Combining Insights from Big Data and Gene-Editing Techniques to Refine Gene-and residue-level Implications of Clonal Hematopoiesis Mutations
Silver, Alexander James
0000-0001-8255-3140
:
2024-07-12
Abstract
Clonal hematopoiesis (CH) is an age-associated phenomenon in which there is an expansion of blood cells with an acquired mutation but no evidence of hematologic malignancy. Clonal hematopoiesis of indeterminate potential (CHIP) is a type of CH defined by mutations in leukemia-associated genes and a variant allele fraction of at least two percent. CHIP is known to increase risk of myeloid malignancy but also a number of diseases of aging, including cardiovascular disease. Because there are many different genes which may be mutated in CHIP, there remain many gaps in our understanding about what populations are more likely to develop certain types of CHIP. It is also poorly understood the extent to which different somatic variants within a given gene have differential association with disease phenotypes. And, at present, there exist no approved therapies that target CHIP clones. Here, we used big data from human cohort studies and genetic editing laboratory techniques to interrogate the phenotypic associations of specific CHIP genes and mutations and determine the feasibility of targeting these using genetic editing. First, we found that TET2-mutant CHIP is enriched two-fold among individuals who have received a solid organ transplant in the past, but is not enriched in people who later get a transplant. These data indicate that solid organ transplant and its attendant immunosuppression lead to selection for TET2-mutant clones. Second, we investigated two ostensibly similar missense mutations in DNMT3A, R882H and R882C, finding that the former mutation leads to heightened inflammatory priming upon knock-in to primary human hematopoietic stem and progenitor cells. Moreover, we observed that R882H, but not R882C, is associated with an increased risk of overall mortality and cardiovascular disease; R882H also exhibited a significantly higher risk of malignant transformation than R882C. Lastly, we pioneered the use of allele-specific gene editing to correct somatic point mutations in human cells without the use of exogenous template sequences. We reverted several CHIP-associated point mutations to their wild-type sequence and show this treatment could prolong survival in a cell-derived xenograft model of leukemia. These results and techniques may be useful in CHIP risk stratification in the future.