Integrated Genomic Profiling Identifies Preferential Expression of the Insulin Receptor in CLL with Deletion 11q.

Chronic lymphocytic leukemia (CLL) is associated with characteristic genomic aberrations as defined by FISH and SNP arrays. CLL with del11q is characterized by a relatively aggressive clinical course, and about one third of cases carry mutations in ATM on the retained allele. Little information is available on additional molecular aberrations associated with del11q in CLL. We have analyzed del11q in a subset of 178 CLL cases using DNA from FACS-sorted CD19+ cells compared with buccal DNA using the Affymetrix 50k SNP array platform. Genomic copy number analysis using dChipSNP identified two non-overlapping minimal deleted regions on 11q, one of which spans ATM. We proceeded to use comparative expression array profiling of RNA derived from sorted CD19+ cells from 10 CLL cases with and nine cases without del11q using the Affymetrix U133 2.0 Plus platform. Analysis of normalized data identified ~85 probe sets with differential expression (del11q versus reference) that displayed a false discovery rate of <0.1. Approximately 70% of these genes were under-expressed and mapped to 11q22–23, thus providing confidence that genes lost through del11q displayed reduced expression under our assay conditions. Three probe sets identified the insulin receptor (INSR) to be expressed at substantially higher levels (log2 scale 2.5–3.1 fold) in del11q CLL as opposed to the reference cases that were used in the expression array-based analysis. Validation of differential INSR expression in CLL was accomplished by Q-PCR using cDNA synthesized from RNA purified from sorted CD19+ cells from 178 CLL cases. Using normalized Ct values for INSR expression (delta Ct INSR-GAPD) and a delta Ct cut-off of <10, 65% of CLL with del11q expressed the INSR as opposed to 15% (del13q14), 6% (del17p), 11% (normal FISH) and 23% (trisomy 12) and ~20% of all CLL cases, independent of genetic subtype. Finally, immunoblot analysis on cellular lysates derived from negatively enriched and >90% pure CLL cells from 10 cases with del11q and with high INSR expression versus cases without del11q and absent expression confirmed the accuracy of Q-PCR-based estimates of INSR expression. Work is in progress to measure effects of INSR expression on CLL survival and insulin-induced signaling in CLL in an effort to dissect functional consequences of INSR expression in CLL.