Investigation of differentiation and migration of hematopoietic cells across tissues at single cell resolution

Abstract

Hematopoiesis is a continuous process where hematopoietic stem cells and progenitor cells (HSPCs) differentiate to mature cells. It requires the coordinated differentiation of HSPCs in multiple tissues. Although differentiation of HSPCs in bone marrow (BM) has been well-studied, our knowledge about the migration and differentiation of HSPCs cross tissues is limited. Here, we collected and integrated single-cell RNA-seq data of human CD34+ cells, which represent HSPCs, from BM, peripheral blood (PB), thymus and mobilized PB (mPB), to investigate the hematopoiesis cross tissues. We constructed a cell atlas of HSPCs cross tissues and found most HSPC subsets in BM had counterparts in PB, indicating migration of HSPCs from BM to PB has a much broad spectrum. We found B progenitors highly expressed CXCR4 for anchoring in BM, while cells with low expression of CXCR4 facilitate their migration out of BM. Among the HSPC subsets from thymus, we only found the counterparts of the earliest thymic progenitor like cells (ETP-like) in BM and PB, potentially indicating that ETP-like were the subsets that migrated from BM to PB and thymus. We found interaction signaling including CD99-CD99, CXCL12-CXCR4 and CCL19-CCR7 played important roles in ETP-like homing to the thymus. Briefly, these data provided a single unified developmental spectrum of hematopoiesis cross different tissues, connected by cell migration. In addition, to explore the cell differentiation and migration during the late hematopoiesis, we collected and integrated single-cell multi-omics data, including single-cell RNA sequencing (scRNA-seq), single-cell B cell receptor sequencing (scBCR-seq) and single-cell T cell receptor sequencing (scTCR-seq) data from thymocytes and immune cells from immune tissues including BM, PB, spleen (SP), thymus, lung-draining lymph node (LLN), and mesenteric lymph node (MLN) with HSPCs. We constructed an atlas of the whole hematopoiesis across tissues and found that cells in BM and PB had the broadest spectrum. HSPCs differentiated to mature cells along lineages with transcriptional change from fundamental biological processed to functional immunological activities. Moreover, BCR and TCR clonotype suggested cell differentiation and migration across tissues in B and T cells.