3211 – MULTIOMIC ANALYSIS OF BONE MARROW HEMATOPOIETIC STEM/PROGENITOR CELLS REVEALS A POTENTIAL EARLY STAGE OF MALIGNANCY OF CLONAL HEMATOPOIESIS OF INDETERMINATE POTENTIAL

Abstract

Clonal hematopoiesis of indeterminate potential (CHIP) increases the risk to develop hematological cancers such as acute myeloid leukemia (AML) tenfold. Since AML has been shown to originate from a hematopoietic stem/progenitor cell (HSPC) we compared the transcriptional landscape of bone marrow HSPCs from a healthy donor and a CHIP carrier (mutations in DNMT3A, 1.1% VAF and TET2, 5.3% VAF) by performing single cell RNA and ATAC sequencing. Cell frequency analysis of HSCP subpopulations, defined by analysis of conserved genes in clusters after dimensional reduction, showed that the proportion of HSC was twofold higher in the CHIP donor whereas the lymphocyte progenitor and pre-B cells compartment was fourfold lower, indicating an overall myeloid bias in the CHIP donor. Gene Ontology analysis of differentially expressed genes in the HSC compartment showed an upregulation of genes involved in metabolic processes in CHIP HSCs, among which genes that are associated with the onset of AML such as MEIS1 and PBX1. Furthermore, the expression levels of genes that are involved in niche retention, such as CD44 and VLA-4 were significantly higher in CHIP HSCs, suggesting alterations in the architecture of CHIP bone marrow. In addition to differences in gene expression, chromatin accessibility analysis showed unique genomic peaks in the CHIP HSC. Analysis of these sequences for binding motifs of transcription factors showed an overabundance of GATA, CEBP and RUNX1 motifs, all believed to play major roles in the onset of AML. The transcriptional landscapes of HSPC from healthy and CHIP donors show distinct differences, indicating that even the absence of signs of hematological disease, changes associated with a possible onset of malignancy can already be observed and provide possible targets for early intervention. Clonal hematopoiesis of indeterminate potential (CHIP) increases the risk to develop hematological cancers such as acute myeloid leukemia (AML) tenfold. Since AML has been shown to originate from a hematopoietic stem/progenitor cell (HSPC) we compared the transcriptional landscape of bone marrow HSPCs from a healthy donor and a CHIP carrier (mutations in DNMT3A, 1.1% VAF and TET2, 5.3% VAF) by performing single cell RNA and ATAC sequencing. Cell frequency analysis of HSCP subpopulations, defined by analysis of conserved genes in clusters after dimensional reduction, showed that the proportion of HSC was twofold higher in the CHIP donor whereas the lymphocyte progenitor and pre-B cells compartment was fourfold lower, indicating an overall myeloid bias in the CHIP donor. Gene Ontology analysis of differentially expressed genes in the HSC compartment showed an upregulation of genes involved in metabolic processes in CHIP HSCs, among which genes that are associated with the onset of AML such as MEIS1 and PBX1. Furthermore, the expression levels of genes that are involved in niche retention, such as CD44 and VLA-4 were significantly higher in CHIP HSCs, suggesting alterations in the architecture of CHIP bone marrow. In addition to differences in gene expression, chromatin accessibility analysis showed unique genomic peaks in the CHIP HSC. Analysis of these sequences for binding motifs of transcription factors showed an overabundance of GATA, CEBP and RUNX1 motifs, all believed to play major roles in the onset of AML. The transcriptional landscapes of HSPC from healthy and CHIP donors show distinct differences, indicating that even the absence of signs of hematological disease, changes associated with a possible onset of malignancy can already be observed and provide possible targets for early intervention.