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

Abstract

AbstractCell 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. UponTet2mutation, a driver of leukemia, or treatment of DSS, an inducer of colitis,Phcis increased and plasticity of HSPCs was enhanced. Quantitative analysis indicates thatTet2mutation 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 forPhcalterations. CellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reversesPhcpromoted byTet2mutation 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 disturbedPhcand CP. (247 words)HighlightsTo guide CP analysis, we introduce a quantizable parameterPhcand a pipeline Snapdragon, which discriminate naive and disturbed hematopoiesis;The Snapdragon pipeline analysis onTet2+/-Lin−cells demonstrates many novel insights, including enhanced HSC plasticity and increased PHC; similar trends are observed in inflammatory Lin−cells;Regulon analysis suggests that transcriptional factor EGR1 is significantly activated to elevated the HSC plasticity and change hematopoietic trajectory;Stress-response-related signaling pathways mediated by receptors IL1R1 or ADRB were obviously activated in the challenged hematopoiesis;CellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reversesPhcpromoted byTet2mutation and inflammation.