High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis

Abstract

Burkitt lymphoma (BL), the most common pediatric cancer in sub-Saharan Africa, is a malignancy of antigen-experienced B lymphocytes. High-throughput sequencing (HTS) of the immunoglobulin heavy (<i>IGH</i>) and light chain (<i>IGK</i>/<i>IGL</i>) loci was performed on genomic DNA from 51 primary BL tumors: 19 from Uganda and 32 from Ghana. Reverse transcription polymerase chain reaction analysis and tumor RNA sequencing (RNAseq) was performed on the Ugandan tumors to confirm and extend the findings from the HTS of tumor DNA. Clonal <i>IGH</i> and <i>IGK</i>/<i>IGL</i> rearrangements were identified in 41 and 46 tumors, respectively. Evidence for rearrangement of the second <i>IGH</i> allele was observed in only 6 of 41 tumor samples with a clonal <i>IGH</i> rearrangement, suggesting that the normal process of biallelic <i>IGHD</i> to <i>IGHJ</i> diversity-joining (DJ) rearrangement is often disrupted in BL progenitor cells. Most tumors, including those with a sole dominant, nonexpressed DJ rearrangement, contained many <i>IGH</i> and <i>IGK</i>/<i>IGL</i> sequences that differed from the dominant rearrangement by < 10 nucleotides, suggesting that the target of ongoing mutagenesis of these loci in BL tumor cells is not limited to expressed alleles. <i>IGHV</i> usage in both BL tumor cohorts revealed enrichment for <i>IGHV</i> genes that are infrequently used in memory B cells from healthy subjects. Analysis of publicly available DNA sequencing and RNAseq data revealed that these same <i>IGHV</i> genes were overrepresented in dominant tumor-associated <i>IGH</i> rearrangements in several independent BL tumor cohorts. These data suggest that BL derives from an abnormal B-cell progenitor and that aberrant mutational processes are active on the immunoglobulin loci in BL cells.