Journal: bioRxiv

Article Title: Selective Immune Silencing by Targeted TGF-β Agonists

doi: 10.64898/2026.01.19.700410

Figure Lengend Snippet: Design and characterization of mouse T cell-targeted TGF- β agonists. a. Schematic of the plasmid construct encoding the MSA–TGM1-targeting-arm fusion protein. b. SDS–PAGE analysis showing the molecular weight and purity of the indicated recombinant proteins. c. SDS–PAGE analysis showing the molecular weight and purity of the indicated recombinant proteins. d. Representative flow cytometry plots showing mouse CD4 and CD8α expression in mouse CD4- or CD8α-transduced HEK293 cells. e. Dose-dependent curves showing GITR, IRF4, and T-bet expression levels in in vitro –cultured CD4 T cells treated with the indicated proteins on day 3. f. Dose-dependent curves showing GITR, IRF4, and T-bet expression levels in in vitro –cultured CD8 T cells treated with the indicated proteins on day 3. g. Dose-dependent curves showing percentages of IFN-γ– and TNF-α–producing cells among in vitro –cultured CD4 T cells treated with the indicated proteins on day 3. h. Dose-dependent curves showing percentages of IFN-γ– and TNF-α–producing cells among in vitro –cultured CD8 T cells treated with the indicated proteins on day 3. i. Dose-dependent curves showing Foxp3 cell percentages in in vitro -cultured CD4 T cells, and Granzyme B–producing cell percentages in in vitro -cultured CD8 T cells treated with the indicated proteins on day 3. Data are presented as mean ± s.e.m.

Article Snippet: The following antibodies were purchased from Miltenyi Biotec: human IgA (130-113-480) and IRF4 (130-100-909).

Techniques: Plasmid Preparation, Construct, SDS Page, Molecular Weight, Recombinant, Flow Cytometry, Expressing, In Vitro, Cell Culture

Journal: bioRxiv

Article Title: Selective Immune Silencing by Targeted TGF-β Agonists

doi: 10.64898/2026.01.19.700410

Figure Lengend Snippet: a. Frequencies of immune cell subsets. b. SCENIC prediction of IRF4 and Blimp1 transcription factor activity. c. Immunoglobulin gene expression. d. UMAP plots showing cell cycle gene signature scores. e. Quantification of cell cycle gene signature scores. f. Scaled signature scores for TGF-β–inducible genes, senescence genes, and apoptosis-related genes, aggregated by sample.

Article Snippet: The following antibodies were purchased from Miltenyi Biotec: human IgA (130-113-480) and IRF4 (130-100-909).

Techniques: Activity Assay, Gene Expression

Journal: bioRxiv

Article Title: Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

doi: 10.1101/2024.06.12.598635

Figure Lengend Snippet: (A) Proteins ranked by their expression differences in HRS compared to GC. The top ten differentially expressed proteins in HRS are listed, with known lymphoma-related markers in bold. (B) Same as A but for SLL compared to GC. (C) Principal component analysis of GC/HRS/SLL cell proteomes. (D) Volcano plot of the proteomic comparison between HRS and SLL. Red dots represent significantly differentially expressed proteins. Proteins with largest fold-change are annotated with their names. Statistical significance was determined using two-sided t -test (FDR<0.05, S0=0.1). (E) The scatter plot of the differential enrichment of proteins in the HRS and SLL populations in comparison to GC. Proteins that show significant expression in HRS (orange), SLL (magenta), and both populations (blue) are highlighted. (F) Expression of IRF4 determined by MS analysis. The box plot displays the distribution of the data from the minimum to the maximum intensity. The horizontal line within each box represents the mean value of the intensity. Statistical significance was determined using one-way ANOVA. F-value (2, 9) = 92.55; **** P < 0.0001. * P < 0.05. (G) Representative images illustrating immunofluorescence staining of CD20, CD30 and IRF4 in non-lesional germinal center regions and tumor areas. Arrows indicate HRS cells. (H) Quantification of staining intensity of IRF4 in GC, HRS and SLL (similar as in F). The horizontal line within each box represents the median value of the intensity. Statistical significance was determined using one-way ANOVA. F (2, 41786) = 4132, **** P < 0.0001. (I) Representative images illustrating immunofluorescence staining of CD20, CD30 and LENG1 in non-lesional germinal center regions and tumor areas. Arrows indicate HRS cells. (J) Quantification of staining intensity of LENG1 in GC, HRS and SLL as (H). F (2, 40108) = 3054, **** P < 0.0001. (K) Expression of LENG1 determined by MS analysis (similar as in F). F (2, 9) = 217.7. (L) Representative immunohistochemistry images of LENG1 in human lymph node tissues, including both normal and lymphoma cases, sourced from the HPA database. (M) Kaplan-Meier analysis to pan-cancer in TCGA using UCSC Xena, with a focus on LENG1 (see main text). The p-values reflect comparisons between two groups through univariate analysis using the log-rank test.

Article Snippet: The tissue was then blocked with 5% BSA for 20 minutes at room temperature and incubated overnight at 4°C with primary antibodies, including anti-CD30 clone Ber-H2 (1:50, M0751, Agilent) with anti-SKIL antibody (1:200, HPA008472, Sigma-Aldrich) / anti-IRF4 antibody (1:100, 11247-2-AP, Proteintech) / anti-LENG1 antibody (1:500, HPA043541, Sigma-Aldrich) / Alexa Fluor® 488 Collagen I (1:1000, ab275996, Abcam) / CD3 (1:500, A0452, Agilent).

Techniques: Expressing, Comparison, Immunofluorescence, Staining, Immunohistochemistry

Journal: bioRxiv

Article Title: Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

doi: 10.1101/2024.06.12.598635

Figure Lengend Snippet: (A) Volcano plot comparing the proteomes of HRS and GC. Orange dots represent significantly differentially expressed proteins, and proteins with largest fold-change are annotated with their names. Statistical significance was determined using two-sided t -test (FDR<0.05, S0=0.1). (B) Interaction between compounds and proteins using STITCH and STRING (see Methods). Interactions are visualized in Cytoscape, representing nodes with gray lines connecting them, where thicker lines signified stronger associations. IRF4 and related proteins appear as circles, while compounds appear as ovals in the visual representation. (C) Volcano plot comparing the proteomes of HRS and GC. Magenta dots represent significantly differentially expressed proteins as in (A). (D) Gene Ontology (GO) enrichment analysis on the upregulated pathways in HRS involving iterative comparisons and functional grouping of these pathways. The plot illustrates -log10 (FDR of term) values, with circle size denoting the percentage of associated upregulated entities in HRS compared to the background entities. (E) Heatmap illustrating entities participating in the cell cycle process pathway identified through GO enrichment analysis. GC, HRS, and SLL are represented with four replicates each, with Z-scores depicted using a gradient color scale. (F) Heatmap of the proteasome subunit proteins. (G) GO enrichment analysis of the upregulated pathways in SLL similar to (D). (H) Interaction between compounds and proteasome proteins.

Article Snippet: The tissue was then blocked with 5% BSA for 20 minutes at room temperature and incubated overnight at 4°C with primary antibodies, including anti-CD30 clone Ber-H2 (1:50, M0751, Agilent) with anti-SKIL antibody (1:200, HPA008472, Sigma-Aldrich) / anti-IRF4 antibody (1:100, 11247-2-AP, Proteintech) / anti-LENG1 antibody (1:500, HPA043541, Sigma-Aldrich) / Alexa Fluor® 488 Collagen I (1:1000, ab275996, Abcam) / CD3 (1:500, A0452, Agilent).

Techniques: Functional Assay