Genomic and Expression Profiling of Hairy Cell Leukemia Revealed Multiple Mechanisms of NFkB Activation

Hairy cell leukemia (HCL) is a rare chronic B-cell lymphoproliferative disorder where the malignant B-cells manifest a “hairy” appearance under the microscope. Recent studies have identified BRAF V600E mutations in most HCL patients, highlighting this abnormality as a molecular hallmark for this disease. However, mutated BRAF occurs widely – already described in several solid tumors, including melanoma, thyroid and colorectal carcinomas, indicating that BRAF V600E is not pathognomonic in HCL. Cell lines originating from HCL patients lack BRAF mutations but retain the typical piliferous morphology and the appropriate HCL immunophenotype (CD19, CD11c, CD103, CD25, CD123), thus constituting tools for identifying alternative mechanisms of leukemogenesis in this disease entity. Genomic aberrations in hematopoietic tumors recurrently target loci bearing genes involved in malignant transformation. These genes may include both candidate biomarkers and potential therapeutic targets. To identify such genes in HCL we here combined genomic profiling and gene expression quantification of a well characterized HCL cell line containing several chromosomal aberrations. The expression levels of genomically targeted genes were compared to HCL control cell lines, identifying 91 deregulated genes. Gene set enrichment analysis of which indicated apoptosis, cell cycle regulation and DNA damage response (DDR) as altered processes in HCL. Accordingly, REL (NFkB and apoptosis), CDK6 and BRAF (cell cycle), ATM and CUTL1 (DDR) comprised prominent target genes overexpressed in this cell line. The same genes were found to be conspicuously expressed in HCL patient samples in silico (Fernandez et al., 2010; Gene Expression Omnibus GSE16455), supporting their clinical significance. Treatments of HCL cell lines for particular siRNA-mediated gene knockdowns and with selective pharmacological inhibitors helped to reveal a regulatory network highlighting NFkB at a central position. Consistently, focused analysis of expression profiling data of several cell lines supported elevated NFkB-pathway activity in HCL and ABC-DLBCL when compared to GC-DLBCL. In conclusion, we identified deregulated genes and multiple mechanisms which contribute to aberrantly activated NFkB-pathway in HCL. Therefore, NFkB may represent a B-cell specific hallmark of HCL and a promising novel therapeutic target most notably in patients lacking BRAF mutations in this entity.