Drugs that target DNA topoisomerase II (Top2), including etoposide (VP-16), doxorubicin, and mitoxantrone, are among the most effective anticancer drugs in clinical use. However, Top2-based chemotherapy has been associated with higher incidences of secondary malignancies, notably the development of acute myeloid leukemia in VP-16-treated patients. This association is suggestive of a link between carcinogenesis and Top2-mediated DNA damage. We show here that VP-16-induced carcinogenesis involves mainly the  rather than the ␣ isozyme of Top2. In a mouse skin carcinogenesis model, the incidence of VP-16-induced melanomas in the skin of 7,12-dimethylbenz[a]anthracene-treated mice is found to be significantly higher in TOP2 ؉ than in skin-specific top2-knockout mice. Furthermore, VP-16-induced DNA sequence rearrangements and double-strand breaks (DSBs) are found to be Top2-dependent and preventable by cotreatment with a proteasome inhibitor, suggesting the importance of proteasomal degradation of the Top2-DNA cleavage complexes in VP-16-induced DNA sequence rearrangements. VP-16 cytotoxicity in transformed cells expressing both Top2 isozymes is, however, found to be primarily Top2␣-dependent. These results point to the importance of developing Top2␣-specific anticancer drugs for effective chemotherapy without the development of treatment-related secondary malignancies.DNA rearrangements ͉ melanoma ͉ skin-specific topoisomerase II-knockout ͉ tumor cell killing ͉ carcinogenesis A nticancer drugs that target DNA topoisomerase II (Top2), including etoposide (VP-16), doxorubicin, and mitoxantrone, are often referred to as Top2 poisons and are among the most effective and widely used anticancer drugs in the clinic. However, life-threatening toxic side effects, including drug-induced secondary malignancies, have been noted in patients receiving Top2-based chemotherapy. An association between infant leukemia and in utero exposure to Top2 poisons has also been reported (reviewed in refs. 1-3). In all cases, the molecular basis underlying carcinogenesis in Top2-based chemotherapy is unclear.Clinical evidence for a direct link between VP-16 treatment and treatment-related acute myeloid leukemia (t-AML) is particularly strong (1-3). VP-16-induced t-AML is frequently associated with balanced translocations between the mixed lineage leukemia (MLL) gene on chromosome 11q23 and Ͼ50 partner genes (the MLL gene is also known as ALL-1, hTRX, or HRX) (4-7). These rearrangements, as well as those found in infant leukemia, cluster within a well characterized 8.3-kb breakpoint cluster region (bcr) (8-16). The bcr of MLL is AT-rich and contains Alu sequences, putative recognition sites of Top2-mediated DNA cleavage, and chromosome scaffold/matrix attachment regions (SAR/MAR) (5,(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). There is substantial evidence that chromosome 11q23 translocations in t-AML and infant leukemia are a consequence of drug-induced formation of double-strand breaks (DSBs) (6-9). VP-16 is known to induce DSBs by the format...