Computing hematopoietic stem and progenitor cell plasticity in response to genetic mutations and environmental stimulations

Abstract

Cell plasticity (CP), describing a dynamic cell state, plays a crucial role in maintaining homeostasis during organ morphogenesis, regeneration and damage-to-repair biological process. Single-cell-omics datasets provide unprecedented resource to empowers analysis on CP. Hematopoiesis offers fertile opportunities to develop quantitative methods for understanding CP with rich supports from experimental ground-truths. In this study we generated high-quality lineage-negative (Lin⁻) single-cell RNA-sequencing datasets under various conditions and introduced a working pipeline named Snapdragon to interrogate naïve and disturbed plasticity of hematopoietic stem and progenitor cells (HSPCs) with mutational or environmental challenges. Utilizing embedding methods UMAP or FA, a continuum of hematopoietic development is visually observed in wildtype where the pipeline confirms a very low Proportion of hybrid-cells (P_hc, with bias range: 0.4-0.6) on a transition trajectory. Upon Tet2 mutation, a driver of leukemia, or treatment of DSS, an inducer of colitis, P_hc is increased and plasticity of HSPCs was enhanced. Quantitative analysis indicates that Tet2 mutation enhances HSC self-renewal capability while DSS treatment results in an enhanced myeloid-skewing trajectory, suggesting their similar but different consequences. We prioritized several transcription factors (i.e the EGR family) and signaling pathways (i.e. receptors IL1R1 and ADRB, inflammation and sympathy-sensing respectively) which are responsible for P_hc alterations. CellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reverses P_hc promoted by Tet2 mutation and inflammation. In conclusion, the study provides high-quality datasets with single-cell transcriptomic matrices for diversified hematopoietic simulations and a computational pipeline Snapdragon for quantifying disturbed P_hc and CP. (247 words)