Developmental trajectories and cooperating genomic events define molecular subtypes of BCR::ABL1-positive ALL.

Distinct diagnostic entities within BCR::ABL1-positive ALL are currently defined (ICC): 'lymphoid-only', with BCR::ABL1 observed exclusively in lymphatic precursors versus 'multilineage', where BCR::ABL1 is also present in other hematopoietic lineages. Here, we analyzed transcriptomes of n=327 BCR::ABL1-positive ALL patients (age: 2 years - 84 years, median: 46) and identified two main gene expression clusters reproducible across four independent patient cohorts. FISH analysis of FACS-sorted hematopoietic compartments showed distinct BCR::ABL1 involvement in myeloid cells for these clusters (n=18/18 vs n=3/16 patients, p<0.001), indicating that a 'multilineage' or 'lymphoid' BCR::ABL1 subtype can be inferred from gene expression. Further subclusters grouped samples according to cooperating genomic events (multilineage: HBS1L deletion or monosomy 7; lymphoid: IKZF1-/- or CDKN2A / PAX5 deletions / hyperdiploidy). A novel HSB1L transcript was highly specific for BCR::ABL1 multilineage cases independent of HBS1L genomic aberrations. Treatment on current GMALL protocols resulted in comparable disease-free survival (DFS) for 'multilineage' vs. 'lymphoid' cluster patients (3-year DFS: 70% vs 61%, p=0.530; n=91). However, the IKZF1-/- enriched lymphoid subcluster was associated with inferior DFS, whereas hyperdiploid cases showed a superior outcome. Thus, gene expression clusters define underlying developmental trajectories and distinct patterns of cooperating events in BCR::ABL1-positive ALL with prognostic relevance.