Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia

Eleonora Khabirova,Matthew D Young,Muzlifah Haniffa,Sarah A Teichmann,Elena Prigmore,Laura Jardine,Owen Williams,Justin Engelbert,Simone Webb,Simon Bomken,Olaf Heidenreich,Tim Coorens ,Sarah Inglott,Jack Bartram,Karin Straathof,Alice Piapi,Taryn D Treger,Tarryn Porter,Grace Collord,Sam Behjati

doi:10.1038/s41591-022-01720-7

Abstract

KMT2A-rearranged infant ALL is an aggressive childhood leukemia with poor prognosis. Here, we investigated the developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia (B-ALL) using bulk messenger RNA (mRNA) meta-analysis and examination of single lymphoblast transcriptomes against a developing bone marrow reference. KMT2A-rearranged infant B-ALL was uniquely dominated by an early lymphocyte precursor (ELP) state, whereas less adverse NUTM1-rearranged infant ALL demonstrated signals of later developing B cells, in line with most other childhood B-ALLs. We compared infant lymphoblasts with ELP cells and revealed that the cancer harbored hybrid myeloid–lymphoid features, including nonphysiological antigen combinations potentially targetable to achieve cancer specificity. We validated surface coexpression of exemplar combinations by flow cytometry. Through analysis of shared mutations in separate leukemias from a child with infant KMT2A-rearranged B-ALL relapsing as AML, we established that KMT2A rearrangement occurred in very early development, before hematopoietic specification, emphasizing that cell of origin cannot be inferred from the transcriptional state.

Highlights

Leukemias are primarily classified by their morphological appearance or immunophenotype, as assessed by flow cytometric analyses of key hematopoietic markers and cytogenetic changes
We adopted the annotation of normal cell types directly from the fetal bone marrow data analysis[9] and supplemented the hematopoietic reference with a control fetal cell type that should not be present in human leukemia samples, Schwann cell precursors (SCPs) derived from human fetal adrenal glands[16]
To further examine the early lymphocyte precursor (ELP) signal in KMT2A-driven infant B-cell acute lymphoblastic leukemia (B-ALL), we examined the ratio of the ELP signal over later stages of B-cell development in each leukemia subtype (Fig. 1c)

Summary

Results

Cell signal analysis of 1,665 leukemia transcriptomes. The starting point of our investigation was a meta-analysis of 1,665 bulk. To validate and further explore this proposition, we performed single-cell RNA-sequencing (scRNA-seq) analysis (10x Genomics) of diagnostic specimens from six infants with KMT2A-rearranged infant B-ALL, including a relapse presentation (case 3) and additional day 8 specimens from responding (case 1) and nonresponding (case 2) patients We compared these to four other leukemias: NUTM1-rearranged infant B-ALL (n = 1), KMT2A-rearranged infant AML (n = 1), megakaryoblastic neonatal AML (n = 1) and childhood ETV6-RUNX1 B-ALL (a common subtype of standard-risk childhood B-ALL; n = 1) (Supplementary Table 3). In the aforementioned subtype of infant B-ALL with a favorable prognosis, NUTM1-rearranged infant B-ALL, single-cell analysis confirmed the shift toward pre-B-cell states and away from ELPs. To further explore the differences between KMT2A- and NUTM1-driven infant B-ALL, we performed independent differential gene expression a.

52 BCR 4 KKMMT2A1 34 -BABL1T2

C PromMOP

Discussion

Methods

Code availability