Integrated Genomic Profiling of Chronic Lymphocytic Leukemia Identifies Subtypes of Deletion 13q14 with Differential Expression of LATS2.

Chronic lymphocytic leukemia (CLL) is a biologically heterogeneous illness with a variable clinical course. Loss of chromosomal material on chromosome 13 at cytoband 13q14 is the most frequent genetic abnormality in CLL but the molecular aberrations underlying del13q14 in CLL remain incompletely characterized. We analyzed 171 CLL cases for LOH and sub-chromosomal copy loss on chromosome 13 in DNA from FACS-sorted CD19+ cells and paired buccal cells using the Affymetrix XbaI 50K SNP array platform. Comparative analysis of SNP-array-derived detection of del13q14 using copy number analysis compared with clinical FISH results for del13q14 demonstrated strong agreement between both methods: FISH detected 91/171=53% overall del13q14 incidence and 77/171=45% del13q14 cases with greater than 25% of cells involved. SNP-arrays detected 82/171=48% del13q14 incidence. SNP-arrays detected 74/77=96% of all CLL cases that were greater than 25% FISH positive and 82/91=90% of all CLL cases that were FISH positive (% positive range for FISH was 2–97%). Finally, SNP-arrays detected 2 CLL cases not previously known to be del13q14 by FISH. The resulting high-resolution genomic maps, together with array-based measurements of expression levels of RNA in CLL cases with and without del13q14 and Q-PCR-based expression analysis of selected genes, support the following conclusions:

• del13q14 is heterogeneous and composed of multiple subtypes (types Ia, Ib and II) with deletion of Rb or the miR15a/16 loci serving as anatomic landmarks, respectively;

• del13q14 type Ia deletions are relatively uniform in length and extend from breakpoints close to the miR15a/16 cluster to a newly identified telomeric breakpoint cluster at ∼50.2–50.5 Mb physical position;

• LATS2 RNA levels are ∼2.6–2.8 fold lower in cases with del13q14 type I that do not delete Rb, as opposed to del13q14 type II lesions or all other CLL cases;

• ∼15% of CLL cases display marked reductions in miR15a/16 expression that are often but not invariably associated with bi-allelic miR15a/16 loss; and

• Bcl-2 levels and miR16/15a locus loss or miR16/15a expression are not correlated.

This data should aid future investigations into biological differences imparted on CLL by different del13q14 subtypes, including investigations into LATS2 as one of the genes found deregulated as part of del13q14 type I and investigations into additional miR16/15a targets.