Single-Cell Multiomics Reveals Increased Plasticity, Resistant Populations and Stem-Cell-like Blasts in KMT2A-Rearranged Leukemia

Abstract

KMT2A-rearranged (KMT2A-r) infant ALL is a devastating malignancy with a dismal outcome, and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to single cell multi-omics analyses. We uncovered the following critical new insights: leukemia cells from patients younger than 6 months have significantly increased lineage plasticity. Steroid response pathways are downregulated in the most immature blasts from younger patients. We identify a hematopoietic stem and progenitor-like (HSPC-like) population in the blood of younger patients that contains leukemic blasts and form an immunosuppressive signaling circuit with cytotoxic lymphocytes. These observations offer a compelling explanation for the ability of leukemias in young patients to evade chemotherapy and immune mediated control. Our analysis also revealed pre-existing lymphomyeloid primed progenitors and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in two patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank AML. These findings provide critical insights into KMT2A-r ALL and have clinical implications for molecularly targeted and immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single cell multi-omics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome. Disclosures Bernt: Merck: Other: Spouse is an employee of Merck.; Syndax: Research Funding.

Poor treatment responses were related to poor outcomes in pediatric B cell acute lymphoblastic leukemia with KMT2A rearrangements

“…Deregulation of these genes initiates the development of leukemia through inhibition of proper hematopoietic development [13,14]. The KMT2Ar fusion genes with their breakpoints code for their related proteins and are regarded as poor factors for both B-ALL and acute myeloid leukemia (AML) [13][14][15].…”

Neonatal congenital leukemia caused by several missense mutations and AFF1‑KMT2A fusion: A case report

“…ALL cases, 70-80% of ALL in infants, 15-20% of childhood AML and 50% of infant AML cases. MLL-r leukemia has long been suspected to originate from an uncommitted precursor (14). MLL-r results in the fusion of the N-terminus of MLL with the C-terminus of a partner.…”

Single-cell multiomics sequencing reveals the reprogramming defects in embryos generated by round spermatid injection

“…So, we used methylation level of GCH sites (1× depth) to define open chromatin regions (NDRs). Because of the sparse nature of single-cell genomic data, we aggregated all cells at the same stage from ICSI/ROSI-derived embryos to define NDRs as previously described ( 13 , 23 , 68 ). As reported in our previous study ( 14 ), we used a sliding window with 100-bp length at 20-bp step size to calculate the significance of difference (chi-square test, P ≤ 10 −15 ) of GCH methylation level compared to the whole genome level.…”

“…For differential methylation analysis between ROSI and ICSI embryos, we aggregated all single-cell data at each stage ( 13 , 23 , 68 ). That meant that we defined the DNA methylation level of each WCG site by the mean level of that in all single cells derived by ICSI or ROSI at the same stage, which could circumvent the variance of genomic coverage among cells to a certain extent.…”