCD4 mice, and their respective Ripk1 FL/FL and Ripk1 FL/FL Casp8 FL/FL littermates with n = 4 mice per group, measured by flow cytometry. ( E ) Representative H&E staining on duodenum sections from aged Ripk1 ΔCD4 mice ( n = 5) and Ripk1 ΔCD4 Casp8 ΔCD4 mice ( n = 4) and their respective littermate controls Ripk1 FL/FL mice ( n = 6) and Ripk1 FL/FL Casp8 FL/FL mice ( n = 5). ( F – H ) Quantification of ( F ) the average crypt depth, ( G ) average villus length, and ( H ) Ki-67+ cells in the duodenum of Ripk1 ΔCD4 Casp8 ΔCD4 mice ( n = 4) and Ripk1 FL/FL Casp8 FL/FL littermates ( n = 5). ( I ) Absolute numbers of TCRβ + CD4 + , TCRβ + CD8β + , TCRβ + CD4 - CD8β - and TCRγδ + IELs in the SI epithelial layer of young Ripk1 ΔCD4 mice ( n = 4) and Ripk1 ΔCD4 Casp8 ΔCD4 mice ( n = 4) and their respective littermate controls Ripk1 FL/FL mice ( n = 4) and Ripk1 FL/FL Casp8 FL/FL mice ( n = 3), measured by flow cytometry. The corresponding statistical analysis is depicted in Fig. . ( J ) Tissue concentrations of TNF in the SI of young Ripk1 ΔCD4 mice ( n = 7) and Ripk1 ΔCD4 Casp8 ΔCD4 mice ( n = 4) and their respective littermates Ripk1 FL/FL ( n = 4) and Ripk1 FL/FL Casp8 FL/FL ( n = 5), measured by multiplex analysis (Meso Scale Discovery). ( K – M ) Quantification of the ( K ) absolute small intestine (SI) length, ( L ) Crypt depth, and ( M ) Villus length, of aged Ripk1 ΔCD4 mice ( n = 8) and Ripk1 FL/FL littermates ( n = 10), and Ripk1 ΔCD4 Tnfr1 −/− mice ( n = 5) and Ripk1 FL/FL Tnfr1 −/− littermates ( n = 5). Data are representative of two ( D , I – M ) or three repeats ( A – C , E – H ). Data are shown as mean ± SEM, with means being represented by bars or horizontal lines and each dot representing an individual mouse. Statistical significance was calculated in Graphpad Prism by two-sided unpaired t-test with Welch’s correction ( F ) p = 0.1821, ( G ) p = 0.123, ( H ) p = 0.9497, or two-way ANOVA on Log 2 -transformed data ( D ) Ripk1 FL/FL vs Ripk1 ΔCD4 : p = 0.0002, Ripk1 ΔCD4 vs Ripk1 ΔCD4 Casp8 ΔCD4 : p < 0.0001, Ripk1 FL/FL Casp8 FL/FL vs Ripk1 ΔCD4 Casp8 ΔCD4 : p = 0.4399; ( I ) corresponding statistical analysis is depicted for each population in Fig. ; ( J ) Ripk1 FL/FL vs Ripk1 ΔCD4 : p = 0.0034, Ripk1 ΔCD4 vs Ripk1 ΔCD4 Casp8 ΔCD4 : p = 0.0182, Ripk1 FL/FL Casp8 FL/FL vs Ripk1 ΔCD4 Casp8 ΔCD4 : p = 0.8625; ( K ) Ripk1 FL/FL vs Ripk1 ΔCD4 ( TNFR1 +/+ ): p < 0.0001, Ripk1 FL/FL vs Ripk1 ΔCD4 ( TNFR1 −/− ): p = 0.0045, TNFR1 +/+ vs TNFR1 −/− ( Ripk1 ΔCD4 ): p = 0.8363; ( L ) Ripk1 FL/FL vs Ripk1 ΔCD4 ( TNFR1 +/+ ): p < 0.0001, Ripk1 FL/FL vs Ripk1 ΔCD4 ( TNFR1 −/− ): p = 0.0004, TNFR1 +/+ vs TNFR1 −/− ( Ripk1 ΔCD4 ): p = 0.3015; ( M ) Ripk1 FL/FL vs Ripk1 ΔCD4 ( TNFR1 +/+ ): p < 0.0001, Ripk1 FL/FL vs Ripk1 ΔCD4 ( TNFR1 −/− ): p = 0.9755, TNFR1 +/+ vs TNFR1 −/− ( Ripk1 ΔCD4 ): p = 0.0009. ns = non-significant, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001. Young mice: 8–12 weeks old. Aged mice: >6 months old. IEL intraepithelial lymphocytes. .

Article Snippet: Tnfr1-deficient mice (Tnfr1 −/− ) , Pfeffer et al, ; purchased from Jackson Laboratory , 002818.

Techniques: Flow Cytometry, Staining, Multiplex Assay, Transformation Assay

Journal: Nature Communications

Article Title: Neural representation of cytokines by vagal sensory neurons

doi: 10.1038/s41467-025-59248-6

Figure Lengend Snippet: a Representative field of view showing neurons that respond to specific cytokines. b Representative traces from individual sensory neurons responding to specific cytokines. c Heatmap demonstrating selective cytokine‐specific responses in normalized neural activity index. White dotted lines indicate the time of cytokine application on the vagus nerve. d Pie chart depicting the proportion of total responsive neurons to specific cytokines, multiple cytokines or nonspecific activity. e Representative confocal microscopy images showing antibody labeling of IL‐1R1 (red) and TNFR1 (green) cytokine receptors on nodose ganglia cell bodies. Scale bar, 50 µm; Zoomed inset scale bar, 25 µm. IHC was repeated independently in 5 mice, quantified over 2 sections each. f Quantification of nodose ganglion cell bodies labeled for IL‐1R1 and TNFR1.

Article Snippet: Tissues were incubated with the following primary antibodies diluted in blocking buffer overnight at 4 °C: rabbit IL1RA (Abcam, Ab124962), mouse TNFR1 or rabbit TNFR1 (Proteintech, 60192-1-Ig), rat IL10RA (Abcam, Ab33738) or rabbit IL10RA (ThermoFisher, PA5-109852), PHOX2B (Abcam, Ab183741) or rabbit PHOX2B Alexa Fluor 647 (Abcam, Ab311130), Rabbit PRDM12 (EMD Millipore, ABE95), and Chicken Anti-GFP (Aves Labs, GFP-1010).

Techniques: Activity Assay, Confocal Microscopy, Antibody Labeling, Labeling

Journal: Nature Communications

Article Title: Neural representation of cytokines by vagal sensory neurons

doi: 10.1038/s41467-025-59248-6

Figure Lengend Snippet: a Representative field of view showing neurons that respond to specific cytokines. b Representative traces from individual sensory neurons responding to specific cytokines. c Heatmap demonstrating selective cytokine‐specific responses in normalized neural activity index. White dotted lines indicate the time of cytokine application on the vagus nerve. d Pie chart depicting the proportion of total responsive neurons to specific cytokines, multiple cytokines or nonspecific activity. e Representative confocal microscopy images showing antibody labeling of IL‐1R1 (red) and TNFR1 (green) cytokine receptors on nodose ganglia cell bodies. Scale bar, 50 µm; Zoomed inset scale bar, 25 µm. IHC was repeated independently in 5 mice, quantified over 2 sections each. f Quantification of nodose ganglion cell bodies labeled for IL‐1R1 and TNFR1.

Article Snippet: Tissues were incubated with the following primary antibodies diluted in blocking buffer overnight at 4 °C: rabbit IL1RA (Abcam, Ab124962), mouse TNFR1 or rabbit TNFR1 (Proteintech, 60192-1-Ig), rat IL10RA (Abcam, Ab33738) or rabbit IL10RA (ThermoFisher, PA5-109852), PHOX2B (Abcam, Ab183741) or rabbit PHOX2B Alexa Fluor 647 (Abcam, Ab311130), Rabbit PRDM12 (EMD Millipore, ABE95), and Chicken Anti-GFP (Aves Labs, GFP-1010).

Techniques: Activity Assay, Confocal Microscopy, Antibody Labeling, Labeling

Journal: Nature Communications

Article Title: Neural representation of cytokines by vagal sensory neurons

doi: 10.1038/s41467-025-59248-6

Figure Lengend Snippet: a Representative field of view showing neurons that respond to specific cytokines. b Representative traces from individual sensory neurons responding to specific cytokines. c Heatmap demonstrating selective cytokine‐specific responses in normalized neural activity index. White dotted lines indicate the time of cytokine application on the vagus nerve. d Pie chart depicting the proportion of total responsive neurons to specific cytokines, multiple cytokines or nonspecific activity. e Representative confocal microscopy images showing antibody labeling of IL‐1R1 (red) and TNFR1 (green) cytokine receptors on nodose ganglia cell bodies. Scale bar, 50 µm; Zoomed inset scale bar, 25 µm. IHC was repeated independently in 5 mice, quantified over 2 sections each. f Quantification of nodose ganglion cell bodies labeled for IL‐1R1 and TNFR1.

Article Snippet: Tissues were incubated with the following primary antibodies diluted in blocking buffer overnight at 4 °C: rabbit IL1RA (Abcam, Ab124962), mouse TNFR1 or rabbit TNFR1 (Proteintech, 60192-1-Ig), rat IL10RA (Abcam, Ab33738) or rabbit IL10RA (ThermoFisher, PA5-109852), PHOX2B (Abcam, Ab183741) or rabbit PHOX2B Alexa Fluor 647 (Abcam, Ab311130), Rabbit PRDM12 (EMD Millipore, ABE95), and Chicken Anti-GFP (Aves Labs, GFP-1010).

Techniques: Activity Assay, Confocal Microscopy, Antibody Labeling, Labeling

Journal: Nature Communications

Article Title: Neural representation of cytokines by vagal sensory neurons

doi: 10.1038/s41467-025-59248-6

Figure Lengend Snippet: a Representative field of view showing neurons that respond to specific cytokines. b Representative traces from individual sensory neurons responding to specific cytokines. c Heatmap demonstrating selective cytokine‐specific responses in normalized neural activity index. White dotted lines indicate the time of cytokine application on the vagus nerve. d Pie chart depicting the proportion of total responsive neurons to specific cytokines, multiple cytokines or nonspecific activity. e Representative confocal microscopy images showing antibody labeling of IL‐1R1 (red) and TNFR1 (green) cytokine receptors on nodose ganglia cell bodies. Scale bar, 50 µm; Zoomed inset scale bar, 25 µm. IHC was repeated independently in 5 mice, quantified over 2 sections each. f Quantification of nodose ganglion cell bodies labeled for IL‐1R1 and TNFR1.

Article Snippet: Tissues were incubated with the following primary antibodies diluted in blocking buffer overnight at 4 °C: rabbit IL1RA (Abcam, Ab124962), mouse TNFR1 or rabbit TNFR1 (Proteintech, 60192-1-Ig), rat IL10RA (Abcam, Ab33738) or rabbit IL10RA (ThermoFisher, PA5-109852), PHOX2B (Abcam, Ab183741) or rabbit PHOX2B Alexa Fluor 647 (Abcam, Ab311130), Rabbit PRDM12 (EMD Millipore, ABE95), and Chicken Anti-GFP (Aves Labs, GFP-1010).

Techniques: Activity Assay, Confocal Microscopy, Antibody Labeling, Labeling