] Briefly, ΔCt [normalized RIP] = (Ct [RIP]‐(Ct [Input]‐Log 2 (Input Dilution Factor))), % Input = 2 (‐ΔCt[normalized RIP]) . e) Addition of Cy5‐labeled 5′UTR of MCL1 enhanced formation of eGFP‐DAP5 + puncta in the buffer containing 100 mM NaCl, 20 mM Tris‐HCl (pH = 7.5), 5% PEG8000 and 2 µM eGFP‐DAP5. Pictures were taken under confocal microscopy. f) The volcano plot depicting transcripts in iTregs with significantly increased translation efficiencies (TE) compared to naïve CD4 + T cells. TE values were determined by combined analysis of Ribo‐seq and RNA‐seq data. Transcripts meeting the criteria of absolute log 2 TE − iTreg TE − na ï ve CD 4 ≥ 2 and adjusted p‐ value < 0.05 were designated as differentially translated. g) Lower panel : the curves displaying the density distributions of transcripts along their relative TE values ( log 2 TE − iTreg TE − na ï ve CD 4 ) (X‐axis). Transcripts were grouped into three categories: DAP5‐bound and hypo‐m 6 A modified, DAP5‐bound and m 6 A modified, and m 6 A modified only; upper panel : box plots comparing TE values of the aforementioned categories of transcripts within three indicated ranges of relative TE values: log 2 TE − iTreg TE − na ï ve CD 4 <‐1, 1≤ log 2 TE − iTreg TE − na ï ve CD 4 <4.4, 4.4≤ log 2 TE − iTreg TE − na ï ve CD 4 ≤10. h) Bar plots displaying efficiencies of in vitro mouse iTreg differentiation induced by FB23‐2 or STM2457. i) Flow cytometric histograms comparing Ki‐67 expression levels between mouse iTregs induced by FB23‐2 and STM2457. P‐ values were determined by two‐tailed student's T ‐test (d and h) or Kolmogorov‐Smirnov test and Kruskal‐Wallis (g), * p <0.05, ** p <0.01, *** p <0.001. " width="100%" height="100%">
Journal: Advanced Science
Article Title: Targeting DAP5 Disrupts Alternate Mode of Translational Initiation in Tregs and Potentiates Antitumor Immunity
doi: 10.1002/advs.202520625
Figure Lengend Snippet: Transcripts bound by DAP5 undergo active translation in Tregs. a) Schematic diagram exhibiting the workflow for the combined RIP‐seq, Ribo‐seq and RNA‐seq experiments. b) Bubble plots displaying enriched GO and KEGG terms that were obtained by performing enrichment analysis with transcripts bound by DAP5 in iTregs. c) Integrative Genomics Viewer (IGV) tracks showing representative binding peaks of DAP5 that are associated with cell survival, proliferation and immunomodulation in human iTreg cells. d) Bar plots showing enriched presence of transcripts bound by DAP5 in iTregs. For histogram plotting, qRT‐PCR assays were performed with DAP5‐RIP assay elutes. The RIP‐qPCR data analysis was performed according to the ΔΔCt method. [ 77 , 78 ] Briefly, ΔCt [normalized RIP] = (Ct [RIP]‐(Ct [Input]‐Log 2 (Input Dilution Factor))), % Input = 2 (‐ΔCt[normalized RIP]) . e) Addition of Cy5‐labeled 5′UTR of MCL1 enhanced formation of eGFP‐DAP5 + puncta in the buffer containing 100 mM NaCl, 20 mM Tris‐HCl (pH = 7.5), 5% PEG8000 and 2 µM eGFP‐DAP5. Pictures were taken under confocal microscopy. f) The volcano plot depicting transcripts in iTregs with significantly increased translation efficiencies (TE) compared to naïve CD4 + T cells. TE values were determined by combined analysis of Ribo‐seq and RNA‐seq data. Transcripts meeting the criteria of absolute log 2 TE − iTreg TE − na ï ve CD 4 ≥ 2 and adjusted p‐ value < 0.05 were designated as differentially translated. g) Lower panel : the curves displaying the density distributions of transcripts along their relative TE values ( log 2 TE − iTreg TE − na ï ve CD 4 ) (X‐axis). Transcripts were grouped into three categories: DAP5‐bound and hypo‐m 6 A modified, DAP5‐bound and m 6 A modified, and m 6 A modified only; upper panel : box plots comparing TE values of the aforementioned categories of transcripts within three indicated ranges of relative TE values: log 2 TE − iTreg TE − na ï ve CD 4 <‐1, 1≤ log 2 TE − iTreg TE − na ï ve CD 4 <4.4, 4.4≤ log 2 TE − iTreg TE − na ï ve CD 4 ≤10. h) Bar plots displaying efficiencies of in vitro mouse iTreg differentiation induced by FB23‐2 or STM2457. i) Flow cytometric histograms comparing Ki‐67 expression levels between mouse iTregs induced by FB23‐2 and STM2457. P‐ values were determined by two‐tailed student's T ‐test (d and h) or Kolmogorov‐Smirnov test and Kruskal‐Wallis (g), * p <0.05, ** p <0.01, *** p <0.001.
Article Snippet: To dissect the function of Dap5 in Tregs in vivo, we generated transgenic mice with specific Dap5 ablation in Tregs ( Dap5 ΔFoxp3 ) by crossing the floxed‐ Dap5 mice with the Foxp3 ‐ Cre (B6.129(Cg)‐ Foxp3 4(YFP/icre)Ayr /J) strain from Jackson Laboratory that are widely used in Treg studies (Figure , Supporting Information).
Techniques: RNA Sequencing, Binding Assay, Quantitative RT-PCR, Labeling, Confocal Microscopy, Modification, In Vitro, Expressing, Two Tailed Test