The Genomic Landscape Of Lineage Switch Acute Leukemia

The regulation of hematopoietic lineage fate and commitment is fundamental to normal and malignant hematopoiesis. Switches between lymphoid and myeloid lineages in leukemia are rare and associated with poor clinical outcome, but potentially very informative regarding the regulation of hematopoietic lineage commitment. In contrast to therapy-related acute leukemia (AL) after a first primary leukemia, lineage-switch ALs arise from a common pre-leukemic or leukemic clone and share a founder mutation, most often rearrangement of MLL at 11q23. The majority of switches are from acute lymphoblastic leukemia (ALL) to acute myeloid leukemia (AML); however, conversions from myeloid to lymphoid and even oscillations between the two lineages have been observed, although the molecular mechanisms underlying lineage switch have not yet been identified. Here we describe a male patient who presented at 9 months of age with a t(4;11)-positive B-ALL and was subsequently treated according to the Interfant06 protocol. He achieved complete remission, but relapsed at the age of 4 years with a t(4;11)-positive AML. He underwent allogeneic BM transplantation and has remained in remission 13 months. Sanger sequencing revealed identical translocation breakpoints in the ALL and AML samples, demonstrating a lymphoid to myeloid lineage switch with a common pre-leukemic or leukaemic cell of origin for both ALs. Interestingly, whereas the AML shows no V(D)J rearrangements, we found incomplete rearrangements in the ALL cells indicating a ProB cell origin. In line with this observation, B-ALL cells expressed 6-fold and 120-fold higher levels of PAX5 and EBF1, respectively, compared to AML blast cells. Microsatellite instability measurements argued against a strong therapy-associated impairment of DNA mismatch repair in the AML. The translocation t(4;11) is the most frequently found chromosomal rearrangement in infant leukaemia and is almost exclusively associated with ALL at presentation, suggesting a strong instructive potential towards the lymphoid cell fate. However, the occurrence of lineage switch in t(4;11) AL demonstrates that this instruction can be overcome by as yet unknown mechanisms.

Exome sequencing identified 16 and 98 novel somatic variants in the diagnostic ALL sample (0.23 mutations per Mb) and AML (1.4 mutations per Mb), respectively, of which 10 were shared. Of the total novel somatic mutations, there were 1 and 12 non-synonymous alterations in the B-ALL and AML, respectively, of which one was shared. RNA sequencing confirmed that all 12 genes with non-synonymous mutations were expressed in AML blast cells, and all belonged to the top 25% of expressed genes in both the AML and B-ALL. Genes carrying non-synonymous somatic AML-specific mutations include CHD4 (12p13, NuRD helicase, chromatin maintenance, DNA repair, lineage fidelity, part of MLL complex), NCOA2 (8q13, also known at TIF2 and part of the MOZ/TIF2 fusion gene, cofactor of nuclear receptors including VDR and NR3C1; control of myeloid differentiation, putative tumour suppressor), CEP164 (11q23, centrosome protein involved in microtubule organization, DNA damage response and chromosome segregation) and PPP1R7 (2q37, regulatory subunit of protein phosphatase 1, control of mitosis, regulator of AURKB). All amino acid residues predicted to be mutated are conserved between several species. Each of the identified mutations is located in functionally relevant regions and may, thus, interfere with protein function. Notably, exome and RNAseq showed that all 12 of the AML-specific non-synonymous mutations were found in at least 40% of the reads covering the corresponding genomic positions (the sample analysed constituted 80% blast material), thus suggesting heterozygosity for each mutation and that all mutations are common to the major leukemic clone.

Taken together, these data suggest that the B-ALL and AML share a common ancestral pre-leukemic or leukemic cell of origin. Whilst the B-ALL revealed few novel somatic mutations, the change in lineage is associated with the acquisition of a substantial number of novel mutations indicating significant clonal evolution preceding the emergence of myeloid neoplasia. These data identify candidate mutations/genes which may overcome lineage instruction by a leukemic master regulator such as MLL/AF4 and which may therefore play an essential role in the control of hematopoietic lineage fate.