Single-Cell Multi-Omics Analysis Reveals Hematopoiesis of Aberrant Mast Cells in Systemic Mastocytosis

Systemic mastocytosis (SM) is a disorder caused by accumulation of aberrant mast cells, leading disfunctions in multiple organs throughout the body. More than 90% patients harbor a D816V mutation in stem cell factor receptor (KIT), which leads to constitutive tyrosine kinase activation, abnormal proliferation and activation of mast cells, causing a series of clinical symptoms. Multilineage involvement of KIT mutation is commonly found, especially in advanced SM patients. Therefore, it is necessary to study the pathogenic mechanism of SM from the origin of abnormal mast cells and the process of hematopoietic development.

To investigate the hematopoiesis in SM patient, we performed a multi-omics study of bone marrow progenitors from SM, combining single-cell transcriptomic data with oligo-conjugated surface antibodies. Using fluorescence-activated cell sorting (FACS), enriched KIT^high mast cells hashing with oligo-barcoded antibody together with a spectrum of lineage^- KIT⁺ hematopoietic progenitors were isolated from bone marrow. All cells were stained with oligo-conjugated surface antibodies including aberrant mast cell characteristic marker CD2 and CD25 before sequence. By integrated analysis of transcriptome and oligo-conjugated surface antibody data, we delineate the bone marrow hematopoietic landscape of SM patients with focus on mast cells. Both transcriptome and oligo-tagged antibody data of CD25 (IL2RA) identified aberrant mast cells and a residual population of phenotypically normal mast cells in SM patients. Comparative analysis between these 2 populations revealed a serious of novel markers that could provide insights in understanding pathogenic mechanisms and offer possible new therapeutic targets.

Furthermore, to further explore the role of KIT D816V mutations in mast cell development in SM, we used long-read sequencing based on 10x Genomics technology. The mutational profile of each cell in the hematopoietic landscape can be captured by integrating long-read sequencing and transcriptome data. This allows us to explore the mechanism of KIT mutation in the development of neoplastic mast cells.

In conclusion, our study integrates single-cell multi-omics analysis and long-read sequencing analysis to reveal the development of aberrant and normal mast cells in the bone marrow of SM patients. Further analysis discovered a series of novel genes in the pathogenesis and progression of SM, which may provide new targets for therapy.

No relevant conflicts of interest to declare.