MicroRNA Profiling of Anaplastic Large Cell Lymphoma
KP Patel, D Ma, BA Barkoh, H Yao, R Sargent, E Drakos, LJ Medeiros, R Luthra. The University of Texas M.D. Anderson Cancer Center, Houston, TX
Background: MicroRNAs (miRNA) are a recently discovered class of naturally occurring short noncoding RNA molecules that negatively regulate eukaryotic gene expression. Recent studies have suggested that dysfunctional expression of miRNA leading to dysregulation of gene expression is a common feature of hematologic malignancies. Anaplastic lymphoma kinase (ALK)+ anaplastic large cell lymphoma (ALCL) is a distinctive type of T-cell lymphoma characterized by CD30 expression, abnormalities of the ALK gene, and a favorable clinical outcome. By contrast, ALK- ALCL, although morphologically and immunophenotypically similar, lacks ALK gene abnormalities and has a worse prognosis. To determine if these clinicopathologic differences were due to differential miRNA expression, we compared the miRNA profiles of ALK+ and ALK- ALCL.
Design: Total RNA was extracted from microdissected paraffin-embedded tissue from 7 ALK+ and 6 ALK- ALCL cases. The miRNA were labeled with Cyanine-3 using miRNA labeling kit (Agilent Technologies, Santa Clara, CA). Human miRNA Microarray Version 3 (Agilent Technologies) containing oligonucleotide probes for 866 human miRNA and 89 human viral miRNAs was used to generate miRNA profiles of the study cases. We performed hierarchical clustering analysis with the ward linkage rule. The robustness of samples clusters was examined by a bootstrapping method with 200 iterations. A beta-uniform mixture method (BUM) was used to control false discovery rate (FDR) to <0.3. The Student's t-test was used to identify miRNAs expressed differentially between the study groups. Potential downstream targets of miRNAs were identified using TargetScan 5.1 (www.targetscan.org) analysis.
Results: The hierarchical clustering analysis identified clusters defined by miRNA expression profiles that were significantly associated with ALK expression (p<0.01). Seven miRNAs expressed differentially between ALK+ and ALK- ALCL were detected (p<0.01). Three of seven miRNAs were upregulated in ALK+ ALCL compared with ALK- ALCL, and four were downregulated. Differentially expressed miRNA included miRNAs that affect multiple cellular processes, such as miR-155 and, new miRNAs whose role has not been studied well, such as miR-720. We also identified miRNAs that appear to target the ALK pathway.
Conclusions: We have identified seven miRNAs with a potential role in the pathogenesis of ALK+ ALCL. Further validation of expression and functions of these miRNAs is in progress.
Monday, March 22, 2010 11:30 AM
Platform Session: Section B, Monday Morning