An immunophenotype-coupled transcriptomic atlas of mouse hematopoietic progenitors

The bone marrow hematopoietic progenitor compartment is a crucial area of study for understanding the development of mature immune cells in health and disease. Recent advancements in single-cell multimodal approaches have allowed researchers to simultaneously capture transcriptomic and proteomic information of this heterogeneous cell population. However, comprehensive studies covering all murine hematopoietic stem and progenitor cells (HSPCs) are limited.

In this study, researchers utilized Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) to create an atlas of 9,281 low-frequency mouse BM HSPCs. This atlas was generated using a 123 antibody-derived tag (ADT) panel combined with genome-wide single-cell transcriptomes. The multimodal analysis revealed 28 progenitor stages across eight blood lineages, each characterized by distinct surface marker and transcription factor (TF) profiles. Novel marker combinations were identified to differentiate closely related progenitor stages.

Classical mouse progenitor surface markers, such as CD117, CD34, and CD115, were found to align with established lineage relationships. However, unexpected findings included the broader expression patterns of CD43 and CD48, as well as the discovery of neglected surface molecules like CD27, CD36, CD106, and PIR-A/B as novel stage-specific markers. When comparing ADT and transcriptome data, transcription-translation inconsistencies were observed for certain markers, including CD54 and CD68.

The CITE-seq-guided gating strategy developed from this research can be used to create FACS-compatible panels for the isolation and functional examination of previously unidentified progenitor stages. Additionally, comprehensive TF network analysis provided insights into lineage- and stage-specific transcriptional programs, shedding light on unresolved ontogenies and functions.

These findings contribute to a better understanding of previously unexplained phenomena, such as the dual lympho-myeloid origin of pDCs or rapid neutrophil turnover. This new and comprehensive resource opens up new avenues for further exploration of mouse hematopoietic progenitor states, potentially leading to discoveries in hematology and immunology.