Clonal hematopoiesis of indeterminate potential (CHIP) was recently identified as a major risk factor for development of both hematologic malignancies and atherosclerotic cardiovascular disease in humans. The most commonly mutated gene in CHIP, DNMT3A, is a de novo DNA methyltransferase. The second most commonly mutated gene is TET2, an enzyme which can lead to loss of DNA methylation, and thus is thought to have an opposing biochemical function to DNMT3A. Surprisingly, mutations in both genes lead to convergent phenotypes, such as clonal expansion of mutated stem cells, increased risk of malignant transformation, and increased risk of coronary heart disease. A molecular mechanism linking CHIP and cardiovascular disease has been explored only for loss of function mutations in the Tet2 gene (Jaiswal et al., NEJM 2017; Fuster et al., Science 2017). Here we tested the ability of null mutations in Dnmt3a to contribute to atherosclerosis in hypercholesteremic mice. We further explored the biological basis for this association through gene expression analyses and single-cell RNA sequencing. To model cardiovascular disease associated with DNMT3A-mutated CHIP, atherosclerosis-prone Ldlr-/- mice received bone marrow from Dnmt3a+/+ mice (WT), or from Dnmt3a-/- mice (KO) and WT mice in a 1:9 ratio to mimic a typical variant allele fraction observed in human CHIP. Mice then consumed a high-fat, high-cholesterol diet (HFD), and underwent assessment of atherosclerosis. At 9 weeks, mice that had received 10% Dnmt3a-/- bone marrow displayed an average lesion size that was 40% larger compared to mice receiving control marrow only (p=0.04). The increase in lesion size resembles that we previously observed in mice receiving Tet2-/- marrow (Jaiswal et al., NEJM 2017). De novo DNA methylation by Dnmt3a can alter gene expression. To elucidate how such changes may accelerate atherosclerosis, we first performed transcriptome analysis using bulk RNA sequencing of cholesterol-stimulated bone marrow derived macrophages (BMDM) from either WT or KO mice. BMDMs lacking Dnmt3a showed significantly augmented expression of genes belonging to the CXC chemokine cluster, Cxcl1, Cxcl2 and Cxcl3, as well as increases in mRNAs encoding canonical pro-inflammatory cytokines Il1b and Il6. These changes mirrored those we saw in macrophages lacking Tet2 (Jaiswal et al., NEJM 2017). We next asked how transcriptomic changes observed using the ex vivo BMDM system translated into the in vivo lesional environment. Single-cell RNA sequencing (10X Genomics) was performed on atherosclerotic aortae from mice that had been competitively transplanted with WT, Dnmt3a-/-, or Tet2-/- marrow at a 1:9 ratio. Clustering demonstrated broad changes in lesional immune cell composition in mice harboring CHIP. Lack of either Tet2 or Dnmt3a substantially expanded the myeloid compartment, containing cells that drive atherogenesis. A reciprocal reduction mainly affecting T lymphocyte populations accompanied this expansion. Within the myeloid cell compartment, Dnmt3a-/- or Tet2-/- donor cells, but not WT donor cells, gave rise to a distinct lesional macrophage population. These cells expressed markers associated with tissue-resident macrophages (Mrc1, Lyve1, F13a1), but also highly expressed several inflammatory mediators (Cxcl1, Pf4, Ccl2, Ccl7, Ccl8), and a characteristic set of transcription factors (Jun, Fos, Egr1). Overall, the present study reveals broad changes to the lesional cellular composition and transcriptome induced by the most common CHIP mutations, and provides novel insight into the mechanisms by which CHIP accelerates atherosclerosis. Despite exerting opposite catalytic functions, lack of Dnmt3a or of Tet2 function lead to a myriad of similar downstream transcriptomic and cellular changes. These results indicate that mutations in Dnmt3a and Tet2 accelerate atherosclerosis through convergent mechanisms. Disclosures No relevant conflicts of interest to declare.

Introduction: Clonal hematopoiesis of indeterminate potential (CHIP) may occur when a hematopoietic stem cell (HSC) acquires a fitness-increasing mutation resulting in its clonal expansion. A diverse set of driver genes, such as regulators of DNA methylation, splicing, and chromatin remodeling, have been associated with CHIP, but it remains largely unknown why HSCs bearing these mutations are positively selected. It has been challenging to identify the genetic and environmental factors mediating clonal expansion in humans, partially due to a lack of large cohorts with longitudinal blood sampling of participants. To circumvent this limitation, we developed a method to infer clonal expansion rate from single timepoint data called PACER (passenger-approximated clonal expansion rate). Methods: PACER is based on the principle that genomic passenger mutations can be used to infer the birth date of pre-malignant clones because these mutations accumulate fairly linearly over time. Thus, an individual with CHIP with a greater number of passenger mutations in the mutant clone is expected to have acquired the clone at a later age than someone with fewer passenger mutations. For two individuals of the same age and with clones of the same size, we expect the clone with more passengers to be more fit, as it expanded to the same size in less time. Typically, one would need to isolate single-cell colonies derived from HSCs in order to calculate the total passenger mutation burden. However, we hypothesized that this measure could also be approximated from whole genome sequencing of blood cell DNA, such as that used in large biobank projects. The expansion rate (PACER) is then estimated by adjusting the total passenger count for age and variant allele fraction in each individual. The ability of passengers to predict future clonal expansion was validated using longitudinal blood samples from 51 CHIP carriers in the Women's Health Initiative taken ~10 years apart (Figure 1). It also accurately predicted the known fitness effects due to different driver mutations in 5,551 CHIP carriers from the Trans-Omics for Precision Medicine (TOPMed) program (Figure 2). Results: Having validated the approach, we next hypothesized that we could identify germline variants influencing PACER, thus revealing genes and pathways mediating clonal expansion. The lead hit in a genome-wide association study (GWAS) of PACER was a common single nucleotide polymorphism (SNP) in the TCL1A promoter that was associated with slower clonal expansion in CHIP overall (Figure 3). TCL1A is an oncogene that is activated via translocation in T-cell prolymphocytic leukemia, but has no known role in CHIP or myeloid malignancies. A gene-level analysis indicated that the TCL1A SNP was associated with slower growth of clones bearing TET2 mutations, but had no effect on DNMT3A-mutant clone growth. We further found that those carrying two copies of the protective SNP had 40-80% reduced odds of having clones with driver mutations in TET2, ASXL1, SF3B1, SRSF2, and JAK2, but not DNMT3A. A concomitant decrease in incident myeloid malignancies was also seen in carriers of this protective SNP. Next, we interrogated how the protective SNP influenced TCL1A activity in HSCs. Normal human HSCs lacked open chromatin at the TCL1A promoter and TCL1A expression, but inducing frameshift mutations in TET2 via CRISPR editing led to accessibility of the promoter and gene/protein expression in HSCs (Figure 4). This effect was abrogated in HSCs from donors of the protective TCL1A SNP in a dose-dependent manner. Finally, we found that HSCs from donors homozygous for the protective SNP had markedly less expansion of phenotypic stem and progenitor cells in vitro after the introduction of TET2 mutations than TET2-edited HSCs from donors with two copies of the reference allele. Conclusions: In summary, we developed a novel method to infer the expansion rate of pre-malignant clones and performed the first ever GWAS for this trait. Our results indicate that the fitness advantage of several common driver genes in CHIP and hematological cancers is mediated through TCL1A activation, which may be a therapeutic target to treat these conditions. PACER is an approach that can be widely adopted to uncover genetic and environmental determinants of pre-malignant clonal expansion in blood and other tissues. Figure 1 Figure 1. Disclosures Desai: Bristol Myers Squibb: Consultancy; Kura Oncology: Consultancy; Agios: Consultancy; Astex: Research Funding; Takeda: Consultancy; Janssen R&D: Research Funding. Natarajan: Blackstone Life Sciences: Consultancy; Boston Scientific: Research Funding; Novartis: Consultancy, Research Funding; AstraZeneca: Consultancy, Research Funding; Apple: Consultancy, Research Funding; Amgen: Research Funding; Genentech: Consultancy; Foresite Labs: Consultancy. Jaiswal: Novartis: Consultancy, Honoraria; AVRO Bio: Consultancy, Honoraria; Genentech: Consultancy, Honoraria; Foresite Labs: Consultancy; Caylo: Current holder of stock options in a privately-held company.