Messenger RNA and micro-RNA expression signatures in endemic Burkitt Lymphoma patients from Western Kenya

Abstract

ABSTRACT: Endemic Burkitt lymphoma (eBL) is a B cell tumour common in region with high Plasmodium falciparum malaria and is characterized by over expression of the c-myc oncogene as a consequence of the t(8:14) IGH/MYC translocation. While MYC is the seminal event, eBL, like all cancers, is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via microRNAs (miRNAs) might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied in eBL tumour cells relative to its normal germinal center (GC) B cells. Western Kenya is one of the high malaria transmission regions in Kenya with high cases of eBL in children. Hence comparing microRNA and mRNA expression profiling in eBL tumours from children in western Kenya relative to GC B cells, may partially explain molecular events involved in eBL oncogenesis. While many transcriptional changes in the oncogenic pathway of eBL have been characterized, comparisons of transcripts expression between eBL and GC B cells have not been performed using more sensitive and specific mRNA and micro-RNA transcriptome deep sequencing. This study aimed at determining the mRNA and miRNA expression profile of eBL tumours from children in western Kenya compared to GC B cells and to identify miRNAs that could contribute to eBL clinical presentation, and poor outcomes. Using the generalized linear model implemented in edgeR package in R, this case-control study compared previously published small and long RNA of a set of 5 GC B cells and 28 eBL tumours (12 jaw and 16 abdominal tumours) and identified 211 differentially expressed (DE) mRNAs (79 upregulated and 132 downregulated) and 49 DE miRNAs (22 up-regulated and 27 down-regulated) in eBL tumour cells. Of these DE genes, the study identified the downregulation of ATM and NLK genes, which represent important regulators in response to DNA damage in eBL tumour cells. These tumour suppressors were targeted by multiple upregulated miRNAs (miR-19b-3p, miR-26a-5p, miR-30b-5p, miR-92a-5p and miR-27b-3p) which could account for their aberrant expression in eBL. One miRNA (miR-10a-5p) was found to be downregulated in eBL jaw tumours and among the non-survivors. Decreased miR-10a expression, relives post-transcriptional regulation to its targets genes (such as CD59 and API5) that would promote tumour cell survival and apoptosis evasion leading to poor eBL patient outcome. Combined loss of p53 induction and function due to miRNA-mediated regulation of ATM and NLK, together with the observed upregulation of TFAP4, may play a central role for human miRNAs in eBL oncogenesis. This would facilitate survival of eBL tumour cells with the IGH/MYC chromosomal translocation and promote MYC-induced cell cycle progression, initiating eBL lymphomagenesis. Given the validated target genes of miR-10a-5p, its altered expression pattern between different tumour sites (jaw versus abdominal tumours) in eBL and in eBL patients with different in-hospital survival outcomes would enhance tumour cell survival and thus, render the tumour less sensitive to chemotherapy. This comprehensive characterization of mRNA and miRNA transcriptomes in eBL relative to GC B cells and among the eBL tumours provides new insights into miRNA-mediated transcript regulation in eBL, which are potentially useful for new improved therapeutic strategies.