-Author name in bold denotes the presenting author
-Asterisk * with author name denotes a Non-ASH member
Clinically Relevant Abstract denotes an abstract that is clinically relevant.

PhD Trainee denotes that this is a recommended PHD Trainee Session.

Ticketed Session denotes that this is a ticketed session.

842 Single-Cell Genomics Details the Maturation Block in BCP-ALL and Identifies Therapeutic Vulnerabilities in DUX4-Rearranged Cases

Program: Oral and Poster Abstracts
Type: Oral
Session: 618. Acute Lymphoblastic Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Novel Disease Subclassifications and Clinical Prognosis
Hematology Disease Topics & Pathways:
Research, Lymphoid Leukemias, ALL, Biological therapies, Translational Research, Chimeric Antigen Receptor (CAR)-T Cell Therapies, bioinformatics, Diseases, Therapies, Lymphoid Malignancies, Technology and Procedures, omics technologies
Monday, December 11, 2023: 3:00 PM

Hanna Thorsson, PhD1*, Rasmus Henningsson, PhD2*, Noelia Puente-Moncada, PhD2*, Ludvig Sjöström2*, Helena Ågerstam1*, Pablo Enrique Peña-Martínez1*, Carl Sandén, PhD2*, Marianne Rissler1*, Anders Castor3*, Hanne Vibeke Marquart, MD, PhD4*, Signe Modvig, MD, PhD4*, Kajsa Paulsson5, Cornelis Pronk, MD, PhD3*, Kjeld Schmiegelow4, Axel Hyrenius Wittsten, PhD6*, Christina Orsmark-Pietras, PhD1*, Henrik PhD Lilljebjörn1* and Thoas Fioretos, MD, PhD1

1Division of Clinical Genetics, Lund University, Lund, Sweden
2Division of Clinical Genetics, Lund University, Lund, SWE
3Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
4Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
5Department of Clinical Genetics, Lund University, Lund, Sweden
6Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden

B cell progenitor acute lymphoblastic leukemia (BCP-ALL) is the most common childhood malignancy. It is initiated by multiple genetic alterations, causing a maturation arrest and accumulation of abnormal progenitor B cells. Current treatment protocols with chemotherapy have led to favorable outcomes, but are associated with significant toxicity and risk of side effects, highlighting the necessity for highly effective, less toxic, targeted drugs that also show efficacy in children experiencing relapse.

We have used multimodal single-cell sequencing to delineate the transcriptional, epigenetic, and immunophenotypic characteristics of 23 childhood BCP-ALLs, including the BCR::ABL1-positive, ETV6::RUNX1-positive, high hyperdiploid, and recently discovered DUX4-rearranged subtypes. In total, 188,546 single cells derived from 23 BCP-ALLs and 9 normal bone marrow samples were profiled using the 10X Genomics platform. Cellranger multi and atac count (10X Genomics) were used to generate read count matrices. Further analysis was performed using Seurat and Signac. The in-house developed program SingleCellProjections was used to create a normal bone marrow reference graph onto which the BCP-ALL data was projected.

Projection of the ALL cells along the normal B cell differentiation axis, revealed a diversity in the maturation block between the different BCP-ALL subtypes. Whereas the BCR::ABL1-, ETV6::RUNX1-positive and high hyperdiploidy cells mainly showed similarities to normal pro-B cells, the DUX4-rearranged ALL cells also displayed a transcriptional signature resembling mature B cells. In addition, the blast population in DUX4-rearranged ALLs showed multilineage priming toward non-hematopoietic cells, myeloid and T cell lineages, but also an activation of PI3K/AKT signaling that sensitized the cells to PI3K inhibition. Finally, we show that chimeric antigen receptor T cell therapy targeting the upregulated myeloid receptor CD371 (CLL-1), effectively eliminates DUX4-rearranged ALL cells. Our results provide a detailed characterization of BCP-ALL at the single-cell level and reveal therapeutic vulnerabilities in the DUX4-rearranged subtype with important implications for the understanding of ALL biology and new therapeutic strategies.

Disclosures: No relevant conflicts of interest to declare.

*signifies non-member of ASH