FATC domain deletion compromises ATM protein stability, lymphocyte development, and promotes lymphomagenesis

ATM kinase is a master regulator of the DNA damage response and loss of ATM leads to primary immunodeficiency and greatly increased risk for lymphoid malignancies. The FATC domain is conserved in Phosphatidylinositol-3-kinase-related protein kinases (PIKKs). Truncation mutation in the FATC domain (R3047X) selectively compromised reactive oxygen species-induced ATM activation in cell-free assays. Here we show that in mouse models, knock-in ATM-R3057X (AtmRX, corresponding to R3047X in human ATM) mutation severely compromises ATM protein stability, and causes T cell development and B cell immunoglobulin class switch recombination defects and infertility resembling ATM-null. The residual ATM R3057X protein retains minimal, yet functional measurable, DNA damage-induced checkpoint activation and significantly delays lymphomagenesis in AtmRX/RX mice compared to Atm-/-. Together, these results support a physiological role of the FATC domain in ATM protein stability and show that minimal ATM activity can prevent growth retardation and delay tumorigenesis without restoring lymphocyte development and fertility. To determine how ATM-RX protein affects the repair phase of CSR, we analyzed thousands of CSR and internal deletion junctions from activated AtmRX/RX, Atm+/+, and Atm-/- control B cells using the high-throughput genome-wide translocation sequencing (HTGTS) technology. Since all our experimental mice carry the preassembled IgH on the 129 background, we replaced the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6-based mm9 with the corresponding region in the AJ851868.3 (NCBI gene accession no. AJ851868.3) 129 IgH sequence (1415966–1592715) to generate the mm9sr (switch region replacement) genome. 1. Hu J, et al. (2016) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 11:853–871. Together, the increased translocation (+ oriented junction), preferential loss of Sμ-Sε junctions, and the increased MH usage in the HTGTS analyses of AtmRX/RX B cells indicate that the R3057X mutation impairs the DNA repair function of ATM during CSR, similar to the loss of ATM.