Article
Author: Schneller, Folker ; Harder, Lana ; Barz, Malwine J. ; Cario, Gunnar ; Baldus, Claudia D. ; Zimmermann, Johannes ; Gökbuget, Nicola ; Stelljes, Matthias ; Bastian, Lorenz ; Denker, Miriam ; Schwartz, Stefan ; Beder, Thomas ; Rohrandt, Christian ; Steffen, Björn ; Hartmann, Alina M. ; Haferlach, Claudia ; Faul, Christoph ; Chitadze, Guranda ; Wittig, Michael ; Brüggemann, Monika ; Bartsch, Lorenz ; Neumann, Martin ; Das Gupta, Dennis ; Pfeifer, Heike ; Iben, Katharina ; Wolgast, Nadine ; Bendig, Sonja ; Walter, Wencke ; Fiedler, Walter ; Brändl, Björn ; Hansen, Björn-Thore ; Müller, Franz-Josef
AbstractDistinct diagnostic entities within BCR::ABL1-positive acute lymphoblastic leukemia (ALL) are currently defined by the International Consensus Classification of myeloid neoplasms and acute leukemias (ICC): “lymphoid only”, with BCR::ABL1 observed exclusively in lymphatic precursors, vs “multilineage”, where BCR::ABL1 is also present in other hematopoietic lineages. Here, we analyzed transcriptomes of 327 BCR::ABL1-positive patients with ALL (age, 2-84 years; median, 46 years) and identified 2 main gene expression clusters reproducible across 4 independent patient cohorts. Fluorescence in situ hybridization analysis of fluorescence-activated cell-sorted hematopoietic compartments showed distinct BCR::ABL1 involvement in myeloid cells for these clusters (n = 18/18 vs n = 3/16 patients; P < .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 German Multicenter Study Group for Adult ALL (GMALL) protocols resulted in comparable disease-free survival (DFS) for multilineage vs lymphoid cluster patients (3-year DFS: 70% vs 61%; P = .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.