-Deficient Nonobese Diabetic Mice Rag1 Underlies Leukemia Initiation in Loss of T Cell Progenitor Checkpoint Control

NOD mice exhibit major defects in the earliest stages of T cell development in the thymus. Genome-wide genetic and transcriptome analyses were used to investigate the origins and consequences of an early T cell developmental checkpoint breakthrough in Rag1-deficient NOD mice. Quantitative trait locus analysis mapped the presence of checkpoint breakthrough cells to several known NOD diabetes susceptibility regions, particularly insulin-dependent diabetes susceptibility genes (Idd)9/11 on chromosome 4, suggesting common genetic origins for T cell defects affecting this trait and autoimmunity. Genome-wide RNA deep-se-quencing of NOD and B6 Rag1-deficient thymocytes revealed the effects of genetic background prior to breakthrough, as well as the cellular consequences of the breakthrough. Transcriptome comparison between the two strains showed enrichment in differentially expressed signal transduction genes, prominently tyrosine kinase and actin-binding genes, in accord with their divergent sensitivities to activating signals. Emerging NOD breakthrough cells aberrantly expressed both stem cell–associated proto-oncogenes, such as Lmo2, Hhex, Lyl1, and Kit, which are normally repressed at the commitment checkpoint, and post–b-selection checkpoint genes, including Cd2 and Cd5. Coexpression of genes characteristic of multipotent progenitors and more mature T cells persists in the expanding population of thymocytes and in the thymic leukemias that emerge with age in these mice. These results show that Rag1-deficient NOD thymocytes have T cell defects that can collapse regulatory boundaries at two early T cell checkpoints, which may predispose them to both leukemia and autoimmunity. A ll T cells arise from a small pool of multipotent progenitors , which undergo proliferation and tightly controlled developmental programming induced and sustained by interactions with the thymic environment rich in Notch ligands and cytokines (1, 2). Thymic precursors are CD4 and CD8 double-negative (DN), and they are defined by sequential changes in surface Kit (CD117), CD25, and CD44 into stages: DN1 (or early T cell progenitor, ETP; Kit hi CD44 hi CD25 2), DN2 (Kit hi CD44 hi CD25 +), DN3 (Kit lo CD44 lo CD25 +), and DN4 (Kit lo CD44 lo CD25 lo) (3, 4). A TCR-independent commitment checkpoint has recently been identified within the DN2 stage, marked by decreased Kit expression from the multipotent DN2a stage to the committed DN2b stage (5) and dependent on Bcl11b (6, 7). DN2a cells, similar to more immature DN1/ETP cells, undergo proliferative expansion and express legacy stem/progenitor genes such as Kit, Lyl1, Tal1, Gfi1b, and Sfpi1 (PU.1). These features decline sharply in the DN2b/DN3 stages when T …