CDKN2 Deletions in Leukemia-Derived Cell Lines: Detection by Fluorescence In Situ Hybridization with Interphase Cells

Abstract

Hemizygous and homozygous deletions of chromosomal band 9p21 have been detected in various tumor types as well as in more than 20% of acute lymphoblastic leukemia. Recently, the CDKN2 gene (pl6^INK4A, MTS I, CDK4I) has been proposed as a candidate tumor suppressor gene because it is frequently deleted in cell lines derived from multiple tumor types. We examined 18 leukemia-derived cell lines (13 T-ALL, 3 B-cell-precursor ALL,1 AML,1 CML-blast crisis) by polymerase chain reaction and Southern blot analysis to further define the frequency and size of 9p deletions in hematological malignancies. Homozygous CDKN2 deletions were detected in 16 cell lines (89%). Interphase fluorescence in situ hybridization (FISH) is a powerful method to detect chromosomal rearrangements, including submicroscopic deletions. Using a cosmid contig of the CDKN2 region, we performed interphase FISH in nine cell lines to study the accuracy of this method in detecting 9p deletions. Interphase FISH determined accurately all deletions of the tumor suppressor region previously detected by Southern blot or PCR. In six cell lines the cosmid contig was completely deleted. In one cell line, the intensity of the hybridization signals was significantly reduced, indicating a partial deletion of the hybridization region. One cell line had a hemizygous deletion which is difficult to detect by molecular techniques. Genomic deletions seem to be the predominant mechanism of CDKN2 inactivation in acute leukemias. Interphase FISH will play an important role in defining the frequency of CDKN2 deletions in primary tumors, because it is able reliably to analyze clinical samples that are contaminated by normal cells.