Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators

Lev Silberstein, Kevin A. Goncalves. Peter V. Kharchenko, Raphael Turcotte, Youmna Kfoury, Francois Mercier, Ninib Baryawno, Nicolas Severe, Jacqueline Bachand, Joel A. Spencer, Ani Papazian, Dongjun Lee, Brahmananda Reddy Chitteti, Edward F. Srour, Jonathan Hoggatt, Tiffany Tate, Cristina Lo Celso, Noriaki Ono, Stephen Nutt, Jyrki Heino, Kalle Sipilä, Toshihiro Shioda, Masatake Osawa, Charles P. Lin, Guo-fu Hu, David T. Scadden


Physiological stem cell function is regulated by secreted factors produced by niche cells. In this study, we describe an unbiased approach based on the differential single-cell gene expression analysis of mesenchymal osteolineage cells close to, and further removed from, hematopoietic stem/progenitor cells (HSPCs) to identify candidate niche factors. Mesenchymal cells displayed distinct molecular profiles based on their relative location. We functionally examined, among the genes that were preferentially expressed in proximal cells, three secreted or cell-surface molecules not previously connected to HSPC biology—the secreted RNase angiogenin, the cytokine IL18, and the adhesion molecule Embigin—and discovered that all of these factors are HSPC quiescence regulators. Therefore, our proximity-based differential single-cell approach reveals molecular heterogeneity within niche cells and can be used to identify novel extrinsic stem/progenitor cell regulators. Similar approaches could also be applied to other stem cell/niche pairs to advance the understanding of microenvironmental regulation of stem cell function.

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