Research Papers:
Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq
PDF | HTML | Supplementary Files | How to cite
Metrics: PDF 4766 views | HTML 6824 views | ?
Abstract
Tobias Gerber1,*, Edith Willscher2,*, Henry Loeffler-Wirth2, Lydia Hopp2, Dirk Schadendorf3, Manfred Schartl4,5,6, Ulf Anderegg7, Gray Camp1, Barbara Treutlein1, Hans Binder2, Manfred Kunz7
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
2Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
3Department of Dermatology, Venereology and Allergology, University Hospital Essen, 45147 Essen, Germany
4Department of Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany
5Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97080 Würzburg, Germany
6Institute for Advanced Study, 3572 Texas A&M University, College Station, Texas 77843-3572, USA
7Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
*These authors contributed equally to this work
Correspondence to:
Manfred Kunz, email: [email protected]
Keywords: melanoma, single cell transcriptome sequencing, stem cells
Received: May 18, 2016 Accepted: November 12, 2016 Published: November 26, 2016
ABSTRACT
Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. Gene expression modules had prognostic relevance when compared with gene expression data from published melanoma samples and patient survival data. We surveyed kinome expression patterns across sub-populations of the BRAF/NRAS wild type sample and found that CDK4 and CDK2 were consistently highly expressed in the majority of cells, suggesting that these kinases might be involved in melanoma progression. Treatment of cells with the CDK4 inhibitor palbociclib restricted cell proliferation to a similar, and in some cases greater, extent than MAPK inhibitors. Finally, we identified a low abundant sub-population in this sample that highly expressed a module containing ABC transporter ABCB5, surface markers CD271 and CD133, and multiple aldehyde dehydrogenases (ALDHs). Patient-derived cultures of the BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant metastases showed more homogeneous single-cell gene expression patterns with gene expression modules for proliferation and ABC transporters. Taken together, our results describe an intertumor and intratumor heterogeneity in melanoma short-term cultures which might be relevant for patient survival, and suggest promising targets for new treatment approaches in melanoma therapy.
All site content, except where otherwise noted, is licensed under a Creative Commons Attribution 4.0 License.
PII: 13666