Mesenchymal Stromal Cell Senescence Induced by Dnmt3a-Mutant Haematopoietic Cells is a Targetable Mechanism Driving Clonal Haematopoiesis and Initiation of Leukemia

Clonal haematopoiesis (CH) is a benign age-related condition occurring due to somatic genetic variation in haematopoietic stem and progenitor cells (HSPCs). In some individuals, CH is a precursor condition for haematologic malignancy, but the mechanisms driving progression of CH to malignancy are incompletely understood. Given that malignant cells reprogram their microenvironment to create a self-reinforcing niche, we hypothesized that HSPCs carrying CH mutations have microenvironment-remodelling properties that promote their clonal advantage and contribute to malignant progression. By single-cell RNA-seq profiling of the non-haematopoietic bone marrow microenvironment in a mouse model of DNMT3A-mutant CH, we identified strong enrichment of a cellular senescence signature in bone marrow mesenchymal stromal cells (MSCs). We find that Dnmt3a-mutant HSPCs induce markers of senescence including SA-b-gal, BCL-2, BCL-xL, Cdkn1a (p21), and Cdkn2a (p16) selectively in MSCs using ex vivo and in vivo assays. This senescence induction phenotype is cell contact-independent and reproduced by IL-6 and TNFa, both of which are soluble factors produced by Dnmt3a-mutant HSPCs. Removal of senescent MSCs using Navitoclax reduced the selective growth advantage of Dnmt3a-mutant hematopoietic cells and reduced myeloproliferation in a Dnmt3a;Npm1-mutant model of myeloid neoplasms. Together, our data demonstrate that Dnmt3a-mutant HSPCs produce specific factors that reprogram their microenvironment through senescence induction, and that this process creates a self-reinforcing niche favouring their growth advantage and progression to malignancy. Overall design: Hematopoietic and bone marrow microenvironment cell populations were enriched using cell sorting 16 weeks post transplantation from 4 Dnmt3a- mutant and 4 Fgd5- control mice transplanted into middle aged CD45.1 recipient mice for single cell RNA-seq.