Journal: Frontiers in Immunology

Article Title: Zapnometinib treatment and influenza A virus infection modulate the HLA class I ligandome in human lung adenocarcinoma cells

doi: 10.3389/fimmu.2026.1790267

Figure Lengend Snippet: Effects of zapnometinib treatment and IAV infection on HLA-I surface expression in Calu-3 cells. Calu-3 cells were treated with zapnometinib and/or infected with IAV H3N2/Fukui, and HLA-I surface expression was analyzed using QIFIKIT-calibrated flow cytometry assay with the W6/32 monoclonal antibody (mAb) (pan-HLA class I specific for HLA-A, -B, and -C alleles). Untreated cells served as baseline for relative fold-change calculations. (A) Representative result of flow cytometry histograms showing HLA-I surface expression analysis (n=3). (B) Absolute quantification of HLA-I molecules on the surface of Calu-3 cells (C) Relative HLA-I surface expression normalized to untreated control (fold changes 1.01-1.13, Brown-Forsythe ANOVA with Dunnett’s T3 multiple comparisons test, all p>0.05). The statistical analysis was performed using Brown-Forsythe ANOVA with Dunnett’s T3 multiple comparisons correction. Flow cytometry data were analyzed using FlowJo software ver. 10.8 (FlowJo LLC, BD). Statistical analysis and visualization were performed using GraphPad Prism software ver. 9.3.

Article Snippet: Comparisons with vehicle controls confirmed that zapnometinib treatment alone ( , middle), as well as combined treatment with IAV H3N2/Fukui infection, displayed similar patterns, with 3% of ligands upregulated and 6–8% downregulated ( , right).

Techniques: Infection, Expressing, Flow Cytometry, Quantitative Proteomics, Control, Software

Journal: Frontiers in Immunology

Article Title: Zapnometinib treatment and influenza A virus infection modulate the HLA class I ligandome in human lung adenocarcinoma cells

doi: 10.3389/fimmu.2026.1790267

Figure Lengend Snippet: Mass spectrometric profiling of the Calu-3 cells HLA-I immunopeptidome following zapnometinib treatment and IAV infection. Calu-3 cells were treated with zapnometinib and/or infected with IAV H3N2/Fukui and HLA-I–bound peptides were isolated and analyzed by LC-MS/MS. Peptides were defined as HLA-I ligands if the NetMHCpan prediction showed percentile rank or IC50 score below ≤2% and 500 nM respectively. (A) Total number of HLA-I ligands (blue bars) and corresponding source proteins (black bars) identified under each condition. Red triangles indicate the purity of identified ligands (the percent of predicted ligands among the total identified peptides. (B) HLA-I allotype distribution of predicted ligands in zapnometinib-treated cells and IAV-infected cells. (C) Venn diagram showing overlap of HLA-I identified ligands between each treatment condition and mock control. (D) HLA-I allotype distribution of exclusively identified ligands under each treatment. (E) Venn diagram showing overlap of source proteins for HLA-I ligands respective for each treatment and infection conditions. A comprehensive list of identified peptides used for generating the figure can be found in the . * Indicates statistical significance.

Article Snippet: Comparisons with vehicle controls confirmed that zapnometinib treatment alone ( , middle), as well as combined treatment with IAV H3N2/Fukui infection, displayed similar patterns, with 3% of ligands upregulated and 6–8% downregulated ( , right).

Techniques: Infection, Isolation, Liquid Chromatography with Mass Spectroscopy, Control

Journal: Frontiers in Immunology

Article Title: Zapnometinib treatment and influenza A virus infection modulate the HLA class I ligandome in human lung adenocarcinoma cells

doi: 10.3389/fimmu.2026.1790267

Figure Lengend Snippet: Qualitative and quantitative influence of zapnometinib treatment and IAV infection on the Calu-3 HLA-I peptidome. Calu-3 cells were treated with zapnometinib and/or infected with IAV H3N2/Fukui and HLA-I–bound peptides were isolated for LC-MS/MS analysis. (A) Volcano plots depicting the modulation and relative abundance of HLA-I identified ligands between the indicated conditions. Each point corresponds to an HLA-I ligand, the x-axis shows log2 fold change in relative abundance, and the y-axis indicates -log10 Benjamini–Hochberg corrected p-value. upregulated ligands (≥ 2-fold increase, adjusted p -value <0.05) are indicated in red and those significantly downregulated (≤-2-fold decrease, adjusted p < 0.05) are in blue. Percentages of significantly modulated ligands are indicated in the respective quadrants. (B) Distribution of HLA-I allotypes among the up- and downmodulated ligands. Data processing and visualization were performed in R (ver. 4.2) using in-house R scripts. A comprehensive list of identified peptides used for generating the figure can be found in the .

Article Snippet: Comparisons with vehicle controls confirmed that zapnometinib treatment alone ( , middle), as well as combined treatment with IAV H3N2/Fukui infection, displayed similar patterns, with 3% of ligands upregulated and 6–8% downregulated ( , right).

Techniques: Infection, Isolation, Liquid Chromatography with Mass Spectroscopy