Fig 1: EBV represses transcription and chromatin of HLA class II gene cluster.(A) Heat map of RNA-seq and ATAC-Seq data from EBV infection of primary B-cells for two independent donors. HLA-II and CIITA genes are shown that have associated changes in both transcription levels and chromatin accessibility during primary infection (r > 0.5). The intensity of purple color for column r is proportional to correlation coefficient. Intensity for gene expression and ATAC signal is a z-score calculated among samples at each experiment (lower right). (B) Proteomic analysis of HLA protein changes in EBV infected LCLs relative to uninfected primary B-cells averaged for 2 donors using label-free quantification. Color is proportional to magnitude of fold change. (C) RT-qPCR analysis of HLA-DRA, -DRB1, -DPA1, -DPB1, -DMA, -DMB, -DOA, and -DOB in B cells (Day 0) and LCLs derived from the B cells (Day 21). Statistical analysis was performed in GraphPad Prism 9. Error bars are standard deviation from mean (SDM) and *** indicates p-values <0.001 using 2-tailed student t-test.
Fig 2: EBNA2 regulates HLA-II through CIITA.(A) RT-qPCR analysis of CIITA levels in B cells (Day 0) and LCLs derived from the B cells (Day 21). (B-C) EREB2.5 cells were treated with (+) or without (-) estradiol (E2) and then assayed by RT-qPCR for CIITA expression relative to GUSB (B) or Western blot for CIITA, EBNA2 or loading control β-actin (C). (D-E) Akata T1 or T2 cells were treated with (+) or without (-) estradiol (E2) and then assayed by RT-qPCR for CIITA expression relative to GUSB (D) or Western blot for CIITA, EBNA2 or loading control β-actin (E). (F) EREB2.5 transduced with either shCIITA or control pLKO.1 (shCtrl) lentivirus was assayed by RT-qPCR for CIITA relative to GUSB (left) or Western blot for CIITA and β-actin control (right). (G) Control or CIITA knockdown EREB2.5 cells were starved from E2 for 48hrs, then replenish with culture medium containing E2 and assayed by RT-qPCR for HLA-DRA, -DRB1, -DQA1 and Myc relative to GUSB. For A-F, 2-tailed student t-test was performed to determine the significance. For G, a 2way ANOVA with Fisher’s LSD test was performed to assess significance. Error bars are SDM, and * p<0.05, *** p<0.001 or ns (not significant).
Fig 3: EBNA2 downregulates the expression of HLA-II.(A-B) EREB2.5 cells were treated with (+) or without (-) estradiol (E2) for 24 or 48 hrs and then assayed by Western blot for EBNA2 or loading control β-actin (A), and by RT-qPCR for HLA-DRA, -DRB1, -DPA1, -DPB1, or HES1 and c-Myc expression relative to GUSB (B). (C-D) Akata T1 or T2 cells were treated with (+) or without (-) estradiol (E2) for 24, 48 or 72 hrs and then assayed by Western blot for EBNA2 or loading control β-actin (C) or RT-qPCR for HLA-DRA, -DRB1, -DPA1, -DPB1, or HES1 expression relative to GUSB (D). Error bars are standard deviation from mean (SDM) and ** p<0.01, *** p <0.001 using 2-tailed student t-test.
Fig 4: CRISPR mutated EBNA2 binding site alters CIITA and HLA-II gene expression.(A) Screenshot of UCSC genome browser with ChIP-seq tracks of EBNA2, EBF1, PU.1, ETS1, RBPJ and GeneHancer interactions at CIITA region. gRNA-targeted region is indicated by a red box. (B) ChIP-qPCR in Ctrl or EBNA2_BS KO EREB2.5 cells with antibodies to either EBNA2, EBF1, PU.1 or IgG. (C) Expression of CIITA, HLA-DRA, DQA1, DPA1, DPB1, and HES1 in Ctrl and EBNA2_BS KO EREB2.5 cells was measured by ∆∆CT method (2-tailed student t test; *** p<0.001 or ns (not significant)). (D) Same as in panel C showing DEXI gene only. (E) Expression of CIITA, HLA-DRA, DQA1, DPA1, DPB1, and DEXI in Ctrl and EBNA2_BS KO BJAB cells was measured by ∆∆CT method (2-tailed student t test; ns (not significant)).
Fig 5: Identification of an HLA-DR+ITGAM+CD68+TREM2+ macrophage.a Merged UMAP plot of scRNA-Seq data of HLA-DRA+ cells (n = 4 independent tumors). b Feature plots for CD207, ITGAM, CD68, and TREM2 from the UMAP that is shown in a. c UMAP plot of scRNA-Seq data of HLA-DRA+ cells from an individual sample. d Feature plots for CD207, ITGAM, CD68, and TREM2 from the UMAP that is shown in c. e CyTOF study design for examining human BCC tumor single-cell suspensions. f TSNE plot of the merged CD45+ cells from BCC samples. g Feature plots for the key CD3+ and HLA-DR+ clusters within the CD45+ fraction. h Quantification of the proportions of CD3+, HLA-DR+, and other cell types by sample. i Feature plots for CD11b, CD206, and TREM2 from the subset of HLA-DR+ cells. j Quantification of the percentages of cells that are HLA-DR+CD11b+, HLA-DR+CD11b+TREM2+, and HLA-DR+CD11b+TREM2+Ki67+. For f, h, i, j, n = 13 independent tumors. Source data are provided as a Source data file.
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