Fig. 4: Impaired innate and adaptive immunity by somatic gene alterations and EBV latent gene expression in NPC. | Nature Communications

Fig. 4: Impaired innate and adaptive immunity by somatic gene alterations and EBV latent gene expression in NPC.

From: Whole-genome profiling of nasopharyngeal carcinoma reveals viral-host co-operation in inflammatory NF-κB activation and immune escape

Fig. 4

A Somatic aberrations and EBV-encoded LMP1 and BNLF2a expression attenuate adaptive and innate immunities in NPC are shown. B By immunohistochemistry analysis, loss of MHC-class I and MHC-class II expression are demonstrated in representative NPC cases with somatic alterations of NLRC5 (n = 3; NPC-6T, NPC-30T, NPC-52T) and CIITA (n = 3; NPC-6T, NPC-52T, NPC-57T), respectively. The experiments were performed twice and similar results were found. Representative images of MHC-class I and MHC-class II expression in the NPC cases with wild-type or somatic alterations of NLRC5 and CIITA genes are illustrated. Scale bar: 20 μm. C RNA-sequencing revealed the expression of BNLF2a in NPC PDXs. The partial EBV transcription profiles illustrating BNLF2a expression in NPC cell line (C666-1) and PDXs (Xeno-23, Xeno-47, Xeno-76, and Xeno-32) were shown. The RISH probe targeted regions (BNLF2a, LMP1) in EBV genome are indicated. By RISH analysis, abundant expression of BNLF2a transcripts was found in the majority of tumor cells in two NPC PDXs, Xeno-32 and Xeno-47. BNLF2a probe was used to illustrate the signal of BNLF2a transcripts in the tumor cells with no LMP1 probe signal. Each tumor was subjected to RISH analysis twice and similar results were found. Representative images of RISH results of BNLF2a and LMP1 in NPCs are illustrated. Scale bar: 10 μm. D Enrichment of BNLF2A-expressing cases in NPCs without somatic alterations in MHC-class I pathway (two-sided Wilcoxon signed-rank p = 0.24). Boxplot is defined as follows: center upper whisker = min(max(x), Q_3+1.5*IQR), lower whisker = max(min(x), Q_1−1.5*IQR); where IQR = Q_3−Q_1, the bounds of the box. BNLF2A expression was determined in NPC specimens (n = 39) by RISH. E Representative NPC tumors (NPC-32T, NPC-44T, NPC-47T) with high BNLF2a expression are shown. An LMP1-expressing xenograft C15 was included for RISH analysis using BNLF2a and LMP1 probes. Each tumor was subjected to RISH analysis twice and similar results were found. Scale bar: 10 μm. Source data are provided as a Source Data file.

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