Dnmt3a Mutant Hematopoietic Stem Cells Produce Hyperactive T Cells with Increased Alloimmune and Anti-Leukemic Activity
Authors: Wallace LaShanale , Engelken Mark , Myers Jacquelyn A. , Harper John , Clark Brandi , Cullins David , Zoine Jaquelyn T. , Shanmugam Raghuvaran , Schattgen Stefan , Velasquez M. Paulina , Sheppard Heather , Crawford Jeremy Chase , Thomas Paul G. , Obeng Esther A. 
Published: December 2024

Clonal hematopoiesis (CH) is the expansion of a hematopoietic stem cell (HSC) clone with an acquired leukemogenic mutation in individuals without any evident hematological abnormalities. CH is an age-related phenomenon associated with an increased risk of death from cardiovascular disease or hematologic malignancies. Epigenetic regulators account for ~80% of the genes mutated in CH, with DNA Methyltransferase 3a (DNMT3A) mutation being the most common. Recent clinical studies have found that, after allogenic stem cell transplantation, CH clones are highly transmitted from donor to recipient. DNMT3A mutations remain the most prevalent and patients with donor-derived CH have an increased risk of acute (Oran et. al. Leukemia 2021) or chronic (Frick et. al. JCO 2018) graft vs host disease (GVHD). A larger study found that recipients of DNMT3A-mutant donor-derived CH had a decreased leukemia relapse risk (Gibson et. al. JCO 2022). These results suggest that DNMT3A-mutant CHIP recipients have hyperactive T cells that may play a role in initiating GVHD or graft vs leukemia effect, but it has not been proven.
To examine whether mutations in DNMT3A affect T cell function leading to GVHD and anti-leukemic effects, we used a murine Dnmt3aR878H/+ model harboring the clinically equivalent point mutation most seen in hematological malignancies (R882H, Loberg et. al. Leukemia 2019). We found that up to 80% of Dnmt3aR878H/+ mice developed a severe ulcerative dermatitis characterized by a hyperplastic epidermis with increased lymphocytic infiltration (p&lt;.02). Further profiling of T cells isolated from the skin of wild type (WT) and mutant mice revealed that Dnmt3aR878H/+ mice had an increase in CD4 effector memory T cells (p&lt;.04). In comparison to the skin, the frequency of T cells in the spleen and thymus was similar between WT and Dnmt3aR878H/+ mice. However, the percentage of activated T cells increased significantly in mutant mice (p&lt;.01). Splenic T cells from Dnmt3aR878H/+ had decreased naïve CD4 and CD8 cells with increased frequency in CD4+ effector memory T cells (p&lt;.001) and CD8+ central memory T cells (p&lt;.02).
To evaluate whether the activation/inflammatory phenotype was due to Dnmt3a-dependent changes in DNA methylation and gene expression, methylation and transcriptome profiling were performed on CD4+ andCD8+ T cells isolated from WT and Dnmt3aR878H/+ mice. Methylation analysis revealed that over 80% of differentially methylated probes (DMPs) were hypomethylated in Dnmt3aR878H/+ mutant T cells, with 3X more DMPs in CD4+ T cells compared to CD8+ T cells. Although there were more upregulated than downregulated genes in CD4+ and CD8+ T cells isolated from Dnmt3aR878H/+ mice, we found 3X more upregulated genes in Dnmt3aR878H/+ CD4+ T cells. Integration of methylation and gene expression analyses showed that 61% of genes were both upregulated and hypomethylated in CD4+ Dnmt3aR878H/+ T cells. Pathways enriched in Dnmt3aR878H/+ CD4+ T cells included interferon g and IL-2 signaling. Single cell RNAseq analysis of WT and Dnmt3aR878H/+ splenic T cells and found that Dnmt3aR878H/+ cells were less abundant in naïve cell clusters, more abundant in effector and memory clusters, and displayed differentially expressed genes involved in T cell activation and effector function.
To functionally assess T cells isolated from Dnmt3aR878H/+ mice, we adoptively transferred naïve CD4+ or CD8+ T cells into NSG mice. We found that mice that received Dnmt3aR878H/+ CD4+ T cells showed a significant increase in activated T cell expansion and developed more severe skin, liver, lung, and gut GVHD compared to WT CD4+ T cell recipients. Similar but less dramatic differences were observed in CD8+ adoptive T cell transfer experiments. In parallel, we evaluated the response of Dnmt3aR878H/+ T cells when challenged with a murine leukemia cell line and found Dnmt3aR878H/+ T cells had increased killing when compared to WT cells in vitro (p&lt;.04). In vivo analysis showed that Dnmt3aR878H/+ mice had a lower leukemic burden (p&lt;0.002) and improved survival compared to WT mice (55 vs 22 days). Single cell RNAseq was notable for increased expansion of cytotoxic CD8+ and effector CD4+ T cells in spleens of Dnmt3aR878H/+ tumor challenged mice. In conclusion, we demonstrate that Dnmt3a-mutant HSCs can give rise to persistently activated T cells that may play both pathogenic and protective roles in allogeneic transplant recipients.