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ACUTE MYELOID LEUKEMIA

Characterization of leukemia progression in the Cbfb-MYH11 knockin mice by single cell RNA sequencing

Leukemia volume 37, pages 1549–1553 (2023)Cite this article

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A recurrent inversion of chromosome 16 fuses the genes CBFB and MYH11 and the resultant CBFβ-SMMHC fusion protein acts as a driver of the M4Eo subtype of acute myeloid leukemia (AML). This study utilized single cell RNA-sequencing (scRNA-seq) to assess gene expression changes during the disease progression from normal to pre-leukemic to overt leukemia in the conditional Cbfb-MYH11 knockin mouse model. The study investigated dynamic shifts in cell types as disease progresses, and gene expression differences between normal and diseased cells. The study identified a novel cell population in the pre-leukemic state with expression of genes involved in immune activation. Overall, this study discovered hematopoietic cells first affected by the expression of CBFβ-SMMHC and identified unique signature genes for the pre-leukemic cells that separate them from the normal hematopoietic cellular milieu.

A subset of acute myeloid leukemias (AMLs) harbor an inversion of chromosome 16, which leads to the expression of the fusion gene CBFB-MYH11 [1, 2]. The in-frame fusion yields a chimeric protein CBFβ-SMMHC that has been shown to drive leukemogenesis in mouse knockin models [3, 4], but there is still much unknown about the mechanisms leading to the onset of leukemia and the activity of the fusion protein itself. The conditional Cbfb-MYH11 knockin mouse model provides the opportunity to study leukemogenic process from the expression of the fusion gene to end-stage disease [4]. We hypothesized that CBFβ-SMMHC induces the formation of a “pre-leukemic” cell population with a distinctive gene expression profile which are precursors of leukemic cells. This scRNA-seq study examined wild-type, pre-leukemic, and leukemic hematopoietic stem and progenitor cells (HSPCs) in the conditional Cbfb-MYH11 knockin mouse model. The results provide insight into the bone marrow stem and progenitor cell types first affected by the presence of the fusion protein and defines cell subtypes associated with disease onset and progression.

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Fig. 1: Comparison of single cell transcriptome of bone marrow Kit+ progenitor/stem cells in wild-type mice and in conditional Cbfb-MYH11 knockin mice at pre-leukemic and leukemic stages.
Fig. 2: Identification of leukemia precursor cells and their candidate markers in the pre-leukemia mice.

Data availability

The datasets generated during and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219043.

References

  1. Liu P, Tarle SA, Hajra A, Claxton DF, Marlton P, Freedman M, et al. Fusion between transcription factor CBF beta/PEBP2 beta and a myosin heavy chain in acute myeloid leukemia. Science. 1993;261:1041–4.

    Article  CAS  PubMed  Google Scholar 

  2. Liu PP, Wijmenga C, Hajra A, Blake TB, Kelley CA, Adelstein RS, et al. Identification of the chimeric protein product of the CBFB-MYH11 fusion gene in inv(16) leukemia cells. Genes Chromosomes Cancer. 1996;16:77–87.

    Article  PubMed  Google Scholar 

  3. Castilla LH, Garrett L, Adya N, Orlic D, Dutra A, Anderson S, et al. The fusion gene Cbfb-MYH11 blocks myeloid differentiation and predisposes mice to acute myelomonocytic leukaemia. Nat Genet. 1999;23:144–6.

    Article  CAS  PubMed  Google Scholar 

  4. Kuo YH, Landrette SF, Heilman SA, Perrat PN, Garrett L, Liu PP, et al. Cbf beta-SMMHC induces distinct abnormal myeloid progenitors able to develop acute myeloid leukemia. Cancer Cell. 2006;9:57–68.

    Article  CAS  PubMed  Google Scholar 

  5. Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017;8:14049.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, et al. Comprehensive integration of single-cell data. Cell. 2019;177:1888–1902.e1821.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, et al. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun. 2019;10:1903.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Becht E, McInnes L, Healy J, Dutertre CA, Kwok IWH, Ng LG, et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat Biotechnol. 2018;37:38–44.

  9. Seita J, Sahoo D, Rossi DJ, Bhattacharya D, Serwold T, Inlay MA, et al. Gene Expression Commons: an open platform for absolute gene expression profiling. PLoS ONE. 2012;7:e40321.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Nestorowa S, Hamey FK, Pijuan Sala B, Diamanti E, Shepherd M, Laurenti E, et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood. 2016;128:e20–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, et al. Mapping the mouse cell atlas by microwell-seq. Cell. 2018;172:1091–1107.e1017.

    Article  CAS  PubMed  Google Scholar 

  12. Zhen T, Cao Y, Ren G, Zhao L, Hyde RK, Lopez G, et al. RUNX1 and CBFbeta-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development. Blood. 2020;136:2373–85.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Hyde RK, Liu PP. RUNX1 repression-independent mechanisms of leukemogenesis by fusion genes CBFB-MYH11 and AML1-ETO (RUNX1-RUNX1T1). J Cell Biochem. 2010;110:1039–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Abdelbaset-Ismail A, Borkowska-Rzeszotek S, Kubis E, Bujko K, Brzezniakiewicz-Janus K, Bolkun L, et al. Activation of the complement cascade enhances motility of leukemic cells by downregulating expression of HO-1. Leukemia. 2017;31:446–58.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The work was supported by the Intramural Research Programs of the National Human Genome Research Institute, National Institute on Deafness and Other Communication Disorders, and Natioal Cancer Institute, NIH. The authors would like to thank Zhi Liu and Jim Mullikin for preliminary STREAM testing, Erika Kwon, Erica Bresciani and Elisabeth Heuston for insightful discussion, as well as Luigi Alvarado (now at 10X Genomics) and the LaRochelle lab at NHLBI (NIH) for critical pilot drop-seq experiments that led to this study. This work used the computational resources of the NIH highperformance computing Biowulf cluster (https://hpc.nih.gov).

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Author notes

  1. Michael Kelly

    Present address: Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Center for Cancer Research, Natioal Cancer Institute, NIH, Bethesda, MD, USA

Authors and Affiliations

  1. Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA

    Jamie L. Diemer, Kai Yu, Tao Zhen, Guadalupe Lopez & Paul Liu

  2. Laboratory of Cochlear Development, Division of Intramural Research, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA

    Michael Kelly

  3. Flow Cytometry Core, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA

    Stacie Anderson

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  1. Jamie L. Diemer
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Contributions

JD performed experiments, analyzed data, and wrote the manuscript, KY analyzed data and prepared several figures for the manuscript, MK assisted in sequencing, read mapping, and downsampling for sequencing depth normalization, TZ and GL prepared the conditional knockin mice used, and SA performed FACS isolation of the cells of interest.

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Correspondence to Paul Liu.

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Diemer, J.L., Yu, K., Kelly, M. et al. Characterization of leukemia progression in the Cbfb-MYH11 knockin mice by single cell RNA sequencing. Leukemia 37, 1549–1553 (2023). https://doi.org/10.1038/s41375-023-01926-9

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