Interstitial deletions of the short arm of chromosome 9 are associated with glioma, acute lymphoblastic leukemia, melanoma, mesothelioma, lung cancer, and bladder cancer. The distal breakpoints of the deletions (in relation to the centromere) in 14 glioma and leukemia cell lines have been mapped within the 400 kb IFN gene cluster located at band 9p2l. To obtain information about the mechanism of these deletions, we have isolated and analyzed the nucleotide sequences at the breakpoint junctions in two glioma-derived cell lines. The A1235 cell line has a complex rearrangement of chromosome 9, including a deletion and an inversion that results in two breakpoint junctions. Both breakpoints of the distal inversion junction occurred within AT-rich regions. In the A172 cell line, a tandem heptamer repeat was found on either side of the deletion breakpoint junction. The distal breakpoint occurred 5' of IFNA2; the 256 bp sequenced from the proximal side of the breakpoint revealed 95% homology to long interspersed nuclear elements. One-and two-base-pair overlaps were observed at these junctions. The possible role of sequence overlaps, and repetitive sequences, in the rearrangements is discussed.Several chromosomal mechanisms leading to the loss of function of putative tumor suppressor genes and the subsequent abnormal growth and proliferation of cancer cells have been described previously (16). Such mechanisms include point mutations, somatic crossing over, deletions and unbalanced translocations, and chromosome nondisjunction. The molecular cloning and characterization of several tumor suppressor genes, such as TP53 on chromosome 17pl3 (19, 43), RB1 on chromosome 13q14 (13), WTI on chromosome 11p13 (5), and APC on chromosome 5 (25), have greatly expanded our understanding of the role of tumor suppressor genes in the development of cancer. However, the molecular mechanisms underlying the interstitial deletions and unbalanced translocations associated with tumor suppressor genes have not been well studied.Recent data indicate that unbalanced translocations or interstitial deletions of the short arm of chromosome 9 [del(9p)] are recurring chromosomal abnormalities in a variety of tumor types, including acute lymphoblastic leukemia, glioma, melanoma, lung cancer, head and neck cancer, mesothelioma, ovarian cancer, and bladder cancer (1,2,7,8,23,28,29,35,40,42). Through molecular analysis, homozygous deletions of DNA sequences or losses of heterozygosity on 9p in a significant proportion of these tumors have been described (4, 10-12, 20, 24, 29, 31-33). Although the lengths and locations of these deletions vary, there is a common region of deletion at band 9p2l. This suggests the presence of a tumor suppressor gene in this region, whose inactivation contributes to the malignant process in all these different tumor types. The molecular studies with the different tumor types have demonstrated that the deletions involving 9p are sometimes interstitial and often include homozygous deletions of all or part of the interferon (IFN)...