Single cell technologies uncover molecular drivers of stem cell function

Novel technologies using single stem cells can now be used together to help define the molecules responsible for stem cell function, according to research from the University of Cambridge, published today in Cell Stem Cell.


Stem cells are essential for the maintenance and repair of all our organs, but they are exceedingly rare and do not look obviously different to other cells.  Stem cell function is typically evidenced by retrospective assays that demonstrate their activity but also destroy the original cell.  This prevents researchers from assessing directly the molecules operative in a stem cell compared to other cells, thereby hindering the development of protocols where stem cells are manipulated to produce clinically useful cells outside of the body.  In a study published today, Professor Bertie Gottgens and colleagues at the Cambridge University Department of Haematology, the Cambridge Institute for Medical Research and the Wellcome Trust/Medical Research Council Stem Cell Institute use for the first time a combination of single cell biology tools to define the molecular signature of functional blood stem cells.

The researchers isolated single cells from rare populations in the bone marrow that are enriched for blood stem cells, and subjected these cells to both single cell gene expression profiling and single cell transplantation assays.  Next, using advanced flow cytometry and computational biology approaches, they were able to define the genes present in single blood stem cells that were capable of creating a new blood system upon transplantation by comparing them to single cells that were unable to do so.  “Linking stem cell function with individual genes in single cells allows us to identify which genes are essential for a blood cell to function as a stem cell.  Such information has tremendous implications for our understanding of the entire blood system, and also how blood stem cell function could be enhanced to improve bone marrow transplantation for cancer patients”, says Nicola Wilson, one of the study’s lead authors. 

The new study is truly interdisciplinary, using many different single cell technologies, including genetic sequencing and single cell culture and transplantation models.  Integration and analysis of these complex datasets was made possible through the development of new computational analysis tools by co-author Dr Florian Buettner from the Helmholtz Institute in Munich. 

David Kent, another lead author, explains that “blood cancers are maintained by leukaemia stem cells, which share some properties with normal blood stem cells.  We are therefore very excited by the possibility that our approach may also, in future, allow us to define the stem cells that drive different classes of leukaemia and treat them specifically.” Professor Gottgens, who directed the study, adds “This work represents the cutting edge of single cell biology where we can finally nail down which molecules are operating in which cells and causing which outcome.  This has major implications for transplantation and cancer biology and provides a novel and powerful paradigm for other stem cell and cancer biologists to follow.”

Dr Matt Kaiser, Head of Research at Leukaemia & Lymphoma Research, said: “Understanding these critical master cells will be vital to improve treatment and deliver cures for many blood cancer patients. New targeted drug treatments can often miss these cells, meaning a complete cure is unlikely. A stem cell transplant can be a last or only resort for some blood cancer patients, but they are not always successful. These important findings could help refine these types of treatment, increasing their effectiveness and reducing harmful side-effects.” 

Work in the Gottgens Lab is supported by Leukaemia and Lymphoma Research; Cancer Research UK; the Kay Kendall Leukaemia Fund; the NIHR Cambridge Biomedical Research Centre; the Leukemia & Lymphoma Society of America; the UK Medical Research and Biotechnology and Biological Sciences Research Councils (MRC and BBSRC); and core support grants by the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute.


Wilson NK, Kent DG, and Buettner F, et al. Combined single cell functional and gene expression analysis resolves heterogeneity within stem cell populations. Cell Stem Cell. 2015

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