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 mice was polyclonal (Figure 1B). A total of > 500 barcoded clones per mouse were detected and in both VF;CARLIN and WT;CARLIN mice, but ~5 individual barcodes accounted for 25% of the cells in all progenitor subsets analyzed (Figure 1B). Overall, clonal composition was similar between WT;CARLIN and VF;CARLIN mice, indicating that clonal selection was not more prominent in JAK2-mutant mice. Importantly, in the offspring of HSCs that accounted for 25% of the cells, we did not observe preferential presence of some barcodes in MkP versus EryP and other barcodes in EryP versus MkP, arguing against the model predicting that erythrocytosis and thrombocytosis originated in different subsets of biased HSCs.

To investigate the question of whether sensitivity or resistance to IFNα could be also due to heterogeneity in HSC subpopulations, we transplanted BM cells from these barcoded VF;CARLIN mice together with an excess of WT competitor cells into irradiated WT recipient mice, and treated them with IFNα or vehicle for 16 weeks. IFNα normalized hemoglobin (122 g/L) compared to vehicle (177 g/L) and reduced VF;CARLIN chimerism in granulocytes from 85% to 44%. BM cells were harvested and the clonal composition is currently being analyzed by NGS in order to identify IFNα resistant and sensitive subclones.

Our barcoding analyses of individual HSCs showed that, during recovery after BM transplantations, a few VF clones dominated, whereas induction of VF expression in situ without transplantation resulted in a polyclonal disease that showed a similar number of HSCs actively contributing to hematopoiesis as in a control experiment with WT mice. The lack of substantial preference in the clonal contribution of individual HSCs to erythropoiesis versus megakaryopoiesis in VF mice suggests that PV and ET are not caused by acquiring JAK2-V617F in HSCs with a pre-existing lineage bias.