Burkitt Lymphoma, DLBCL and FL – integrative sequencing analysis identifies alterations in microRNA and microRNA regulated mRNA which contributes to lymphomagenesis

Lymphomas display molecular heterogeneity, therefore many patients have poor responses to our commonly used treatment strategies. Novel therapeutic targets and new biomarkers need to be identified so as to improve the accuracy of diagnosis and treatment selection.

K. Hezaveh (Heinrich-Heine University), A. Kloetgen (Heinrich-Heine University), Stephan H. Bernhart (University of Leipzig), et al. carried out Next-Generation Sequencing (NGS) within the framework of the International Cancer Genome Consortium Project “Determining Molecular Mechanisms in Malignant Lymphoma by Sequencing” to identify microRNA (miRNA) signatures in Burkitt Lymphoma (BL), Diffuse Large B-Cell Lymphoma (DLBCL) and Follicular Lymphoma (FL), and correlate these to Messenger RNA (mRNA) expression and genomic mutations. Also, by using PAR-CLIP and intersecting the results with mRNA/miRNA expression profiles derived from patients, specific miRNA-mRNA target pairs in BL and DLBCL could be identified. Their findings were published in Haematologica in November 2016.

Tumor samples were profiled from 16 BLs, 19 DLBCLs (including 7 with germinal center DLBCL, 10 activated B-cell DLBCL and 2 with type III DLBCL), and 21 FLs (mainly grade 1/2).

• When comparing their miRNA classifiers that separate the BL, DLBCL, and FL to previous array- and qRT-PCR based studies, 5 miRNA (hsa-miRs-23a/29b/146a/155/222) were repeatedly identified to differentiate BL from DLBCL and 2 miRNA (hsa-miR-92/150) that separated FL from DLBCL
• BLs were separated from DLBCL/FL by 22 unique miRNA, of which 13 have been shown to be regulated by MYC
• Hsa-miR-143 was very highly expressed across the majority of Lymphoma samples; expression ranged from 0.8% to 68.2% (mean 8.9%) of all reads mapping to miRNA for this miRNA alone with no significant differences between mean expression for BL (10.8%), FL (8.9%), and DLBCL (8.9%)
• Ten mutations in miRNA, detectable at DNA and RNA levels, were identified in 8 patients (6 mutations in 5 DLBCL patients, 4 mutations in 3 FL patients) with a total of four miRNA affected (hsa-miR-142/-612/-3655/-4322)
• The most commonly mutated miRNA was hsa-miR-142 with 6 different mutations in 5/40 DLBCL/FL patients (3/19 DLBCL, 2/21 FL)
• Found expression of three previously unreported microRNA
  • Downregulation of novel-miR-1 and novel-miR-2 resulted in two (EIF3C, MPEG1) and three (HLA-DRB5, PFKFB4, PPP1R35) upregulated mRNA, respectively
  • Upregulation of novel-miR-1 led to the downregulation of 55 coding mRNA whereas overexpression of novel-miR-2 only resulted in two downregulated mRNA (SLCO2B1, UPP1)
• Argonaute-2 PAR-CLIP experiments found, at the individual gene level, microRNA directly targeted 328 mRNA in non-BL models and 208 mRNA in BLs
• Multiple regulatory pathways involved in lymphomagenesis and commonly deregulated by mutations in lymphoma were identified in this integrative analysis such as Ras, PI3K-Akt and MAPK signaling pathways

These findings show that mRNA deregulation via miRNA is potentially involved in lymphomagenesis; the identified recurrent mutations in has-miR-142 in FL and DLBCL, and editing of the has-miR-376 cluster, indicated microRNA editing contributes to lymphomagenesis. Moreover, novel-miR-1 presented as a possible contributor to lymphomagenesis and therefore, a potential therapeutic target; it was detected in a B-lymphoblastoid, SU-DHL-4, and Namalwa cell lines, and was found to regulate numerous lymphoma genes such as CARD11, E2F2, MCM2, and MCM7.