Literature DB >> 33782565

Bridging the gap between cancer cell line models and tumours using gene expression data.

Javad Noorbakhsh1, Francisca Vazquez1, James M McFarland2.   

Abstract

Cancer cell line models are a cornerstone of cancer research, yet our understanding of how well they represent the molecular features of patient tumours remains limited. Our recent work provides a computational approach to systematically compare large gene expression datasets to better understand which cell lines most closely resemble each tumour type, as well as identify potential gaps in our current cancer models.
© 2021. The Author(s), under exclusive licence to Cancer Research UK.

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Year:  2021        PMID: 33782565      PMCID: PMC8329170          DOI: 10.1038/s41416-021-01359-0

Source DB:  PubMed          Journal:  Br J Cancer        ISSN: 0007-0920            Impact factor:   7.640


  11 in total

Review 1.  From cell lines to living biosensors: new opportunities to prioritize cancer dependencies using ex vivo tumor cultures.

Authors:  Yuen-Yi Tseng; Jesse S Boehm
Journal:  Curr Opin Genet Dev       Date:  2019-03-28       Impact factor: 5.578

2.  Defining a Cancer Dependency Map.

Authors:  Aviad Tsherniak; Francisca Vazquez; Phil G Montgomery; Barbara A Weir; Gregory Kryukov; Glenn S Cowley; Stanley Gill; William F Harrington; Sasha Pantel; John M Krill-Burger; Robin M Meyers; Levi Ali; Amy Goodale; Yenarae Lee; Guozhi Jiang; Jessica Hsiao; William F J Gerath; Sara Howell; Erin Merkel; Mahmoud Ghandi; Levi A Garraway; David E Root; Todd R Golub; Jesse S Boehm; William C Hahn
Journal:  Cell       Date:  2017-07-27       Impact factor: 41.582

3.  CELLector: Genomics-Guided Selection of Cancer In Vitro Models.

Authors:  Hanna Najgebauer; Mi Yang; Hayley E Francies; Clare Pacini; Euan A Stronach; Mathew J Garnett; Julio Saez-Rodriguez; Francesco Iorio
Journal:  Cell Syst       Date:  2020-05-20       Impact factor: 10.304

4.  Next-generation characterization of the Cancer Cell Line Encyclopedia.

Authors:  Mahmoud Ghandi; Franklin W Huang; Judit Jané-Valbuena; Gregory V Kryukov; Christopher C Lo; E Robert McDonald; Jordi Barretina; Ellen T Gelfand; Craig M Bielski; Haoxin Li; Kevin Hu; Alexander Y Andreev-Drakhlin; Jaegil Kim; Julian M Hess; Brian J Haas; François Aguet; Barbara A Weir; Michael V Rothberg; Brenton R Paolella; Michael S Lawrence; Rehan Akbani; Yiling Lu; Hong L Tiv; Prafulla C Gokhale; Antoine de Weck; Ali Amin Mansour; Coyin Oh; Juliann Shih; Kevin Hadi; Yanay Rosen; Jonathan Bistline; Kavitha Venkatesan; Anupama Reddy; Dmitriy Sonkin; Manway Liu; Joseph Lehar; Joshua M Korn; Dale A Porter; Michael D Jones; Javad Golji; Giordano Caponigro; Jordan E Taylor; Caitlin M Dunning; Amanda L Creech; Allison C Warren; James M McFarland; Mahdi Zamanighomi; Audrey Kauffmann; Nicolas Stransky; Marcin Imielinski; Yosef E Maruvka; Andrew D Cherniack; Aviad Tsherniak; Francisca Vazquez; Jacob D Jaffe; Andrew A Lane; David M Weinstock; Cory M Johannessen; Michael P Morrissey; Frank Stegmeier; Robert Schlegel; William C Hahn; Gad Getz; Gordon B Mills; Jesse S Boehm; Todd R Golub; Levi A Garraway; William R Sellers
Journal:  Nature       Date:  2019-05-08       Impact factor: 49.962

5.  Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

Authors:  Laleh Haghverdi; Aaron T L Lun; Michael D Morgan; John C Marioni
Journal:  Nat Biotechnol       Date:  2018-04-02       Impact factor: 54.908

6.  Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling.

Authors:  Steven M Corsello; Rohith T Nagari; Ryan D Spangler; Jordan Rossen; Mustafa Kocak; Jordan G Bryan; Ranad Humeidi; David Peck; Xiaoyun Wu; Andrew A Tang; Vickie M Wang; Samantha A Bender; Evan Lemire; Rajiv Narayan; Philip Montgomery; Uri Ben-David; Colin W Garvie; Yejia Chen; Matthew G Rees; Nicholas J Lyons; James M McFarland; Bang T Wong; Li Wang; Nancy Dumont; Patrick J O'Hearn; Eric Stefan; John G Doench; Caitlin N Harrington; Heidi Greulich; Matthew Meyerson; Francisca Vazquez; Aravind Subramanian; Jennifer A Roth; Joshua A Bittker; Jesse S Boehm; Christopher C Mader; Aviad Tsherniak; Todd R Golub
Journal:  Nat Cancer       Date:  2020-01-20

7.  Exploring patterns enriched in a dataset with contrastive principal component analysis.

Authors:  Abubakar Abid; Martin J Zhang; Vivek K Bagaria; James Zou
Journal:  Nat Commun       Date:  2018-05-30       Impact factor: 14.919

8.  Global computational alignment of tumor and cell line transcriptional profiles.

Authors:  Allison Warren; Yejia Chen; Andrew Jones; Tsukasa Shibue; William C Hahn; Jesse S Boehm; Francisca Vazquez; Aviad Tsherniak; James M McFarland
Journal:  Nat Commun       Date:  2021-01-04       Impact factor: 14.919

9.  Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value.

Authors:  Laetitia Marisa; Aurélien de Reyniès; Alex Duval; Janick Selves; Marie Pierre Gaub; Laure Vescovo; Marie-Christine Etienne-Grimaldi; Renaud Schiappa; Dominique Guenot; Mira Ayadi; Sylvain Kirzin; Maurice Chazal; Jean-François Fléjou; Daniel Benchimol; Anne Berger; Arnaud Lagarde; Erwan Pencreach; Françoise Piard; Dominique Elias; Yann Parc; Sylviane Olschwang; Gérard Milano; Pierre Laurent-Puig; Valérie Boige
Journal:  PLoS Med       Date:  2013-05-21       Impact factor: 11.069

Review 10.  The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Authors:  Orit Rozenblatt-Rosen; Aviv Regev; Philipp Oberdoerffer; Tal Nawy; Anna Hupalowska; Jennifer E Rood; Orr Ashenberg; Ethan Cerami; Robert J Coffey; Emek Demir; Li Ding; Edward D Esplin; James M Ford; Jeremy Goecks; Sharmistha Ghosh; Joe W Gray; Justin Guinney; Sean E Hanlon; Shannon K Hughes; E Shelley Hwang; Christine A Iacobuzio-Donahue; Judit Jané-Valbuena; Bruce E Johnson; Ken S Lau; Tracy Lively; Sarah A Mazzilli; Dana Pe'er; Sandro Santagata; Alex K Shalek; Denis Schapiro; Michael P Snyder; Peter K Sorger; Avrum E Spira; Sudhir Srivastava; Kai Tan; Robert B West; Elizabeth H Williams
Journal:  Cell       Date:  2020-04-16       Impact factor: 66.850

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  1 in total

Review 1.  Immuno-oncology trends: preclinical models, biomarkers, and clinical development.

Authors:  Maryland Rosenfeld Franklin; Suso Platero; Kamal S Saini; Giuseppe Curigliano; Steven Anderson
Journal:  J Immunother Cancer       Date:  2022-01       Impact factor: 13.751

  1 in total

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