I have sequenced tens of single cells of bladder cancer, and got the gene expression profile of each single cell. I am trying to speculate the cancer stem cells mixed in these cells using clustering method, which needs a priori list of "stemness genes". If there are some available common or specific stemness signatures can be used in this analysis? Many thanks.
You can try looking for CD47, Oct/Sox etc.. However, I am not sure if you will find 'CSC' signature in 10 cells.. In general CSCs are 1-5% of total population therefore finding CSCs in 10 or for that matter 100 cells may be a challenging task..
Oct4, Sox2 are embryonic stem cell markers. Oct4 is not expressed in adult stem cells, contrary to many published reports. Also, the Jaenisch lab clearly showed that Oct4 is dispensable for all adult stem cells. Cancer stem cells are defined functionally, by their ability to transplant the tumor in isografts. I am not an expert here, but I don't think there is a stemness marker that defines all cancer stem cells, they are likely to be tissue and sub-type specific.
Surely Oct4, Nanog and Sox2 belong to the stem cell marker molecules expressed in ES cells, but you should choose molecules exclusively related to cancer stem-like cells. CD44 is expected to be a useful cancer stem cell marker whether or not bladder cancer cells are epithelial or mesenchymal.
Article Bladder Cancer Stem Cells: Biological and Therapeutic Perspectives
Thank you Go J Yoshida and Shi Lei. Actually I have sorted the "cancer stem-like cells" as CD44+ by FACS, as well as CD44- cancer cells and normal epithelial cells. But CD44 is just a marker to enrich CSCs. So I need a more comprehensive gene list to infer the more likely CSCs in these sorted cells.
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