CDKN1B Encoding the Cyclin-Dependent Kinase Inhibitor 1B (p27) but Not ETV6 Is Located in the Minimally Deleted Region of 12p Abnormalities in Myeloid Malignancies and Its Expression Is Associated with Outcome in Acute Myeloid Leukemia (AML).

Abstract 275

Cytogenetic abnormalities – translocations as well as deletions – involving the short arm of chromosome 12 are common in a wide variety of hematologic malignancies. However, data on the minimal deleted region and on expression of candidate genes in this region are limited. Therefore, we analyzed 590 myeloid malignancies with FISH probes flanking the breakpoints within the ETV6 gene which is located on the short arm of chromosome 12. 114 cases showed a deletion of the telomeric and the centromeric probe while in 7 cases a deletion of the probe localized centromeric of ETV6 was observed while the telomeric probe was retained, suggesting a small interstitial 12p deletion. These cases were further analysed using SNP microarrays (Affymetrix Genome-Wide Human SNP Array 6.0). The median size of the deletion was 1.6 Mb (range: 1.2 – 10.6 Mb). The minimal deleted region was narrowed down to 815 kb (physical map position start: 12005749 bp from pter; end: 12820773 bp from pter) and encompasses the following genes: BCL2L14, LRP6, MANSC1, DUSP16, CREBL2, GPR19, CDKN1B, APOLD1 and hsa-mir-613. The expression of these genes was further evaluated by gene expression microarrays (Affymetrix HG-U133 Plus 2.0) in 781 patients with hematological malignancies. Only three genes, CREBL2, MANSC1 and CDKN1B were expressed in more than 15% of cases. As CDKN1B plays an important role in multiple fundamental cellular processes, including cell proliferation, cell differentiation, and apoptosis and moreover is a putative tumor suppressor. Thus, it is an interesting candidate gene for playing an important pathogenetic role in cases with 12p deletions. Therefore, we first analyzed CDKN1B expression in more detail. The median CDKN1B expression intensity was 1,582 (range 83 – 4498) in 399 myeloid malignancies (286 AML, 113 MDS). Karyotypes in AML were t(15;17)(q22;q12) (n=15), t(8;21)(q22;q22) (n=16), inv(16)(p13q22) (n=7), t(11q23)/MLL-rearrangement (n=10), complex aberrant karyotype (n=53), normal karyotype (n=99), and various other chromosome abnormalities (n=86) and in MDS del(5q) sole (n=20), −7 sole (n=5), normal karyotype (n=46) and various other chromosome abnormalities (n=42). 99 cases showed an expression intensity of CDKN1B below 1160 (first quartile) (83 AML, 16 MDS). In this cohort cases with t(8;21) (n=11), t(15;17) (n=11) or t(11q23)/MLL-rearrangement (n=6) were over-represented (Chi-square: p<0.0001, p<0.0001, and p=0.009, respectively), while cases with normal karyotype (n=28) were under-represented (Chi-square: p=0.048). In addition, an association of FLT3-TKD with low CDKN1B expression was observed (7/13 FLT3-TKD+ cases showed a low CDKN1 expression compared to 54/213 FLT3-TKD- cases, p=0.025), while no correlation to other molecular mutations was found (NPM1, FLT3-ITD, CEPBA, MLL-PTD). With respect to clinical data in AML, median overall survival (OS) and event-free survival (EFS) was longer in CDKN1B low expressers (not reached vs. 14.8 months; p=0.005 and 31 months vs. 9.7 months; p=0.013). In MDS, a tendency towards a longer OS was also observed (not reached vs. 55.9 months; p=0.29). For CREBL2 and MANSC1 no association of expression and survival was observed. In conclusion, the minimal deleted region on 12p in myeloid malignancies encompasses only 3 genes which are expressed in myeloid malignancies: CDKN1B, CREBL2 and MANSC1. Low CDKN1B expression is more frequently found in AML with t(8;21), t(15;17) or t(11q23)/MLL-rearrangement and is associated with a favorable outcome which might be due to a higher susceptibility to cytotoxic agents as low CDKN1B expression enhances cell cycle progression.