Collaborative Pathways that Lead to Leukemia

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

Mini-chromosome maintenance component 2 (Mcm2) is a DNA replication licensing factor that is part of the Mcm2-7 complex which functions as a DNA helicase, unwinding genomic DNA at the replication fork. Not surprisingly, homozygous deletion of Mcm2 is lethal. However, insertion of a cre cassette into the 3' UTR of Mcm2 leads to ~ 50% reduction in Mcm2 protein, and cells with two copies of the cre knock-in allele are hypomorphic, in that these cells express only 20-30% as much Mcm2 protein compared to wild-type cells. Mice with two copies of the Mcm2 cre allele (Mcm2cre/cre) invariably develop pre-T lymphoblastic leukemia/lymphoma (pre-T LBL) and, when crossed with mice that express a NUP98::HOXD13 (NHD13) fusion oncogene, develop B cell precursor acute lymphoblastic leukemia (BCP ALL). Copy number alteration (CNA) analysis demonstrated a pattern of gains and losses, predominantly losses 10-1000 kb in length. Notably, there is a recurrent loss of Pax5 and Ptpn1 in BCP ALL. The observation that Ptpn1 loss frequently occurred in double mutant Mcm2cre/cre; NHD13 mice suggested that Ptpn1 loss might predispose NHD13 mice to develop BCP ALL. To test this hypothesis, we crossed an NHD13 transgene onto a Ptpn1-/- background. Almost 70% of the NHD13+/Ptpn1-/- mice developed BCP-ALL within a year, demonstrating a strong genetic collaboration between these two mutations. Although PTPN1 deletions have not been reported in human BCP-ALL, deletions of the closely related PTPN2 co-occur with NUP214-ABL1 fusions, and PTPN2 was identified as a negative regulator of the NUP214-ABL1 kinase (Nat Genet 42:530-5, 2010). A manuscript describing these findings was recently submitted for publication. We have generated a panel of Mcm2cre/cre T-ALL cell lines that display the CNA mutator phenotype. Although CRISPR screens are an excellent mechanism to detect phenotypes produced by gene loss, they will not detect phenotypes produced by gene copy number gains. Therefore, we have begun a study to identify copy number loss and gains associated with chemotherapy resistance. These studies revealed methotrexate resistance associated with specific copy number gains of the Dhfr gene, vincristine and etoposide resistance associated with focal gains of the Abcb1a (previously known as MDR1) gene, and loss of Nr3c1 associated with prednisone resistance. An unexpected finding stemmed from study of cytarabine resistant cells, which had acquired splice mutations and/or copy number loss of the Dck gene, which phosphorylates cytidine and cytarabine. The Dck deficient cells showed a novel, specific mutator phenotype. These findings have been published in abstract form, and a manuscript describing these findings in additional detail will be submitted for publication soon. We have also demonstrated that treatment of mice with the investigational azanucleoside ATC (see project 1) leads to BCP ALL, due to acquired mutations in genes well known to be relevant for human BCP ALL, such as Trp53, Pax5, Ikzf1, and Jak1/3. A manuscript describing these findings in currently in press. Finally, in collaboration with Dr. Suming Huang, we have shown that NUP98-rearragned leukemic transformation can act through the HoxBlinc lndRNA (PMID: 39883527).