1. Genome-Wide Analysis Uncovers Novel Recurrent Alterations in Primary Central Nervous System Lymphomas
- Author
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Yan W. Asmann, Riccardo Valdez, Esteban Braggio, Ellen D. McPhail, M. Beatriz S. Lopes, Paul A. Decker, Jan B. Egan, Jackline Ayres Da Silva, Raoul Tibes, Bruce W. Eckloff, David Schiff, A. Keith Stewart, Thomas E. Witzig, Juhi Ojha, Rafael Fonseca, Brian P. O'Neill, and Scott Van Wier
- Subjects
Cancer Research ,DNA Copy Number Variations ,Karyotype ,Biology ,Article ,Central Nervous System Neoplasms ,immune system diseases ,CDKN2A ,hemic and lymphatic diseases ,medicine ,Humans ,Exome ,Exome sequencing ,Chromosome Aberrations ,Comparative Genomic Hybridization ,Lymphoma, Non-Hodgkin ,Lymphocyte differentiation ,Primary central nervous system lymphoma ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Prognosis ,medicine.disease ,Lymphoma ,PRKCD ,Oncology ,Mutation ,Immunology ,Cancer research ,Chromosomes, Human, Pair 6 ,Genome-Wide Association Study ,Comparative genomic hybridization - Abstract
Purpose: Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin lymphoma confined to the central nervous system. Whether there is a PCNSL-specific genomic signature and, if so, how it differs from systemic diffuse large B-cell lymphoma (DLBCL) is uncertain. Experimental Design: We performed a comprehensive genomic study of tumor samples from 19 immunocompetent PCNSL patients. Testing comprised array-comparative genomic hybridization and whole exome sequencing. Results: Biallelic inactivation of TOX and PRKCD was recurrently found in PCNSL but not in systemic DLBCL, suggesting a specific role in PCNSL pathogenesis. In addition, we found a high prevalence of MYD88 mutations (79%) and CDKN2A biallelic loss (60%). Several genes recurrently affected in PCNSL were common with systemic DLBCL, including loss of TNFAIP3, PRDM1, GNA13, TMEM30A, TBL1XR1, B2M, CD58, activating mutations of CD79B, CARD11, and translocations IgH-BCL6. Overall, B-cell receptor/Toll-like receptor/NF-κB pathways were altered in >90% of PNCSL, highlighting its value for targeted therapeutic approaches. Furthermore, integrated analysis showed enrichment of pathways associated with immune response, proliferation, apoptosis, and lymphocyte differentiation. Conclusions: In summary, genome-wide analysis uncovered novel recurrent alterations, including TOX and PRKCD, helping to differentiate PCNSL from systemic DLBCL and related lymphomas. Clin Cancer Res; 21(17); 3986–94. ©2015 AACR.
- Published
- 2015