Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2017 May;15(5):563-576.
doi: 10.1158/1541-7786.MCR-16-0305.

Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences

Yasin Kaymaz  1 , Cliff I Oduor  2   3 , Hongbo Yu  4 , Juliana A Otieno  5 , John Michael Ong'echa  2 , Ann M Moormann  6 , Jeffrey A Bailey  7   8
Affiliations
Comparative Study

Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences

Yasin Kaymaz et al. Mol Cancer Res. 2017 May.

Abstract

Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein-Barr virus (EBV), unlike sporadic Burkitt lymphoma (sBL) that occurs with a lower incidence in developed countries. Given these differences and the variable clinical presentation and outcomes, we sought to further understand pathogenesis by investigating transcriptomes using RNA sequencing (RNAseq) from multiple primary eBL tumors compared with sBL tumors. Within eBL tumors, minimal expression differences were found based on: anatomical presentation site, in-hospital survival rates, and EBV genome type, suggesting that eBL tumors are homogeneous without marked subtypes. The outstanding difference detected using surrogate variable analysis was the significantly decreased expression of key genes in the immunoproteasome complex (PSMB9/β1i, PSMB10/β2i, PSMB8/β5i, and PSME2/PA28β) in eBL tumors carrying type 2 EBV compared with type 1 EBV. Second, in comparison with previously published pediatric sBL specimens, the majority of the expression and pathway differences was related to the PTEN/PI3K/mTOR signaling pathway and was correlated most strongly with EBV status rather than geographic designation. Third, common mutations were observed significantly less frequently in eBL tumors harboring EBV type 1, with mutation frequencies similar between tumors with EBV type 2 and without EBV. In addition to the previously reported genes, a set of new genes mutated in BL, including TFAP4, MSH6, PRRC2C, BCL7A, FOXO1, PLCG2, PRKDC, RAD50, and RPRD2, were identified. Overall, these data establish that EBV, particularly EBV type 1, supports BL oncogenesis, alleviating the need for certain driver mutations in the human genome.

Implications: Genomic and mutational analyses of Burkitt lymphoma tumors identify key differences based on viral content and clinical outcomes suggesting new avenues for the development of prognostic molecular biomarkers and therapeutic interventions.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Expression heatmap for all known EBV genes for 26 eBL, 4 sBL and 3 long-term BL cultures (Daudi, Raji, Namalwa) that were found to be EBV positive. This correlation based clustering heatmap using log2 transformed FPKM values demonstrates a predominant expression pattern resembling latency I for most of the BLs while two eBLs (eBL_23 and eBL_25) and cell lines have elevated expression in other genes. eBL_02 and eBL_20 show intermediate level lytic genes such as BMRF1, BALF2, and BSLF2/BMLF1 in addition to the two eBLs that cluster with cell lines.
Figure 2
Figure 2
Sample to sample clustering of BL tumors based on expression profiles of top 10,000 genes with highest correlation of variation (CV) values (calculated using regularized log transformed expression data). While 2 sBLs (sBL_u1 and sBL_u2) separate out from 28 eBLs, eBL tumor expression profiles demonstrate greater correlation within eBLs (r > 0.95, Pearson correlation; Dark red is 1.0) compared to sBLs, which might be due to differences in biopsy and preservation methods or biology. Overall gene expression correlations between eBLs does not reveal significant clustering consistent with no major underlying molecular subtypes nor clustering correlating with tumor presentation site, treatment outcome, or EBV type.
Figure 3
Figure 3
Clustering heatmap of significantly differentially expressed human genes between factors of phenotypes. Sample wise scaled log2 expression values range between lowest as light green and highest as dark red. Clustering dendrogram based on Pearson correlation demonstrates tumor grouping proper to the phenotype of interest. A) Significantly differentially expressed genes between Survivors and Nonsurvivors (BH Padj < 0.1). B) Significantly differentially expressed human genes between eBL tumors carrying EBV Type 1 and eBL tumor with EBV Type 2 (BH Padj < 0.1).
Figure 4
Figure 4
Gene set enrichment plot and expression heatmap of corresponding genes in the enriched gene set. Left panels include the running enrichment score throughout the gene set and projection of genes in the geneset to the complete list of genes rank ordered based on signal to noise ratio. Leading edge genes that build up the enrichment score of the geneset (RES at the peak) are the most important genes for these tumor sample comparison. On the expression heatmap (columns are tumors, rows are genes in the gene set), dark red represent higher expression while dark blue lower expression. A) Genes in this enrichment have been shown to be downregulated upon PTEN knockdown, and are observed to be downregulated in EBV positive BLs relative to EBV negative BLs (ES = 0.438, Nominal P = 0.00, FDR q = 0.0959) and B) Hallmark gene set enrichment showing mTOR complex 1 signaling genes to be relatively more activated in EBV positive BLs compared to negative BLs (ES = −0.439, Nominal P = 0.0665, FDR q = 0.151). Enrichment of genes associated with mTOR activation supports the enrichment of genes linked to PTEN inhibition.
Figure 5
Figure 5
Mutational landscape of BL tumors. A) This panel demonstrates mutated gene distribution in each tumor sample (columns) are tumors and rows are frequently mutated genes (>10% of samples mutated at least once). Tumor samples were grouped based on their EBV content and second color bar shows the subtype of the tumor. Red squares represent mutated gene while blue is for no mutation detected. Barplot on the right measures the frequency of mutated tumor samples and compares regarding the subtype of BLs (Percent frequency). Similarly, barplot on the left compares the mutated tumor frequencies for each gene stratified by EBV status (* P < 0.05, Fisher's Exact). B) Average number of mutated genes per BL tumor by EBV type. Error bars represent standard error (*** P < 0.01, t-test). C) Schematic overview of the proposed key pathways and frequently mutated genes in eBL pathogenesis. Genes in the boxes are found to be frequently mutated (likely gain of function and loss of function, represented by green and light-red boxes, respectively). Likely key interactions with EBV components are shown are in red connections. Possible interactions are shown in grey.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Burkitt D, Denis B. MALIGNANT LYMPHOMA IN AFRICAN CHILDREN. Lancet. 1961;277:1410–1.
    1. Satou A, Akira S, Naoko A, Atsuko N, Tomoo O, Masahito T, et al. Epstein-Barr Virus (EBV)-positive Sporadic Burkitt Lymphoma. Am J Surg Pathol. 2015;39:227–35. - PubMed
    1. Ferry JA. Burkitt's lymphoma: clinicopathologic features and differential diagnosis. Oncologist. 2006;11:375–83. - PubMed
    1. Boerma EG, van Imhoff GW, Appel IM, Veeger NJGM, Kluin PM, Kluin-Nelemans JC. Gender and age-related differences in Burkitt lymphoma – epidemiological and clinical data from The Netherlands. Eur J Cancer. 2004;40:2781–7. - PubMed
    1. Chen B-J, Chang S-T, Weng S-F, Huang W-T, Chu P-Y, Hsieh P-P, et al. EBV-associated Burkitt lymphoma in Taiwan is not age-related. Leuk Lymphoma. 2016;57:644–53. - PubMed

Publication types