Modeling Clonal Hematopoietic Disorders in Zebrafish Using Color Barcoding

Myeloid neoplasms, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), are clonal hematopoietic disorders that arise from abnormal hematopoietic stem and progenitor cells (HSPCs)with acquired somatic mutations. To follow the hematopoietic output of HSPC clones endogenously, we have developed a novel marking strategy in which each HSPC clone is labeled in a unique fluorescent hue. The transgenic zebrafish line Zebrabow uses a Cre/lox system where stochastic recombination of multiple transgenic insertions harboring three fluorescent proteins (dTomato, YFP and CFP) provide stable and heritable color barcodes. Tissue-specificity is ensured by tamoxifen-induced Cre activation under the draculin promoter which is highly expressed in zebrafish HSPCs throughout development. The result of Zebrabow labeling is a collection of colored blood cells, which are grouped by their hue, and largely cluster in various groups, each representing a clonal population of cells that arise from a specific HSPC. To induce clonal hematopoietic states in zebrafish assessed by color dominance in hematopoietic cells, we introduced combinations of known genetic mutations founds in MDS and AML into Zebrabow embryos. Embryos at the 1-cell stage were injected with combinations of mutations and HSPC color labeling was performed at 36 to 48 hours post fertilization, during peak emergence of definitive blood stem cells from the dorsal aorta. The injected mutations were grouped by known co-occurence in patients with MDS and AML. The transgenic overexpression of Jak2^V617F, FLT3ITD, IDH2^R140Q, HOXA9 or HOXB4 under the zebrafish blood-specific promoter draculin, was combined with somatic mutagenesis of endogenous tet2, asxl1, dnmt3a, ezh2, ptena/b and tp53 via the CRISPR/Cas9 system. Mosaic combinations of these mutations resulted in the expansion of single color clones, contributing to ≥30% of granulocytes, with concomittant myeloid expansion in a third of these zebrafish. The majority of zebrafish exhibiting clonal expansion harbored frame-shift mutations in asxl1 with >25% variant allelic frequency identified by next-generation sequencing. Similarly, combinations including Jak2^V617F, tet2, or asxl1 mutations lead to single color expansion in kidney marrow cells in 30% of injected zebrafish, with the occasional presence of a blast-like population of cells in the marrow and spleen. We have successfully modeled early stages of clonal hematopoietic expansion with myeloproliferation in the presence of Jak2^V617F and asxl1 deletion using the unique color barcoding system in zebrafish.