Distinct Stromal Cell Populations Define the B-cell Acute Lymphoblastic Leukemia Microenvironment

Processed single-cell RNA-seq from the study 

• 10X Genomics CellRanger output (barcodes.tsv, genes.tsv, matrix.mtx) for each each sample
• Metadata
• Seurat object of the integrated scRNAseq dataset
• Xenium object of the spatial transcriptomic data

Distinct Stromal Cell Populations Define the B-cell Acute Lymphoblastic Leukemia Microenvironment

Mauricio N. Ferrao Blanco¹, Bexultan Kazybay¹, Mirjam Belderbos¹, Olaf Heidenreich¹, Hermann Josef Vormoor^1,2

¹ Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands

² University Medical Center Utrecht, Utrecht, the Netherlands

Abstract

The bone marrow microenvironment plays a critical role in B-cell acute lymphoblastic leukemia (B-ALL) progression, yet its cellular heterogeneity remains poorly understood. Using single-cell RNA sequencing on patient-derived of bone marrow aspirates from pediatric B-ALL patients, we identified two distinct mesenchymal stromal cell (MSC) populations: early mesenchymal progenitors and adipogenic progenitors. Spatial transcriptomic analysis further revealed the localization of these cell types and identified a third stromal population, osteogenic-lineage cells, exclusively present in the bone biopsy. Functional ex vivo assays using sorted stromal populations derived from B-ALL patient bone marrow aspirates demonstrated that both early mesenchymal and adipogenic progenitors secrete key niche-supportive factors, including CXCL12 and Osteopontin, and support leukemic cell survival and chemoresistance. Transcriptomic profiling revealed that B-ALL cells interact differently with stromal subtypes. Notably, adipogenic progenitors, but not early mesenchymal progenitors, provide support to leukemic cells through interleukin-7 and VCAM1 signaling. Stromal cells from B-ALL patients exhibited an enhanced adipogenic differentiation capacity compared to healthy controls. Moreover, co-culture experiments showed that B-ALL cells induce adipogenic differentiation in healthy MSCs through a cell contact-dependent mechanism. Adipogenic progenitors were also enriched in relapse samples, implicating them in disease progression. These findings highlight the complexity of the B-ALL microenvironment and identify different specialized stromal niches with which the leukemic cells can engage.