Cellular Barcoding of JAK2-V617F Hematopoietic Stem Cells Reveals No Substantial Preferences in the Contribution of Individual Stem Cell Clones to Erythroid Versus Megakaryocytic Lineages

JAK2-V617F is the most frequent driver gene mutation in patients with myeloproliferative neoplasms (MPN) but the phenotypic manifestation is heterogeneous with some patients presenting as polycythemia vera (PV), whereas others with essential thrombocythemia (ET) or myelofibrosis (MF). JAK2-V617F is acquired in a hematopoietic stem cell (HSC) and leads to clonal expansion of HSCs and progenitor cells that gain dominance over unmutated hematopoiesis. We tested the hypothesis that the preferential expansion of megakaryopoiesis in ET versus erythropoiesis in PV could be due to the acquisition of JAK2-V617F in different subsets of HSCs with inherent bias towards megakaryopoiesis or erythropoiesis. In addition, we addressed the question of whether sensitivity or resistance to interferon-α (IFNα), currently the only treatment that can induce a deep molecular remission in some MPN patients, could be also due to heterogeneity in HSC subpopulations. We used a mouse model of JAK2-V617F driven MPN in combination with molecular barcoding that allowed us to monitor expansion and lineage contribution of individual HSC subclones. First, we genetically barcoded HSCs from our tamoxifen-inducible SclCre; JAK2-V617F ( VF) mice with a lentiviral vector, and transplanted 2'000 HSCs into lethally irradiated recipient mice. After 12 weeks we sequenced the barcodes in bone marrow (BM) progenitors by next generation sequencing (NGS). We observed a strong selection of 1-2 HSCs clones per recipient mouse, which alone contributed to > 80% of all the myeloid cells. Since cytokine storm after irradiation and aplasia during the reconstitution with lentivirally transduced BM may favor such oligo-clonal dominance observed in this experiment, we characterized the clonal composition of JAK2-mutant HSCs in non-transplanted MPN mice. To this end, we crossed a CRISPR-based genetic barcoding mouse line ( CARLIN) (Bowling, S. et al, Cell 2020) with our VF mice to obtain VF;CARLIN mice. Cas9-mediated barcoding in VF;CARLIN or in CARLIN mice with wildtype Jak2 (WT;CARLIN) was induced with doxycycline and immediately followed by the activation of the JAK2-V617F by tamoxifen (Figure 1A). After 12 weeks, when the mice developed full PV phenotype (hemoglobin 195 g/L; platelets 4.3x10 12 /L and neutrophils 10.5x10 9/L), we performed scRNAseq on lin- cKit+ BM cells using the 10X-platform to retrieve the cellular barcodes and transcriptomic profiles. MPN hematopoiesis in these non-transplanted VF;CARLIN m