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A topological view of human CD34+ cell state trajectories from integrated single-cell output and proteomic data

David J.H.F. Knapp, Colin A. Hammond, Fangwu Wang, Nima Aghaeepour, Paul H. Miller, Philip A. Beer, Davide Pellacani, Michael VanInsberghe, Carl Hansen, Sean C. Bendall, Garry P. Nolan and Connie J. Eaves

Key points

  • Paired functional and proteomic measurements of single human CD34+ CB cells reveal variable processes leading to lineage-restricted states.

  • Signaling profiles of individual CD34+ CB cells suggest external cues contribute to the lineage restriction pathways they pursue.

Abstract

Recent advances in single-cell molecular analytical methods and clonal growth assays are enabling more refined models of human hematopoietic lineage restriction processes to be conceptualized. Here, we report the results of integrating single-cell proteome measurements with clonally-determined lymphoid, neutrophilic/monocytic, and/or erythroid progeny outputs from over 1,000 index-sorted CD34+ human cord blood cells in short-term cultures with and without stromal cells. Surface phenotypes of functionally examined cells were individually mapped onto a molecular landscape of the entire CD34+ compartment constructed from single-cell mass cytometric measurements of 14 cell surface markers, 20 signaling/cell cycle proteins and 6 transcription factors in approximately 300,000 cells. This analysis demonstrated that conventionally defined subsets of CD34+ CB cells are quite heterogeneous in their functional properties, transcription factor content, and signaling activities. Importantly, this molecular heterogeneity was reduced, but not eliminated in phenotypes that we showed display highly restricted lineage outputs. Integration of the complete proteomic and functional datasets obtained revealed a continuous probabilistic topology of change that includes a multiplicity of lineage restriction trajectories. Each of these reflects progressive but variable changes in the levels of specific signaling intermediates and transcription factors, but shared features of decreasing quiescence. Taken together, our results suggest a model in which increasingly narrowed hematopoietic output capabilities in neonatal CD34+ cord blood cells are determined by a history of external stimulation in combination with innately programmed cell state changes.

  • Submitted October 4, 2018.
  • Accepted December 23, 2018.