Genetic Analysis of Plasmablastic Lymphomas in HIV (+) Patients Reveals Novel Driver Regulators of the Noncanonical NF-κB Pathway

Introduction: Plasmablastic lymphoma (PL) is an aggressive variant of lymphoma, with strong association with HIV. Despite significant improvements in the survival of other lymphomas, PL has a short overall survival (14 months). The association with Epstein-Barr virus (EBV) infection and MYC chromosomal translocations are defining features of PL. However, the genetic causes and the role of specific mutation in PL are largely unknown. This limitation hinders the design of therapeutic approaches aimed to improve PL survival. Therefore, we performed a comprehensive analysis of the genetic landscape in PL.

Methodology: Whole exon sequencing of 52 de novo PL tumors from HIV+ patients and matched normal tissues (15%) using high throughput sequencing on the Illumina platform. Of these 52 patient samples, 10 tumor and 4 normal control samples were removed due to poor sequencing quality. Mapping and variant calls were performed using BWA and Varscan softwares. Variants call filtering criteria include: exon location, minimum coverage of 5%, and onside T-test P value ≤ of 0.01 or 0.02). For immunohistochemistry, we use p-TAK1 Thr184-187 (Cell signaling) and p-BTK Tyr551(Termofisher) antibodies.

Results: Analysis of exome sequencing data identified 1562 recurrent somatic mutations (p-value ≤0.01) in 711 genes, including 304 mutations previously identified in cancer driving genes. The most common recurrent pathways affected within the top 2000 gene mutations with p≤0.02 comprised mainly of NF-κB signaling followed by immune response (antigen presentation by MHC class II and the alternative and lectin induced complement pathways), reverse signaling by Ephrin B, mTOR/PTEN and EGFR/RAS pathways.

Based on the lack of canonical NF-κB activation previously reported (Chapman J et al. Leukemia 2015; 29: 2270-2273) and the important role of MYD88-p100 signaling pathway in B cell differentiation into plasmablast (Guo et al. Oncogene 2016. 36(29):4224-4232), we investigated the status of p100 signaling in PL using a published gene expression dataset (Chapman J. et al Leukemia 2015). Our analysis demonstrated that most PL (70%) manifest constitutive p100 signaling. Therefore, we focused on mutations in genes involved in the NF-κB activation. Mutations in the NF-κB pathway were identified in all the analyzed cases with an average of 4 mutated genes in each tumor. Consistent with the previously reported downregulation in RNA expression of genes implicated in the BCR and canonical NF-κB signaling, we found deleterious mutations in genes in the BCR pathway that have been previously reported in lymphomas, including MATL1, FYN and SYK (24%, 16% and 15%, respectively). In contrast, we found frequent gene mutations in the MYD88-PI3P pathway that never have been reported in lymphomas, including SHIP2, DOCK8, PLCG2 in 50%, 39% and 37% of the cases, respectively. These findings are of relevance, as this mutations are expected to results in increased MYD88/TAK1 and BTK signaling (Shinners NP et al J. Imm. 2007, 179 (6) 3872-3880) and can be targeted by specific inhibitors. To evaluate the status of phosphorylation of TAK1 and BTK in these tumors, we performed immunohistochemistry analysis in 15 PL, demonstrating high levels of phosphorylation of these proteins in all tumors analyzed.

Conclusion: To our knowledge, this is the first in-depth analysis of PL genome. Our data provide the most comprehensive genetic portrait of PL, provides potential genetic causes of this disease and identify potential druggable targets that deserve further clinical exploration.