GENOME-WIDE ANALYSIS UNCOVERS RECURRENT ALTERATIONS IN PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMAS (PCNSL)

Abstract

BACKGROUND: Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin lymphoma (NHL) confined to the CNS. Whether there is a PCNSL-specific genomic signature and, if so, how it differs from systemic DLBCL is uncertain. To address this gap in critical knowledge we performed a comprehensive genomic study in a cohort of 19 immunocompetent PCNSL patients by combining aCGH, whole exome sequencing and mate-pair whole genome sequencing. METHODS: 1) Tumor samples from 19 immunocompetent (HIV-, EBV-) PCNSL. 2) DNA from frozen tissue or from formalin-fixed paraffin embedded (FFPE) tissues. 3) All samples analyzed using a combination of aCGH, whole exome sequencing, mate-pair whole genome sequencing, targeted sequencing and FISH. 4) Overall survival estimated using Kaplan Meier method. RESULTS: We found a complex karyotype with a median of 21 copy-number abnormalities, 6 structural abnormalities and 3.3 non-synonymous mutations per Mb. We found a remarkably high prevalence of MYD88 activating mutations (79%) and CDKN2A biallelic loss (60%). Biallelic losses of TOX (a regulator of T-cell development), PRKCD (protein kinase C delta) and chromosomal breakpoints in DLGAP1 (discs large-associated protein 1) were recurrently found in PCNSL but not in systemic DLBCL, suggesting a specific role in PCNSL pathogenesis. Several other genes recurrently affected in PCNSL are common with systemic DLBCL of the ABC-type, such as loss of TNFAIP3, PRDM1, GNA13, TMEM30A, TBL1XR1, B2M and CD58, activating mutations of CD79B, CARD11, BRAF3 and translocations of IgH-BCL6. Overall, components of the NF-□B signaling pathway were altered in >90% of PNCSL, highlighting the potential value of this pathway for targeted therapeutic approaches. Furthermore, integrated analysis also showed an enrichment of networks associated with immune response, proliferation, regulation of apoptosis, and lymphocyte differentiation. CONCLUSIONS: We report a PCNSL genomic landscape closely related to ABC-DLBCL but with critical elements that support the existence of a subset of PCNSL-specific abnormalities, helping to genetically differentiate PCNSL from systemic DLBCL and related lymphomas. SECONDARY CATEGORY: Immunobiology & Immunotherapy.