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Chronic myelogenous leukemia

Aberrant RAG-mediated recombination contributes to multiple structural rearrangements in lymphoid blast crisis of chronic myeloid leukemia


Blast crisis of chronic myeloid leukemia is associated with poor survival and the accumulation of genomic lesions. Using whole-exome and/or RNA sequencing of patients at chronic phase (CP, n = 49), myeloid blast crisis (MBC, n = 19), and lymphoid blast crisis (LBC, n = 20), we found 25 focal gene deletions and 14 fusions in 24 patients in BC. Deletions predominated in LBC (83% of structural variants). Transcriptional analysis identified the upregulation of genes involved in V(D)J recombination, including RAG1/2 and DNTT in LBC. RAG recombination is a reported mediator of IKZF1 deletion. We investigated the extent of RAG-mediated genomic lesions in BC. Molecular hallmarks of RAG activity; DNTT-mediated nucleotide insertions and a RAG-binding motif at structural variants were exclusively found in patients with high RAG expression. Structural variants in 65% of patients in LBC displayed these hallmarks compared with only 5% in MBC. RAG-mediated events included focal deletion and novel fusion of genes associated with hematologic cancer: IKZF1, RUNX1, CDKN2A/B, and RB1. Importantly, 8/8 patients with elevated DNTT at CP diagnosis progressed to LBC by 12 months, potentially enabling early prediction of LBC. This work confirms the central mutagenic role of RAG in LBC and describes potential clinical utility in CML management.

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Fig. 1: Global transcriptomic shift at blast crisis towards myeloid or lymphoid lineage.
Fig. 2: The V(D)J recombination pathway is upregulated at lymphoid blast crisis.
Fig. 3: Bioinformatic identification of RAG-mediated genomic deletions.
Fig. 4: The molecular signature of V(D)J recombination is enriched at oncogenic genomic lesions in patients with high RAG1 expression.
Fig. 5: RAG1/2 and DNTT expression corresponds to acquisition of oncogenic lesions.
Fig. 6: High RAG1 or DNTT expression at diagnosis predicts imminent LBC.
Fig. 7: RAG is constitutively upregulated by reinforced regulatory activation.
Fig. 8: Cytosine deamination is seen in CML patients irrespective of disease phase but not consistent with the mutational signature of AID.


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This work was funded by the National Health and Medical Research Council of Australia APP1027531 and APP1117718 (S.B.), APP1135949 (T.P.H.) and APP1023059 (H.S.S.), the Ray and Shirl Norman Cancer Research Trust and the Royal Adelaide Hospital Research Foundation. T.P.H. and H.S.S have the financial support of Cancer Council SA’s Beat Cancer Project on behalf of its donors and the State Government of South Australia through the Department of Health. ACRF Cancer Genomics Facility was established with funding from Therapeutic Innovation Australia and the Australian Cancer Research Foundation (ACRF). We would like to thank Verity Saunders for preparation of some patient samples and David Yeung and Deborah White for critically reading the manuscript.

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DWT and SB conceptualized the research, analyzed and interpreted the data, and wrote the manuscript. DWT designed and performed bioinformatics analyses. AWS, PPSW, and DWT developed bioinformatics pipelines. NHS and CW performed laboratory experiments and interpreted data. AWS, NHS, HSS, CW, MED, NS, and TPH provided scientific insight and contributed to manuscript preparation. All authors critically reviewed the manuscript.

Corresponding author

Correspondence to Susan Branford.

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Conflict of interest

SB: Member of the advisory board of Qiagen, Novartis and Bristol-Myers Squibb, and consultant for Cepheid and received honoraria from Qiagen, Novartis, Bristol-Myers Squibb, and Cepheid. Research support from Novartis. TPH: Holds a consultancy role and has received research funding and honoraria from Novartis, Bristol-Myers Squibb, and Ariad. HSS received honoraria from Celgene. NS received travel support from Novartis, Bristol-Myers Squibb, Amgen, and Janssen. Other authors declare no conflicts of interest.

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Thomson, D.W., Shahrin, N.H., Wang, P.P.S. et al. Aberrant RAG-mediated recombination contributes to multiple structural rearrangements in lymphoid blast crisis of chronic myeloid leukemia. Leukemia 34, 2051–2063 (2020).

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