Single-cell gene expression signatures reveal melanoma cell heterogeneity

Oncogene

Volumn 34, Issue 25, 2015, Pages 3251-3263

  Ennen, M ^a   Keime, C ^a   Kobi, D ^a   Mengus, G ^a   Lipsker, D ^a,b   Thibault Carpentier, C ^a   Davidson, I ^a  

^a INSERM   (France)

^b HÔPITAL CIVIL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CELL HETEROGENEITY; CELL INVASION; CELL PROLIFERATION; CELL SUBPOPULATION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENE SWITCHING; HUMAN; HUMAN CELL; IN VITRO STUDY; MELANOMA; MICROFLUIDICS; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SINGLE CELL ANALYSIS; TUMOR XENOGRAFT; ANIMAL; CELL TRANSFORMATION; GENETICS; METABOLISM; PATHOLOGY; TUMOR CELL LINE;

MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR;

ANIMALS; CELL LINE, TUMOR; CELL TRANSFORMATION, NEOPLASTIC; GENE EXPRESSION PROFILING; HUMANS; MELANOMA; MICE; MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR; SINGLE-CELL ANALYSIS;

EID: 84931562619     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2014.262     Document Type: Article

References (31)

1. Meacham CE, Morrison SJ. Tumour heterogeneity and cancer cell plasticity. Nature 2013; 501: 328-337.
2. Nazarian R, Shi H, Wang Q, Kong X, Koya RC, Lee H et al. Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation. Nature 2010; 468: 973-977.
3. Somasundaram R, Villanueva J, Herlyn M. Intratumoral heterogeneity as a therapy resistance mechanism: role of melanoma subpopulations. Adv Pharmacol 2012; 65: 335-359.
4. Hoek KS, Goding CR. Cancer stem cells versus phenotype-switching in melanoma. Pigment Cell Melanoma Res 2010; 23: 746-759.
5. Quintana E, Shackleton M, Foster HR, Fullen DR, Sabel MS, Johnson TM et al. Phenotypic heterogeneity among tumorigenic melanoma cells from patients that is reversible and not hierarchically organized. Cancer Cell 2010; 18: 510-523.
6. Hoek KS, Eichhoff OM, Schlegel NC, Dobbeling U, Kobert N, Schaerer L et al. In vivo switching of human melanoma cells between proliferative and invasive states. Cancer Res 2008; 68: 650-656.
7. Widmer DS, Cheng PF, Eichhoff OM, Belloni BC, Zipser MC, Schlegel NC et al. Systematic classification of melanoma cells by phenotype-specific gene expression mapping. Pigment Cell Melanoma Res 2012; 25: 343-353.
8. Goodall J, Carreira S, Denat L, Kobi D, Davidson I, Nuciforo P et al. Brn-2 represses microphthalmia-associated transcription factor expression and marks a distinct subpopulation of microphthalmia-associated transcription factor-negative melanoma cells. Cancer Res 2008; 68: 7788-7794.
9. Javelaud D, Alexaki VI, Pierrat MJ, Hoek KS, Dennler S, Van Kempen L et al. GLI2 and M-MITF transcription factors control exclusive gene expression programs and inversely regulate invasion in human melanoma cells. Pigment Cell Melanoma Res 2011; 24: 932-943.
10. Cheli Y, Guiliano S, Botton T, Rocchi S, Hofman V, Hofman P et al. Mitf is the key molecular switch between mouse or human melanoma initiating cells and their differentiated progeny. Oncogene 2011; 30: 2307-2318.
11. Ohanna M, Cheli Y, Bonet C, Bonazzi VF, Allegra M, Giuliano S et al. Secretome from senescent melanoma engages the STAT3 pathway to favor reprogramming of naive melanoma towards a tumor-initiating cell phenotype. Oncotarget 2013; 4: 2212-2224.
12. Chen KG, Valencia JC, Gillet JP, Hearing VJ, Gottesman MM. Involvement of ABC transporters in melanogenesis and the development of multidrug resistance of melanoma. Pigment Cell Melanoma Res 2009; 22: 740-749.
13. Perego M, Tortoreto M, Tragni G, Mariani L, Deho P, Carbone A et al. Heterogeneous phenotype of human melanoma cells with in vitro and in vivo features of tumor-initiating cells. J Invest Dermatol 2010; 130: 1877-1886.
14. Thurber AE, Douglas G, Sturm EC, Zabierowski SE, Smit DJ, Ramakrishnan SN et al. Inverse expression states of the BRN2 and MITF transcription factors in melanoma spheres and tumour xenografts regulate the NOTCH pathway. Oncogene 2011; 30: 3036-3048.
15. Strub T, Giuliano S, Ye T, Bonet C, Keime C, Kobi D et al. Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. Oncogene 2011; 30: 2319-2332.
16. Kobi D, Steunou AL, Dembele D, Legras S, Larue L, Nieto L et al. Genome-wide analysis of POU3F2/BRN2 promoter occupancy in human melanoma cells reveals Kitl as a novel regulated target gene. Pigment Cell Melanoma Res 2010; 23: 404-418.
17. Thies A, Moll I, Berger J, Wagener C, Brummer J, Schulze HJ et al. CEACAM1 expression in cutaneous malignant melanoma predicts the development of metastatic disease. J Clin Oncol 2002; 20: 2530-2536.
18. Caramel J, Papadogeorgakis E, Hill L, Browne GJ, Richard G, Wierinckx A et al. A switch in the expression of embryonic EMT-inducers drives the development of malignant melanoma. Cancer Cell 2013; 24: 466-480.
19. Chiaverini C, Beuret L, Flori E, Busca R, Abbe P, Bille K et al. Microphthalmiaassociated transcription factor regulates RAB27A gene expression and controls melanosome transport. J Biol Chem 2008; 283: 12635-12642.
20. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 2011; 29: 1120-1127.
21. Castro FV, Al-Muftah M, Mulryan K, Jiang HR, Drijfhout JW, Ali S et al. Regulation of autologous immunity to the mouse 5T4 oncofoetal antigen: implications for immunotherapy. Cancer Immunol Immunother 2012; 61: 1005-1018.
22. Perez-Lorenzo R, Gill KZ, Shen CH, Zhao FX, Zheng B, Schulze HJ et al. A tumor suppressor function for the lipid phosphatase INPP4B in melanocytic neoplasms. J Invest Dermatol 2013; 134: 1359-1368.
23. Liu S, Ren S, Howell P, Fodstad O, Riker AI. Identification of novel epigenetically modified genes in human melanoma via promoter methylation gene profiling. Pigment Cell Melanoma Res 2008; 21: 545-558.
24. Carreira S, Goodall J, Denat L, Rodriguez M, Nuciforo P, Hoek KS et al. Mitf regulation of Dia1 controls melanoma proliferation and invasiveness. Genes Dev 2006; 20: 3426-3439.
25. Haass NK, Beaumont KA, Hill DS, Anfosso A, Mrass P, Munoz MA et al. Real-time cell cycle imaging during melanoma growth, invasion, and drug response. Pigment Cell Melanoma Res (e-pub ahead of print 5 June 2014; doi:10.1111/pcmr.12274).
26. McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS et al. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics 2013; 29: 461-467.
27. Herquel B, Ouararhni K, Martianov I, Le Gras S, Ye T, Keime C et al. Trim24- repressed VL30 retrotransposons regulate gene expression by producing noncoding RNA. Nat Struct Mol Biol 2013; 20: 339-346.
28. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105-1111.
29. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.
30. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010; 11: R106.
31. Denecker G, Vandamme N, Akay O, Koludrovic D, Taminau J, Lemeire K et al. Identification of a ZEB2-MITF-ZEB1 transcriptional network that controls melanogenesis and melanoma progression. Cell Death Differ 2014; 21: 1250-1261.