New Functional Signatures for Understanding Melanoma Biology from Tumor Cell Lineage-Specific Analysis

被引:70
作者
Rambow, Florian [1 ,2 ,3 ,4 ]
Job, Bastien [5 ]
Petit, Valerie [1 ,2 ,3 ,4 ]
Gesbert, Franck [1 ,2 ,3 ,4 ]
Delmas, Veronique [1 ,2 ,3 ,4 ]
Seberg, Hannah [7 ]
Meurice, Guillaume [5 ]
Van Otterloo, Eric [7 ]
Dessen, Philippe [5 ]
Robert, Caroline [6 ]
Gautheret, Daniel [5 ]
Cornell, Robert A. [7 ]
Sarasin, Alain [8 ,9 ]
Larue, Lionel [1 ,2 ,3 ,4 ]
机构
[1] Inst Curie, Normal & Pathol Dev Melanocytes, F-91405 Orsay, France
[2] CNRS, UMR3347, F-91405 Orsay, France
[3] Univ Paris 11, INSERM, U1021, F-91405 Orsay, France
[4] Equipe Labellisee Ligue Natl Canc, F-91405 Orsay, France
[5] UMS AMMICA, Plateforme Bioinformat, F-94805 Villejuif, France
[6] Inst Gustave Roussy, INSERM, U981, F-94805 Villejuif, France
[7] Univ Iowa, Dept Anat & Cell Biol, Iowa City, IA 52242 USA
[8] CNRS, UMR8200, F-94805 Villejuif, France
[9] Univ Paris 11, F-94805 Villejuif, France
来源
CELL REPORTS | 2015年 / 13卷 / 04期
关键词
CANCER STEM-CELLS; TRANSCRIPTION FACTOR; GENE-EXPRESSION; NEURAL CREST; PHENOTYPE; PATHWAY; MITF; MICROPHTHALMIA; MECHANISMS; MODELS;
D O I
10.1016/j.celrep.2015.09.037
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Molecular signatures specific to particular tumor types are required to design treatments for resistant tumors. However, it remains unclear whether tumors and corresponding cell lines used for drug development share such signatures. We developed similarity core analysis (SCA), a universal and unsupervised computational framework for extracting core molecular features common to tumors and cell lines. We applied SCA to mRNA/miRNA expression data from various sources, comparing melanoma cell lines and metastases. The signature obtained was associated with phenotypic characteristics in vitro, and the core genes CAPN3 and TRIM63 were implicated in melanoma cell migration/invasion. About 90% of the melanoma signature genes belong to an intrinsic network of transcription factors governing neural development (TFAP2A, DLX2, ALX1, MITF, PAX3, SOX10, LEF1, and GAS7) and miRNAs (211-5p, 221-3p, and 10a-5p). The SCA signature effectively discriminated between two subpopulations of melanoma patients differing in overall survival, and classified MEKi/BRAFi-resistant and -sensitive melanoma cell lines.
引用
收藏
页码:840 / 853
页数:14
相关论文
共 58 条
  • [1] Mechanisms regulating GABAergic neuron development
    Achim, Kaia
    Salminen, Marjo
    Partanen, Juha
    [J]. CELLULAR AND MOLECULAR LIFE SCIENCES, 2014, 71 (08) : 1395 - 1415
  • [2] An Integrated Approach to Uncover Drivers of Cancer
    Akavia, Uri David
    Litvin, Oren
    Kim, Jessica
    Sanchez-Garcia, Felix
    Kotliar, Dylan
    Causton, Helen C.
    Pochanard, Panisa
    Mozes, Eyal
    Garraway, Levi A.
    Pe'er, Dana
    [J]. CELL, 2010, 143 (06) : 1005 - 1017
  • [3] RAB7 Controls Melanoma Progression by Exploiting a Lineage-Specific Wiring of the Endolysosomal Pathway
    Alonso-Curbelo, Direna
    Riveiro-Falkenbach, Erica
    Perez-Guijarro, Eva
    Cifdaloz, Metehan
    Karras, Panagiotis
    Osterloh, Lisa
    Megias, Diego
    Canon, Estela
    Calvo, Tonantzin G.
    Olmeda, David
    Gomez-Lopez, Gonzalo
    Grana, Osvaldo
    Sanchez-Arevalo Lobo, Victor Javier
    Pisano, David G.
    Wang, Hao-Wei
    Ortiz-Romero, Pablo
    Tormo, Damia
    Hoek, Keith
    Rodriguez-Peralto, Jose L.
    Joyce, Johanna A.
    Soengas, Maria S.
    [J]. CANCER CELL, 2014, 26 (01) : 61 - 76
  • [4] The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
    Barretina, Jordi
    Caponigro, Giordano
    Stransky, Nicolas
    Venkatesan, Kavitha
    Margolin, Adam A.
    Kim, Sungjoon
    Wilson, Christopher J.
    Lehar, Joseph
    Kryukov, Gregory V.
    Sonkin, Dmitriy
    Reddy, Anupama
    Liu, Manway
    Murray, Lauren
    Berger, Michael F.
    Monahan, John E.
    Morais, Paula
    Meltzer, Jodi
    Korejwa, Adam
    Jane-Valbuena, Judit
    Mapa, Felipa A.
    Thibault, Joseph
    Bric-Furlong, Eva
    Raman, Pichai
    Shipway, Aaron
    Engels, Ingo H.
    Cheng, Jill
    Yu, Guoying K.
    Yu, Jianjun
    Aspesi, Peter, Jr.
    de Silva, Melanie
    Jagtap, Kalpana
    Jones, Michael D.
    Wang, Li
    Hatton, Charles
    Palescandolo, Emanuele
    Gupta, Supriya
    Mahan, Scott
    Sougnez, Carrie
    Onofrio, Robert C.
    Liefeld, Ted
    MacConaill, Laura
    Winckler, Wendy
    Reich, Michael
    Li, Nanxin
    Mesirov, Jill P.
    Gabriel, Stacey B.
    Getz, Gad
    Ardlie, Kristin
    Chan, Vivien
    Myer, Vic E.
    [J]. NATURE, 2012, 483 (7391) : 603 - 607
  • [5] An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules
    Basu, Amrita
    Bodycombe, Nicole E.
    Cheah, Jaime H.
    Price, Edmund V.
    Liu, Ke
    Schaefer, Giannina I.
    Ebright, Richard Y.
    Stewart, Michelle L.
    Ito, Daisuke
    Wang, Stephanie
    Bracha, Abigail L.
    Liefeld, Ted
    Wawer, Mathias
    Gilbert, Joshua C.
    Wilson, Andrew J.
    Stransky, Nicolas
    Kryukov, Gregory V.
    Dancik, Vlado
    Barretina, Jordi
    Garraway, Levi A.
    Hon, C. Suk-Yee
    Munoz, Benito
    Bittker, Joshua A.
    Stockwell, Brent R.
    Khabele, Dineo
    Stern, Andrew M.
    Clemons, Paul A.
    Shamji, Alykhan F.
    Schreiber, Stuart L.
    [J]. CELL, 2013, 154 (05) : 1151 - 1161
  • [6] Transcription Factor/microRNA Axis Blocks Melanoma Invasion Program by miR-211 Targeting NUAK1
    Bell, Rachel E.
    Khaled, Mehdi
    Netanely, Dvir
    Schubert, Steffen
    Golan, Tamar
    Buxbaum, Amir
    Janas, Maja M.
    Postolsky, Benny
    Goldberg, Michael S.
    Shamir, Ron
    Levy, Carmit
    [J]. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 2014, 134 (02) : 441 - 451
  • [7] Genomic code for Sox10 activation reveals a key regulatory enhancer for cranial neural crest
    Betancur, Paola
    Bronner-Fraser, Marianne
    Sauka-Spengler, Tatjana
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (08) : 3570 - 3575
  • [8] Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival
    Bogunovic, Dusan
    O'Neill, David W.
    Belitskaya-Levy, Ilana
    Vacic, Vladimir
    Yu, Yi-Lo
    Adams, Sylvia
    Darvishian, Farbod
    Berman, Russell
    Shapiro, Richard
    Pavlick, Anna C.
    Lonardi, Stefano
    Zavadil, Jiri
    Osman, Iman
    Bhardwaj, Nina
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (48) : 20429 - 20434
  • [9] Mitf regulation of Dia1 controls melanoma proliferation and invasiveness
    Carreira, Suzanne
    Goodall, Jane
    Denat, Laurence
    Rodriguez, Mercedes
    Nuciforo, Paolo
    Hoek, Keith S.
    Testori, Alessandro
    Larue, Lionel
    Goding, Colin R.
    [J]. GENES & DEVELOPMENT, 2006, 20 (24) : 3426 - 3439
  • [10] Human gas7 isoforms homologous to mouse transcripts differentially induce neurite outgrowth
    Chao, CCK
    Chang, PY
    Lu, HHP
    [J]. JOURNAL OF NEUROSCIENCE RESEARCH, 2005, 81 (02) : 153 - 162