Acute lymphoblastic leukemia

Single-cell analysis identifies CRLF2 rearrangements as both early and late events in Down syndrome and non-Down syndrome acute lymphoblastic leukaemia


Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5–15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We have previously reported the genomic landscape of patients with CRLF2 rearrangements (CRLF2-r) using both whole genome and exome sequencing, which identified a number of potential clonal and sub-clonal genomic alterations. In this study, we aimed to assess when the CRLF2-r; IGH-CRLF2 or P2RY8-CRLF2, arose during the evolution of both Down syndrome-ALL (DS-ALL) and non-DS-ALL. Using fluorescence in situ hybridisation, we were able to track up to four structural variants in single cells from 47 CRLF2-r B-ALL patients, which in association with our multiplex single-cell analysis of a further four patients, permitted simultaneous tracking of copy number alterations, structural and single nucleotide variants within individual cells. We observed CRLF2-r arising as both early and late events in DS and non-DS-ALL patients. Parallel evolution of discrete clones was observed in the development of CRLF2-r B-ALL, either involving the CRLF2-r or one of the other tracked abnormalities. In-depth single-cell analysis identified both linear and branching evolution with early clones harbouring a multitude of abnormalities, including the CRLF2-r in DS-ALL patients.

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Data sharing not applicable to this article as no datasets were generated or analysed during the current study.


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The authors would like to thank The Kay Kendall Leukaemia Fund, Leuka, Children with Cancer UK and Bloodwise (formerly Leukaemia and Lymphoma Research) for financial support. Lisa J Russell has a John Goldman Fellowship from Leuka. We also thank member laboratories of the United Kingdom Cancer Cytogenetic Group (UKCCG) for providing cytogenetic data and material. We are grateful to all the members of the NCRI Haematological Oncology Adult ALL Subgroup and the NCRI Childhood Cancer and Leukaemia Group (CCLG) Leukaemia Subgroup. Primary childhood leukaemia samples used in this study were provided by the Bloodwise Childhood Leukaemia Cell Bank working with the laboratory teams in the Bristol Genetics Laboratory, Southmead Hospital, Bristol: Molecular Biology Laboratory, Royal Hospital for Sick Children, Glasgow: Molecular Haematology Laboratory, Royal London Hospital, London: Molecular Genetics Service and Sheffield Children’s Hospital, Sheffield. We also thank the Central England Haemato-Oncology Research Biobank for providing patient samples. Finally, we thank all the clinicians who entered patients into the trial and the patients and families who agreed to take part.

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Correspondence to L. J. Russell.

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Potter, N., Jones, L., Blair, H. et al. Single-cell analysis identifies CRLF2 rearrangements as both early and late events in Down syndrome and non-Down syndrome acute lymphoblastic leukaemia. Leukemia 33, 893–904 (2019).

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