The genomic landscape of hypodiploid acute lymphoblastic leukemia

Abstract

The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.

Figure 1. Mutation spectrum of whole genome sequenced hypodiploid ALL

a, Circos plots of representative near haploid (top left), masked near haploid (top right), low hypodiploid (bottom left) and masked low hypodiploid (bottom right) cases. Depicted are structural genetic variants, including DNA copy number alterations, intra- and inter-chromosomal translocations, and sequence alterations. b, Whole genome sequenced cases are depicted from left to right. Colored bars represent number of specific lesions identified in each case as indicated. Masked hypodiploid cases here refer to cases with either a pure doubled hypodiploid clone or cases harboring a doubled clone constituting at least 30%.

Figure 2. Genome-wide DNA copy number alterations and gene expression profiling of hypodiploid ALL

a, Log₂ ratio DNA copy number heatmap showing SNP 6.0 microarray data for the tumor samples from the pediatric hypodiploid ALL cohort. Chromosomes 1–22, X and Y are depicted from top to bottom, and individual samples are shown from left to right. An asterisk (*) indicates tumor samples with less than 70% blasts. LH, low hypodiploid. Blue indicates loss of genetic material and red, gain. Dicentric chromosomes most frequently involved chromosome arms 9p, and either 12p or 20q, and were predominantly observed in near diploid karyotypes. Copy-neutral loss-of-heterozygosity was observed of diploid chromosomes in masked hypodiploid cases (Supplementary Table 10 and Supplementary Fig. 2) consistent with duplication of the hypodiploid clone. b, Left panel: Unsupervised principal component analysis (PCA) of gene expression data from all hypodiploid ALL cases with available high quality RNA (N=94). PCA analysis using 1000 representative probesets selected by k means distinguishes near haploid/masked near haploid, low hypodiploid/masked low hypodiploid and near diploid subgroups. Right panel: Weighted Pair-Group Method with Arithmetic mean hierarchical clustering analysis performed using the 10,000 most variable probesets. Masked hypodiploid cases here refer to cases with a doubled hypodiploid clone constituting at least 30%.

Figure 3. Recurrent alterations of Ras- and RTK signaling in near haploid ALL

a, Protein domain plot of NF1 depicting identified alterations. The recurrent exon 15–35 deletion in NF1 is indicated by a double-headed arrow. b, SNP 6.0 microarray heatmap showing deletions in NF1. Blue indicates DNA loss. Cases with simultaneous NF1 deletion and sequence mutation are indicated by a Y. Masked hypodiploid cases here include all cases harboring a doubled clone constituting at least 30%. mNH, masked near haploid; LH, low hypodiploid; mLH, masked low hypodiploid. c, The genomic breakpoints for the NF1 deletions cluster in two regions. The individual breakpoints are indicated by arrows. The 5′-break (upper panel) is most frequently present in intron 14, and the 3′-break (lower panel) in intron 35. Immediately internal to the 5′- and 3′-breakpoints are putative, partially conserved RAG heptamer recombination signal sequences (RSS) present, and an insertion of a variable number of non-consensus nucleotides in between the two breakpoints were seen for all these cases. d, RT-PCR on cases harboring an NF1 exon 15–35 deletion, using forward and reverse primers complementary to regions in NF1 exons 14 and 36, respectively, rendering a 648 bp fragment. e–h, Protein domain- and alteration plots for other Ras- and RTK signaling related genes recurrently targeted by sequence mutations in hypodiploid ALL, including NRAS, KRAS, FLT3 and PTPN11 (schematic of MAPK1 can be found in Supplementary Fig. 4). Blue line indicates alterations present also in non-tumor cells.

Figure 4. Frequent mutations in TP53 in low hypodiploid ALL

a–b, Protein domain plots of p53 with alterations identified in (a) pediatric hypodiploid ALL and (b) adult ALL. Known LFS alterations are indicated in red. Alterations present in non-tumor cells are indicated by blue lines. Arrows indicate alterations identified in adult low hypodiploid cases in b. c, Pedigree of a family with an inherited TP53 mutation. N, number of siblings. d, Electropherograms showing the inherited TP53 g.13886delG mutation (resulting in p.G302fs) in the proband (child; leukemic bone marrow (top) and normal skin biopsy(middle)) and father (lower panel). Wild-type (Wt) DNA and amino acid (aa) sequences (seq) are depicted at the top of the panel. Δ indicates the deleted nucleotide. e, Histologic examination of tumor from the proband’s father indicated a diagnosis of glioblastoma. Poorly differentiated glial cells are admixed with sparse cells showing an astrocytic phenotype. Many neoplastic cells are GFAP-immunopositive, and all express the mutant TP53 and IDH1 (p.Arg132His) gene products. Scale bar corresponds to 50 microns. HE, hematoxylin and eosin. f, Immunoblot of p53 on primary hypodiploid ALL samples harboring either wild-type TP53 or a TP53 missense mutation as indicated. g, Flow cytometric analysis of spleen samples from xenografted mice and NALM-16 detecting p53 levels. Only cells positive for human CD45 and CD19 were analyzed. Known nonsense and missense alterations in p53 are indicated. BM, bone marrow.

Figure 5. Recurrent deletions of the IKAROS family genes IKZF2 (HELIOS) and IKZF3 (AIOLOS)

a–c, SNP 6.0 microarray heatmaps (left panel) and schematics (right panel) of the alterations identified in the IKAROS family members IKZF1 (IKAROS, a), IKZF2 (HELIOS, b) and IKZF3 (AIOLOS, c). Blue indicates loss of DNA in the heatmaps. One IKZF1 altered case harbors a simultaneous deletion and sequence mutation, indicated by a Y in the left hand panel of a. d, Immunoblot analysis on primary hypodiploid ALL patient samples using the antibodies sc-9866 detecting HELIOS (left), and sc-101982 detecting AIOLOS (right). Deletions in the respective gene are indicated by “+” and lack thereof by “−”.

Figure 6. Recurring mutations in hypodiploid ALL

a, Data are shown for the entire hypodiploid ALL cohort split up in the near haploid (including masked near haploid cases), low hypodiploid (and masked low hypodiploid) and near diploid subgroups. b, Data matrix as above, but only including genes involved in histone modification identified in samples sequenced by either whole genome- or exome sequencing. SV, structural variation; Indel, insertion/deletion mutation; SNV, single nucleotide variation; Age, Age at diagnosis; Ind. failure, Induction treatment failure; NGS, next-generation sequencing; WGS, whole genome sequencing; WES, whole exome sequencing; GEP, gene expression profiling.

Figure 7. Activation of Ras signaling

a–b, Flow cytometric analyses of spleen samples from xenografted mice and the near haploid cell line NALM-16 detecting pERK (a) and pS6 (b)levels. Only cells positive for human CD45 were analyzed. *Cases with a known mutation in the Ras signaling pathway. IKZF2 and IKZF3 deletions are indicated by “+” and lack thereof by “−”. c, Immunoblot showing levels of Ras-GTP as assessed by a Raf-Ras binding domain bead pulldown assay in low hypodiploid and near haploid ALL xenograft samples and NALM-16. Presence of Ras pathway (pwy) and IKZF2 alterations are indicated by “+”. d–e, Detection of pERK (d) and pS6 (e) in non-stimulated NALM-16 with and without treatment with the PI3K inhibitor GDC-0941 (0.7uM) and the PI3K/mTOR inhibitor BEZ235 (0.3uM) for 1 hour. The drug concentrations correspond to the respective IC₅₀ value gained from proliferation assays on NALM-16 (Supplementary Table 23). f, ex vivo proliferation assay on near haploid (upper, SJHYPO037-X2) and low hypodiploid (lower, SJHYPO077-X1) xenograft cells harboring the indicated mutations (Supplementary Table 12). BM, bone marrow; NH, near haploid; LH, low hypodiploid.