title: Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators.
abstract: 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.
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Lev
authors.initials: L
authors.lastname: Silberstein
authors.affiliation: Graduate Program in Cellular and Molecular Physiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA; Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA.
authors.forename: Kevin A
authors.initials: KA
authors.lastname: Goncalves
authors.affiliation: Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.affiliation: Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02445, USA.
authors.forename: Raphael
authors.initials: R
authors.lastname: Turcotte
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Youmna
authors.initials: Y
authors.lastname: Kfoury
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Francois
authors.initials: F
authors.lastname: Mercier
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Ninib
authors.initials: N
authors.lastname: Baryawno
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Severe
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Bachand
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Joel A
authors.initials: JA
authors.lastname: Spencer
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Ani
authors.initials: A
authors.lastname: Papazian
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Dongjun
authors.initials: D
authors.lastname: Lee
authors.affiliation: Indiana University, Indianapolis, IN 46202, USA.
authors.forename: Brahmananda Reddy
authors.initials: BR
authors.lastname: Chitteti
authors.affiliation: Indiana University, Indianapolis, IN 46202, USA.
authors.forename: Edward F
authors.initials: EF
authors.lastname: Srour
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hoggatt
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Tiffany
authors.initials: T
authors.lastname: Tate
authors.affiliation: Imperial College London, London SW7 2AZ, UK.
authors.forename: Cristina
authors.initials: C
authors.lastname: Lo Celso
authors.affiliation: School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Noriaki
authors.initials: N
authors.lastname: Ono
authors.affiliation: Walter and Eliza Hall Research Institute, Parkville, VIC 3052, Australia.
authors.forename: Stephen
authors.initials: S
authors.lastname: Nutt
authors.affiliation: University of Turku, Turku 20014, Finland.
authors.forename: Jyrki
authors.initials: J
authors.lastname: Heino
authors.affiliation: University of Turku, Turku 20014, Finland.
authors.forename: Kalle
authors.initials: K
authors.lastname: Sipilä
authors.affiliation: Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Shioda
authors.affiliation: Gifu University, Gifu 501-1193, Japan.
authors.forename: Masatake
authors.initials: M
authors.lastname: Osawa
authors.affiliation: Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02445, USA.
authors.forename: Charles P
authors.initials: CP
authors.lastname: Lin
authors.affiliation: Graduate Program in Cellular and Molecular Physiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA; Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA. Electronic address: guo-fu.hu@tufts.edu.
authors.forename: Guo-Fu
authors.initials: GF
authors.lastname: Hu
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02445, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: david_scadden@harvard.edu.
authors.forename: David T
authors.initials: DT
authors.lastname: Scadden
mesh_terms: D000818:Animals; D001854:Bone Marrow Cells / Q000166:cytology; D001842:Bone and Bones / Q000166:cytology; D019070:Cell Lineage / Q000235:genetics; D000066673:Cell Self Renewal / Q000235:genetics; D002469:Cell Separation; D017353:Gene Deletion; D020869:Gene Expression Profiling; D006412:Hematopoietic Stem Cells / Q000166:cytology* / Q000378:metabolism; D020382:Interleukin-18 / Q000378:metabolism; D008562:Membrane Glycoproteins / Q000378:metabolism; D012259:Ribonuclease, Pancreatic / Q000378:metabolism; D059010:Single-Cell Analysis / Q000379:methods*; D055153:Stem Cell Niche; D013997:Time Factors; D014158:Transcription, Genetic; D019010:Vascular Cell Adhesion Molecule-1 / Q000378:metabolism
chemical_list: D020382:Interleukin-18; D008562:Membrane Glycoproteins; D019010:Vascular Cell Adhesion Molecule-1; C046366:angiogenin; D012259:Ribonuclease, Pancreatic