Type: Oral
Session: 605. Molecular Pharmacology and Drug Resistance: Lymphoid Neoplasms: Mechanisms of Therapy Resistance in Lymphoma
Hematology Disease Topics & Pathways:
Lymphoid Leukemias, ALL, Diseases, Lymphoid Malignancies
Methods: To comprehensively investigate the genomic basis of variability in leukemia CD22 expression and thus B-ALL sensitivity to InO, we performed a multi-omic characterization of 196 primary human B-ALL samples, using whole transcriptome sequencing (RNAseq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), coupled with ex vivo profiling of InO sensitivity. Additionally, genomic editing studies were performed in Nalm6 and REH B-ALL cell lines, and patient derived xenograft (PDX) models were used for in vitro and in vivo validations.
Results: Applying digital cytometry to leukemia bulk RNAseq data to infer the B-ALL developmental state, we found that blast cells with early Pre-pro-B-like signature had low levels of CD22 expression and were resistant to InO. As B-cell differentiation is controlled by stage-specific transcription factors (TFs), we performed a targeted CRISPR library screen of 1,639 TF genes and identified EBF1 as a key activator of CD22 expression (FDR=7.1x10-4). In primary B-ALL samples, EBF1 expression was significantly correlated with CD22 expression (R=0.69, P<0.0001) and leukemia response to InO (measured as LC50, R=-0.42, P<0.0001). In addition, TF footprint analysis of leukemia ATAC-seq data identified EBF1 as the most differentially activated TF comparing InO-sensitive and -resistant B-ALL cases (P=8x10-174). Blocking the EBF1 binding sites within the CD22 promoter by CRISPR interference resulted in a 50-fold and 49-fold decrease in cell surface CD22 expression, and a 22-fold and 25.7-fold increase in InO LC50 for Nalm6 and REH, respectively, confirming the direct impact of EBF1 on CD22 transcription and InO sensitivity.
Because BCR::ABL1-positive ALL showed the greatest variability in InO sensitivity among all B-ALL subtypes, we further investigate the role of the EBF1/CD22 axis on InO sensitivity within this subtype. Unsupervised clustering of gene expression profiles revealed two distinct groups, namely BCR::ABL1 ALL with multilineage (BCR::ABL1-M) or lymphoid only (BCR::ABL1-L) involvement [PMID: 38153913]. Compared to BCR::ABL1-L, BCR::ABL1-M displayed markedly reduced CD22 expression (P=8.3×10-11) and resistance to InO (P=1.9×10-4), likely due to the lower expression and frequent somatic alteration of EBF1. Finally, we established PDX models for representative cases of BCR::ABL1-M and BCR::ABL1-L. Strikingly, InO treatment did not affect leukemia progression in the BCR::ABL1-M PDX model, whereas the BCR::ABL1-L PDX model achieved complete remission and has remained leukemia free to date.
Conclusion: Collectively, these data demonstrate the direct impact of EBF1 on CD22 expression during B-cell development, and explain the heterogeneity of InO sensitivity, even within the same molecular B-ALL subtype.
Disclosures: Stock: Adaptive: Consultancy, Honoraria; Kura: Research Funding; Kura, Servier, Newave, Adaptive, Jazz, Asofarma: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees. Konopleva: Curis: Consultancy; Adaptive: Consultancy; MEI Pharma: Consultancy, Membership on an entity's Board of Directors or advisory committees; Servier: Speakers Bureau; Novartis: Membership on an entity's Board of Directors or advisory committees; Auxenion GmbH: Membership on an entity's Board of Directors or advisory committees; Legend Biotech: Membership on an entity's Board of Directors or advisory committees; AbbVie: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: clinical trials, Research Funding; Intellisphere: Speakers Bureau; Menarini Group: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Other: clinical trials; Vincerx: Consultancy; Sanofi Aventis: Consultancy; Klondike Biopharma: Research Funding; Syndax: Membership on an entity's Board of Directors or advisory committees; Dark Blue Therapeutics: Membership on an entity's Board of Directors or advisory committees. Litzow: Abbvie: Research Funding; Amgen: Research Funding, Speakers Bureau; Actinium: Research Funding; Astellas: Research Funding; Pluristem: Research Funding; Sanofi: Research Funding; Beigene: Speakers Bureau; Biosight: Other: Data Safety Monitoring Committee. Inaba: Jazz: Consultancy; Servier: Consultancy, Research Funding; Incyte: Research Funding.