TY - JOUR
T1 - Single-molecule transcript counting of stem-cell markers in the mouse intestine
AU - Itzkovitz, Shalev
AU - Lyubimova, Anna
AU - Blat, Irene C.
AU - Maynard, Mindy
AU - Van Es, Johan
AU - Lees, Jacqueline
AU - Jacks, Tyler
AU - Clevers, Hans
AU - Van Oudenaarden, Alexander
N1 - Funding Information:
The authors would like to thank H. Youk, S. Semrau, S. Klemm and K. Hilgendorf for comments on the manuscript, and X. Wu, Z. Peng Fan and A. Yang for help with the cell segmentation software. This work was supported by the National Institutes of Health (NIH)/National Cancer Institute Physical Sciences Oncology Center at MIT (U54CA143874) and an NIH Pioneer award (1DP1OD003936) to A.v.O., and in part by Cancer Center Support (core) grant P30-CA14051 from the National Cancer Institute. S.I. acknowledges support from a European Molecular Biology Organization postdoctoral fellowship, the International Human Frontiers Science Program Organization and the Machiah Foundation. I.C.B. acknowledges support from the Howard Hughes Medical Institute Gilliam fellowship. T.J. is the D. H. Koch Professor of Biology and a D. K. Ludwig Scholar.
PY - 2012/1
Y1 - 2012/1
N2 - Determining the molecular identities of adult stem cells requires technologies for sensitive transcript detection in tissues. In mouse intestinal crypts, lineage-tracing studies indicated that different genes uniquely mark spatially distinct stem-cell populations, residing either at crypt bases or at position +4, but a detailed analysis of their spatial co-expression has not been feasible. Here we apply three-colour single-molecule fluorescent in situ hybridization to study a comprehensive panel of intestinal stem-cell markers during homeostasis, ageing and regeneration. We find that the expression of all markers overlaps at crypt-base cells. This co-expression includes Lgr5, Bmi1 and mTert, genes previously suggested to mark distinct stem cells. Strikingly, Dcamkl1 tuft cells, distributed throughout the crypt axis, co-express Lgr5 and other stem-cell markers that are otherwise confined to crypt bases. We also detect significant changes in the expression of some of the markers following irradiation, indicating their potential role in the regeneration process. Our approach can enable the sensitive detection of putative stem cells in other tissues and in tumours, guiding complementary functional studies to evaluate their stem-cell properties.
AB - Determining the molecular identities of adult stem cells requires technologies for sensitive transcript detection in tissues. In mouse intestinal crypts, lineage-tracing studies indicated that different genes uniquely mark spatially distinct stem-cell populations, residing either at crypt bases or at position +4, but a detailed analysis of their spatial co-expression has not been feasible. Here we apply three-colour single-molecule fluorescent in situ hybridization to study a comprehensive panel of intestinal stem-cell markers during homeostasis, ageing and regeneration. We find that the expression of all markers overlaps at crypt-base cells. This co-expression includes Lgr5, Bmi1 and mTert, genes previously suggested to mark distinct stem cells. Strikingly, Dcamkl1 tuft cells, distributed throughout the crypt axis, co-express Lgr5 and other stem-cell markers that are otherwise confined to crypt bases. We also detect significant changes in the expression of some of the markers following irradiation, indicating their potential role in the regeneration process. Our approach can enable the sensitive detection of putative stem cells in other tissues and in tumours, guiding complementary functional studies to evaluate their stem-cell properties.
UR - http://www.scopus.com/inward/record.url?scp=84355162740&partnerID=8YFLogxK
U2 - 10.1038/ncb2384
DO - 10.1038/ncb2384
M3 - Article
C2 - 22119784
AN - SCOPUS:84355162740
SN - 1465-7392
VL - 14
SP - 106
EP - 114
JO - Nature Cell Biology
JF - Nature Cell Biology
IS - 1
ER -