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Clonal Hematopoiesis Mutation Study in Blood Cells Points to Promotion of Abnormal Blood Cells

NEW YORK — Mutations affecting a DNA methyltransferase that commonly arise in blood stem cells may lead to disease through changes in methylation and gene expression, a new study has found.

Mutations at the DNMT3A R882 hotspot are common in clonal hematopoiesis (CH), an aging-related condition in which blood stem cells undergo clonal expansion. CH is linked to an increased risk of myeloid malignancies and is suspected to represent an early stage of neoplastic development. DNMT3A R882 hotspot mutations are also an early change seen in acute myeloid leukemia.

In a new paper appearing in Nature Genetics on Thursday, researchers from the New York Genome Center sought to characterize the effects of DNMT3A R882 hotspot mutations in CH and thus the effects of somatic driver mutations in clonal mosaicism more broadly.

"These findings help us understand how these mutated cells outgrow normal cells and pave the way for possible future interventions targeting these cells to prevent cancers and other clonal outgrowth-related conditions," senior author Dan Landau, a hematologist and medical oncologist at Weill Cornell Medicine and a core faculty member of the New York Genome Center, said in a statement.

But studying CH can be challenging, as individuals with the condition have normal blood production and typically do not undergo bone marrow biopsies. To skirt that issue, the researchers instead examined samples obtained from a cohort of 136 multiple myeloma patients with CH but whose disease was in remission. For their analyses, the researchers in particular focused on samples from four patients who harbored DNMT3A R882 hotspot mutations and had a high enough variant allele frequency to permit single-cell RNA sequencing analysis.

They isolated more than 27,000 CD34+ cells for "genotyping of transcriptomes" (GoT) analysis, an approach that combines genotyping with high-throughput single-cell RNA sequencing. In all, they generated genotyping data for 6,430 of these cells while also capturing transcriptomic and methylome data.

By mapping this data to the hematopoietic differentiation tree, the researchers found that cells with DNMT3A R882 hotspot mutations exhibited a myeloid over lymphoid bias, as has been suggested by previous mouse studies. Additionally, mutated immature myeloid progenitors showed a megakaryocytic-erythroid lineage bias, also as previous mouse studies have found.

As DNMT3A encodes a DNA methyltransferase, the researchers in particular examined the effects of hotspot mutations on methylation patterns and gene expression. DNMT3A R882 hotspot mutations led to hypomethylation at polycomb repressive complex 2 (PRC2) targets as well as at a certain CpG flanking motif. This motif was enriched in the binding motifs of hematopoietic transcription factors like MYC/MAX, HIF1A/ARNT, and USF1/2. Further, hypomethylation at sites like MYC/MAX led to increased expression of their transcriptional targets.

This could provide a mechanism tying DNMT3A R882 hotspot mutations to atypical transcriptional phenotypes, the researchers said.

But as the researchers' analyses relied on samples from multiple myeloma patients, they also confirmed their findings in a mouse model and in a bone marrow sample from a patient with DNMT3A-mutated CH but no hematological disorder.

"Our hope is that by uncovering molecular signatures like these we'll be able to target these clonal outgrowths and prevent cancer development in people who are still healthy," study co-first author Anna Nam from the Weill Cornell Medicine said in a statement.

The researchers added that they plan other studies focused on other clonal mutations and that they are working to speed and scale up their multiomic approach.