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

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 ( Phc , 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, Phc 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 Phc alterations. CellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reverses Phc 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 Phc and CP. (247 words) Highlights 1. To guide CP analysis, we introduce a quantizable parameter Phc and a pipeline Snapdragon, which discriminate naive and disturbed hematopoiesis; 2. The Snapdragon pipeline analysis on Tet2+/- Lin− cells demonstrates many novel insights, including enhanced HSC plasticity and increased PHC; similar trends are observed in inflammatory Lin− cells; 3. Regulon analysis suggests that transcriptional factor EGR1 is significantly activated to elevated the HSC plasticity and change hematopoietic trajectory; 4. Stress-response-related signaling pathways mediated by receptors IL1R1 or ADRB were obviously activated in the challenged hematopoiesis; 5. CellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reverses Phc promoted by Tet2 mutation and inflammation. * CP : Cell Plasticity Phc : Proportion of hybrid-cells on a transition trajectory UMAP : Uniform Manifold Approximation and Projection, an embedding method FA : Force Atlas, another embedding method VIT : Vision-Transformer TOSICA : Transformer for One Stop Interpretable Cell type Annotation, a VIT-based predictor of cell types TF : Transcriptional factor SP : Signaling pathway TET2 : Ten-Eleven-Translocation (TET) methyl-cytosine dioxygenase 2 EGR : Early Growth Response, a transcriptional factor family IL1R1 : Interleukine-1 Receptor 1 ADRB : Adrenergic Receptor Beta BM : Bone Marrow HSPC : Hematopoietic Stem and Progenitor Cell Lin− : Lineage-negative Pro_Mk : Megakaryocyte progenitor cell ErP : Erythrocyte progenitor cell Pro_Mast : Progenitor Mast cell Pro_NE : Progenitor Neutrophil Pro_Mono : Progenitor Monocyte Pro_DC : Progenitor Dendritic Cell Pro_B : Progenitor B cell