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Single-cell gene expression signatures reveal melanoma cell heterogeneity

Oncogene volume 34, pages 3251–3263 (2015)Cite this article

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Abstract

It is well established that tumours are not homogenous, but comprise cells with differing invasive, proliferative and tumour-initiating potential. A major challenge in cancer research is therefore to develop methods to characterize cell heterogeneity. In melanoma, proliferative and invasive cells are characterized by distinct gene expression profiles and accumulating evidence suggests that cells can alternate between these states through a process called phenotype switching. We have used microfluidic technology to isolate single melanoma cells grown in vitro as monolayers or melanospheres or in vivo as xenografted tumours and analyse the expression profiles of 114 genes that discriminate the proliferative and invasive states by quantitative PCR. Single-cell analysis accurately recapitulates the specific gene expression programmes of melanoma cell lines and defines subpopulations with distinct expression profiles. Cell heterogeneity is augmented when cells are grown as spheres and as xenografted tumours. Correlative analysis identifies gene-regulatory networks and changes in gene expression under different growth conditions. In tumours, subpopulations of cells that express specific invasion and drug resistance markers can be identified amongst which is the pluripotency factor POUF51 (OCT4) whose expression correlates with the tumorigenic potential. We therefore show that single-cell analysis can be used to define and quantify tumour heterogeneity based on detection of cells with specific gene expression profiles.

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Acknowledgements

We thank D Dembélé for help with data analysis, all the staff of the IGBMC common facilities, as well as F Kardouz and the staff of the Strasbourg Hospital Dermatology Clinic, This work was supported by institutional grants from the Centre National de la Recherche Scientifique, the Institut National de Sante et de la Recherche Médicale, the Université de Strasbourg, the Association pour la Recherche contre le Cancer, the Ligue Nationale contre le Cancer, the Institut National du Cancer PAIR-melanoma grant, the ANR-10-LABX-0030-INRT French state fund through the Agence Nationale de la Recherche under the frame programme Investissements d’Avenir labelled ANR-10-IDEX-0002-02. The IGBMC high throughput sequencing facility is a member of the ‘France Génomique’ consortium (ANR10-INBS-09-08). ID is an ‘équipe labellisée’ of the Ligue Nationale contre le Cancer. ME was supported by a fellowship from the Ligue Nationale contre le Cancer.

Author Contributions

ID, ME and CK designed the experiments. ME, CK, CT-C developed methodologies and performed the experiments. CK and ME performed the bioinformatics and computational analyses. DL provided the human melanoma samples and analysed the images. ID, ME and CK wrote the paper.

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Authors and Affiliations

  1. Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France

    M Ennen, C Keime, D Kobi, G Mengus, D Lipsker, C Thibault-Carpentier & I Davidson

  2. Faculté de Médecine and Service de Dermatologie, Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France

    D Lipsker

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  1. M Ennen
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Correspondence to I Davidson.

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Supplementary Information accompanies this paper on the Oncogene website

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Ennen, M., Keime, C., Kobi, D. et al. Single-cell gene expression signatures reveal melanoma cell heterogeneity. Oncogene 34, 3251–3263 (2015). https://doi.org/10.1038/onc.2014.262

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