Fig. 2 | Scientific Reports

Fig. 2

From: Latent EBV reactivation drives aberrant B-cell proliferation during ex vivo tumor-infiltrating lymphocyte expansion from EBV-negative rectal cancer tumor tissue

Fig. 2The alternative text for this image may have been generated using AI.

Bulk RNA-seq data analysis of lcl_burn0214, 10 B95-8_LCLs, 5 EBV + and 5 EBV- B cell lymphoma cell lines. A Hierarchical clustering of the SNP sites across the EBV genome extracted from Rna-seq data of 10 lymphoblastoid cells obtained by infection PBMC with B95-8 EBV strain (B95-8_LCLs) from Geuvadis consortium dataset, 5 EBV + lymphoma cell lines infected with wild-type EBV from Quentmeier H. dataset and spontaneous lcl_burn0214 cell line. Each row in the heatmap represents an SNP position, and each column represents a cell line. Reference alleles are colored dark blue, while non-reference alleles are colored light blue. The reference genome sequence is the type 1 EBV surrogate genome sequence (NC_007605), constructed based on the B95-8 and Raji EBV genomes. B Similarity of malignant and non-malignant B cell lines by principal component analysis of the following samples: B95-8_LCLs, lcl_burn0214, EBV-negative and EBV-positive lymphomas. C Similarity of malignant and non-malignant B cell lines by hierarchical clustering of transcriptome correlation of the following samples: B95-8_LCLs, tum_burn0214, lcl_burn0214, EBV-negative and EBV-positive lymphomas. The correlation plot is symmetric on one diagonal. Correlation is pointed by color the more red the greater correlation between the two samples. Cell lines are color-coded according to their cellular origin: B_NHL, green; HL, orange; B95-8_LCLs, blue; lcl_burn0214, violet. D, E Box plots show the estimated correlation between groups of samples with lcl_burn0214. Pearson correlation coefficients and 95% confidence intervals were estimated using a random effects mixed likelihood (REML) model. The best model for measuring the correlation was the full model (E), which includes the following groups or samples: the B95-8_LCL group; the LBC_susp group, consisting of the Bonna-12, HC-1, MEC-1, and PGA-1 cell lines; the B_NHL group, consisting of the REC-1, NU-DHL-1, DOHH-2, BC-3, and CRO-AP2 cell lines; the HL cell line HDLM-2; and the tum_burn0214 sample. Lcl_burn0214 showed the strongest correlation with the B95-8_LCL group (r = 0.88 [0.87–0.90]) and the LBC_susp group (r = 0.86 [0.84–0.89]). Correlations with the B_NHL, HL, and tum_burn0214 samples were 0.73 [0.71–0.76], 0.69 [0.63–0.74], and 0.63 [0.57–0.69], respectively. The reduced model (D) includes the following groups or samples: the B95-8_LCL group; the B_NHL group, consisting of the REC-1, NU-DHL-1, DOHH-2, BC-3, and CRO-AP2 cell lines, along with the Bonna-12, HC-1, MEC-1, and PGA-1 cell lines; the HL cell line HDLM-2; and the tum_burn0214 sample.

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