Fig. 4

Apoptosis and cell cycle control are rewired in cyclophosphamide-treated TCA and TCP mice. Cyclophosphamide treatment induces a robust p53 response in CLL cells isolated from TC animals, evidenced by transcriptional upregulation of the p53 target genes Mdm2, Bax, and Cdkn1a. S-phase cyclins and mitotic genes are downregulated in cyclophosphamide-treated TC-derived CLL cells. In contrast, TCA animals lack a detectable repression of S-phase cyclins and mitotic genes in response to cyclophosphamide. Furthermore, TCP-derived CLL cells lack a transcriptional signature of a p53 response, fail to downregulate S-phase cyclins and mitotic genes and instead display an increased expression of the S-phase genes Cdc6 and Ccne2. a Significantly differentially expressed KEGG pathways between CLL cells isolated from spleens of untreated (n = 3 for TC, TCA, and TCP) and cyclophosphamide-treated animals (n = 3 for TC, TCA, and n = 2 for TCP) of all three genotypes. Splenocytes were isolated 12 h after a single dose of 200 mg/kg cyclophosphamide. b Differentially expressed genes between untreated and treated samples of each genotype. Significantly differentially expressed components of the KEGG pathways “p53 signaling pathway” and “cell cycle” are highlighted (transparent circles) and a selected set of these genes was annotated (colored circles). A complete list of the significantly and differentially expressed genes is provided in Supplementary Table 1. c Expression levels of cell cycle and apoptosis genes in splenocytes of untreated and cyclophosphamide-treated animals (genotype-stratified). d Simplified illustration of the cellular response to genotoxic stress observed in leukemic clones that develop in TC, TCA, a`nd TCP animals. Integrated signals from multiple pathways activated by DNA damage lead to the activation of p53, which mediates cell cycle arrest and apoptosis. This p53-mediated response is partially impaired in Atm-deficient cells and completely abolished in the p53-deficient setting. e Significantly differentially expressed components of the base excision repair (BER) pathway between the different genotypes are highlighted. A complete list of differentially expressed genes of the KEGG pathway “base excision repair” is provided in Supplementary Table 2. Error bars represent standard deviation. Student’s t-test, *p ≤ 0.05, **p ≤ 0.01