Clinical and biological relevance of genomic heterogeneity in chronic lymphocytic leukemia

• Published in: PloS one 2013-02, Vol.8 (2), p.e57356-e57356
• Main Authors: Friedman, Daphne R, Lucas, Joseph E, Weinberg, J Brice
• Format: Article
• Language: English
• Subjects: Aberration; Bioinformatics; Biological properties; Biology; Cancer; Chronic lymphocytic leukemia; Clinical outcomes; Clustering; Datasets; Gene expression; Gene Expression Profiling; Genetic Heterogeneity; Genomes; Heterogeneity; Humans; Leukemia; Leukemia, Lymphocytic, Chronic, B-Cell - genetics; Leukemia, Lymphocytic, Chronic, B-Cell - pathology; Lymphatic leukemia; Lymphocytes B; Lymphoma; Malignancy; Medical prognosis; Medical treatment; Medicine; Pathways; Patients; Polymorphism, Single Nucleotide; Principal components analysis; Standard deviation; Subgroups; Variability
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0057356

Chronic lymphocytic leukemia (CLL) is typically regarded as an indolent B-cell malignancy. However, there is wide variability with regards to need for therapy, time to progressive disease, and treatment response. This clinical variability is due, in part, to biological heterogeneity between individual patients' leukemias. While much has been learned about this biological variation using genomic approaches, it is unclear whether such efforts have sufficiently evaluated biological and clinical heterogeneity in CLL. To study the extent of genomic variability in CLL and the biological and clinical attributes of genomic classification in CLL, we evaluated 893 unique CLL samples from fifteen publicly available gene expression profiling datasets. We used unsupervised approaches to divide the data into subgroups, evaluated the biological pathways and genetic aberrations that were associated with the subgroups, and compared prognostic and clinical outcome data between the subgroups. Using an unsupervised approach, we determined that approximately 600 CLL samples are needed to define the spectrum of diversity in CLL genomic expression. We identified seven genomically-defined CLL subgroups that have distinct biological properties, are associated with specific chromosomal deletions and amplifications, and have marked differences in molecular prognostic markers and clinical outcomes. Our results indicate that investigations focusing on small numbers of patient samples likely provide a biased outlook on CLL biology. These findings may have important implications in identifying patients who should be treated with specific targeted therapies, which could have efficacy against CLL cells that rely on specific biological pathways.