CRISPR/Cas9 screen for small molecule inhibitors of clonal hematopoiesis of indeterminate potential

Abstract

Clonal hematopoiesis of indeterminate potential (CHIP) is a novel clinical entity, in which distinct somatic mutations occur at a variant allele fraction of at least 2% in the peripheral blood of healthy individuals. While individuals with CHIP do not have overt hematologic disease, the cells that harbor these mutations can undergo clonal expansion over time, acquire additional mutations and ultimately transform to frank malignancy. In addition, population studies have shown that these individuals have decreased overall survival due to an increased rate of cardiovascular disease. The most commonly mutated genes in CHIP include DNMT3a, TET2, ASXL1, PPM1D, and TP53. While individuals with CHIP are at a greater risk of developing hematologic malignancies and cardiovascular disease, the precise molecular mechanisms of CHIP that drive its associated disease states are largely unknown. We hypothesize that genes implicated in CHIP are potential targets for small molecule compounds to prevent clonal expansion. We modeled CHIP using Hoxb8 immortalized murine bone marrow derived hematopoietic progenitors, together with CRISPR/Cas9 to generate targeted loss of function mutations in Dnmt3a, Tet2, Ppm1d, and Tp53. With our model, we found differential sensitivity of Tp53 loss of function mutant cells to immunomodulatory imide drugs (IMiDs). Treatment with lenalidomide resulted in marked resistance and outgrowth of Tp53(-/-) mutant clones. However, the Tp53(-/-) mutant population exhibited sensitivity to pomalidomide, and a lesser degree of resistance compared to lenalidomide. These findings suggest a potential role for pomalidomide towards slowing the progression of Tp53 mutant CHIP, as well as in treatment of high risk TP53 mutant myeloid disease. Understanding the molecular mechanisms that drive CHIP and its interactions with small molecule drugs will offer new insight into targetable pathways, as well as the mechanisms that drive myeloid malignancy.