Abstract

Chronic myeloid leukaemia (CML) arises after transformation of a haemopoietic stem cell (HSC) by the protein-tyrosine kinase BCR–ABL. Direct inhibition of BCR–ABL kinase has revolutionized disease management, but fails to eradicate leukaemic stem cells (LSCs), which maintain CML. LSCs are independent of BCR–ABL for survival, providing a rationale for identifying and targeting kinase-independent pathways. Here we show—using proteomics, transcriptomics and network analyses—that in human LSCs, aberrantly expressed proteins, in both imatinib-responder and non-responder patients, are modulated in concert with p53 (also known as TP53) and c-MYC regulation. Perturbation of both p53 and c-MYC, and not BCR–ABL itself, leads to synergistic cell kill, differentiation, and near elimination of transplantable human LSCs in mice, while sparing normal HSCs. This unbiased systems approach targeting connected nodes exemplifies a novel precision medicine strategy providing evidence that LSCs can be eradicated.

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Accessions

Primary accessions

European Nucleotide Archive

Gene Expression Omnibus

Data deposits

The CML and normal CD34+ mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001502, PXD001503, PXD001504; SCOPE3/SCOPE4 data are also available using PXD001505 and PXD002782 respectively. Transcriptomic data are publicly available via the accession codes E-MTAB-2581, E-MTAB-2508, E-MIMR-17 at ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GSE47927, GSE5550, GSE24739, GSE14671 at GEO (http://www.ncbi.nlm.nih.gov/geo/). RNA-seq data (fastq) have been deposited in the European Nucleotide Archive under accession number PRJEB9942.

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Acknowledgements

We thank all CML patients and UK haematology departments who contributed samples; A. Hair for sample processing; J. Cassels for cell sorting; A. Michie and V. Helgason for assisting with the in vivo research and providing cord blood samples; C. Wells, P. Bailey and J. Cole for discussions regarding the RNA-seq analysis. We acknowledge the Cancer Research UK (CR-UK) Glasgow Centre (C596/A18076) and the CR-UK Beatson Institute (C596/A17196) for providing animal care and housing facilities. We acknowledge Constellation Pharmaceuticals for providing CPI-203, CPI-0610 and part funding M.E.D., Roche for providing RG7112, RG7388 and part funding M.E.D. and the SPIRIT Trials Management Group for access to CML samples. This study was supported by the Glasgow and Manchester Experimental Cancer Medicine Centres (ECMC), which are funded by CR-UK and the Chief Scientist’s Office (Scotland). We acknowledge the funders who have contributed to this work: MRC stratified medicine infrastructure award (A.D.W.), CR-UK C11074/A11008 (F.P., L.E.M.H., T.L.H., A.D.W.); LLR08071 (S.A.A., E.C.); LLR11017 (M.C.); SCD/04 (M.C.); LLR13035 (S.A.A., K.D., A.D.W. and A.P.); LLR14005 (M.T.S., D.V.); KKL690 (L.E.P.); KKL698 (P.B.); LLR08004 (A.D.W., A.P. and A.J.W.); MRC CiC (M.E.D.); The Howat Foundation (fluorescence-activated cell sorting (FACS) support); Friends of Paul O’Gorman (K.D. and FACS support); ELF 67954 (S.A.A.); British Society for Haematology start-up fund (S.A.A.); MR/K014854/1 (K.D.).

Author information

Author notes

    • Sheela A. Abraham
    • , Lisa E. M. Hopcroft
    •  & Anthony D. Whetton

    These authors contributed equally to this work.

Affiliations

  1. Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Gartnavel General Hospital, 1053 Great Western Road, Glasgow G12 0YN, UK

    • Sheela A. Abraham
    • , Lisa E. M. Hopcroft
    • , Mark E. Drotar
    • , Karen Dunn
    • , Koorosh Korfi
    • , Laura E. Park
    • , Mary T. Scott
    • , Francesca Pellicano
    • , Mhairi Copland
    •  & Tessa L. Holyoake
  2. Stem Cell and Leukaemia Proteomics laboratory, University of Manchester, Manchester M20 3LJ, UK

    • Emma Carrick
    • , Andrew J. K. Williamson
    • , Andrew Pierce
    •  & Anthony D. Whetton
  3. Manchester Precision Medicine Institute, University of Manchester, Manchester M20 3LJ, UK

    • Emma Carrick
    • , Andrew J. K. Williamson
    • , Andrew Pierce
    •  & Anthony D. Whetton
  4. Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK

    • Koorosh Korfi
    • , Pablo Baquero
    • , Craig Nourse
    •  & David Vetrie
  5. University of Melbourne Centre for Cancer Research, University of Melbourne, Victoria 3010, Australia

    • Sean M. Grimmond
  6. Stoller Biomarker Discovery Centre, University of Manchester, Manchester M20 3LJ, UK

    • Anthony D. Whetton

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Contributions

A.D.W. and T.L.H. supervised the entire study and research. S.A.A., L.E.M.H., A.D.W. and T.L.H. designed the research, analysed and interpreted data, and wrote the manuscript. S.A.A. conceived the hypothesis, supervised in vivo research, prepared samples for proteomic and RNA-seq, performed all in vitro work including western blotting, immunofluorescence, cloning and knockdown studies, clonogenic studies, flow cytometry and all mouse in vivo studies including tissue processing-FISH preparation and slide interpretation, engraftment determination and analysis of primitive stem cell subsets. L.E.M.H. designed and performed all in silico work including global omics handling, integration and analysis (MS, RNA-seq and microarray data); network analyses; correlation/MI calculations; functional enrichment analyses and permutation experiments for calculation of P values. E.C. performed proteomic work. A.J.K.W. performed proteomic work and generated relative proteomic quantification. M.E.D. performed virus preparation, prepared drugs for in vivo work and assisted with in vivo studies. K.D. provided maintenance and care for all mouse colonies and assisted with in vivo work. P.B. and L.E.P. provided assistance with in vivo studies and D-FISH preparation. F.P. and M.T.S. provided assistance with in vivo studies. D.V. provided analysed datasets and analysed/interpreted RNA-seq data. S.M.G. supervised and interpreted RNA-seq. C.N. performed RNA-seq experiments. K.K. and M.C. provided analysed datasets. A.P. supervised proteomic studies. All authors reviewed/edited the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Tessa L. Holyoake.

Extended data

Supplementary information

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  1. 1.

    Supplementary Information

    This file contains the raw data for Figure 2a and Extended Data Figures 2a, 3a, 3b, Supplementary Tables 1, 3, 4, 8 and legends for Supplementary Tables 2, 5, 6 and 7 (see separate excel files).

Excel files

  1. 1.

    Supplementary Table 2

    This file contains the candidate network statistics (see Supplementary Information file for legend).

  2. 2.

    Supplementary Table 5

    This file shows the molecular deregulation of P53/apoptosis-related signatures and pathways (see Supplementary Information file for legend).

  3. 3.

    Supplementary Table 6

    This file shows the molecular deregulation of MYC-related signatures and pathways (see Supplementary Information file for legend).

  4. 4.

    Supplementary Table 7

    This file shows the molecular deregulation of differentiation-related signatures and pathways (see Supplementary Information file for legend).

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DOI

https://doi.org/10.1038/nature18288

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