Fig. 2
Mass spectrometry analysis of HLA Class II epitopes in PDAC tumor tissues. MaxQuant was used to identify the peptide sequences. The MS analysis of eluted HLA-II peptides showed an average of 490 peptide sequences (ranging between 249 and 689), corresponding to an average of 116 proteins (ranging between 62 and142) from six PDAC tissue samples. A Histograms show the numbers of different lengths of peptides affinity purified by anti-HLA Class II antibody from two representative human PDAC tissue samples, Pan13 and Pan14. B Numbers of total HLA class I peptides, HLA class II peptides, and completely overlapped peptides between HLA-I and HLA-II peptides were indicated. Three representative PDAC samples were shown. The sources of six selected peptides were indicated. C Ability of selected, HLA class I/II-overlapped peptides in stimulating single cells to express IFN-y, IL-2 and TNF-a in FluoroSpot assays was shown in the histograms. PBMC samples from three representative patients were shown. Spot forming unit (SFU) is the number of spots per 106 PBMCs. Shown is SFU of each peptide after subtracting that of a negative control peptide; and error bars represent the percentages of deviation. “Unstimulated” indicates the reaction in absence of peptides. If the SFU of a peptide in a sample is less than that of the negative control peptide, it is set as zero; and such a result would be considered “unstimulated”. Unpaired t test and 1-way ANOVA was used for comparing between stimulated and unstimulated peptide/samples. *p < 0.05, **p < 0.01, ***p < 0.001