Literature DB >> 24406433

Reconciliation of classification systems defining molecular subtypes of colorectal cancer: interrelationships and clinical implications.

Anguraj Sadanandam1, Xin Wang2, Felipe de Sousa E Melo3, Joe W Gray4, Louis Vermeulen5, Douglas Hanahan6, Jan Paul Medema3.   

Abstract

Recently we published two independent studies describing novel gene expression-based classifications of colorectal cancer (CRC). Notably, each study stratified CRC into a different number of subtypes: one reported 3 subtypes, whereas the second highlighted 5. Given that each ascribed clinical significance, distinctive biology, and therapeutic prognosis to the different subtypes, we sought to reconcile this apparent incongruity in subtype stratification of CRC, and to interrelate the results. To do so, we each evaluated the other's data sets and analytical methods and discovered that the subtypes and their classifiers are, in fact, clearly related to each other; indeed, the 5 subtype outcomes can be coalesced into the same three. In addition to presenting this clarification, we briefly discuss how both classification methods can be viewed within the broader literature on CRC subtypes, and potentially applied.

Entities:  

Keywords:  CIMP; MSI; cancer subtypes; cetuximab; colorectal cancer; consensus clustering; serrated pathway; therapy resistance

Mesh:

Year:  2014        PMID: 24406433      PMCID: PMC3956531          DOI: 10.4161/cc.27769

Source DB:  PubMed          Journal:  Cell Cycle        ISSN: 1551-4005            Impact factor:   4.534


  12 in total

Review 1.  Microsatellite instability in colorectal cancer.

Authors:  C Richard Boland; Ajay Goel
Journal:  Gastroenterology       Date:  2010-06       Impact factor: 22.682

2.  Adjusting batch effects in microarray expression data using empirical Bayes methods.

Authors:  W Evan Johnson; Cheng Li; Ariel Rabinovic
Journal:  Biostatistics       Date:  2006-04-21       Impact factor: 5.899

Review 3.  Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?

Authors:  Christos Sotiriou; Martine J Piccart
Journal:  Nat Rev Cancer       Date:  2007-07       Impact factor: 60.716

4.  Frozen robust multiarray analysis (fRMA).

Authors:  Matthew N McCall; Benjamin M Bolstad; Rafael A Irizarry
Journal:  Biostatistics       Date:  2010-01-22       Impact factor: 5.899

5.  The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse.

Authors:  Anna Merlos-Suárez; Francisco M Barriga; Peter Jung; Mar Iglesias; María Virtudes Céspedes; David Rossell; Marta Sevillano; Xavier Hernando-Momblona; Victoria da Silva-Diz; Purificación Muñoz; Hans Clevers; Elena Sancho; Ramón Mangues; Eduard Batlle
Journal:  Cell Stem Cell       Date:  2011-03-17       Impact factor: 24.633

6.  KRAS wild-type state predicts survival and is associated to early radiological response in metastatic colorectal cancer treated with cetuximab.

Authors:  W De Roock; H Piessevaux; J De Schutter; M Janssens; G De Hertogh; N Personeni; B Biesmans; J-L Van Laethem; M Peeters; Y Humblet; E Van Cutsem; S Tejpar
Journal:  Ann Oncol       Date:  2007-11-12       Impact factor: 32.976

7.  A colorectal cancer classification system that associates cellular phenotype and responses to therapy.

Authors:  Anguraj Sadanandam; Costas A Lyssiotis; Krisztian Homicsko; Eric A Collisson; William J Gibb; Stephan Wullschleger; Liliane C Gonzalez Ostos; William A Lannon; Carsten Grotzinger; Maguy Del Rio; Benoit Lhermitte; Adam B Olshen; Bertram Wiedenmann; Lewis C Cantley; Joe W Gray; Douglas Hanahan
Journal:  Nat Med       Date:  2013-04-14       Impact factor: 53.440

8.  Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions.

Authors:  Felipe De Sousa E Melo; Xin Wang; Marnix Jansen; Evelyn Fessler; Anne Trinh; Laura P M H de Rooij; Joan H de Jong; Onno J de Boer; Ronald van Leersum; Maarten F Bijlsma; Hans Rodermond; Maartje van der Heijden; Carel J M van Noesel; Jurriaan B Tuynman; Evelien Dekker; Florian Markowetz; Jan Paul Medema; Louis Vermeulen
Journal:  Nat Med       Date:  2013-04-14       Impact factor: 53.440

9.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

10.  Expression of epiregulin and amphiregulin and K-ras mutation status predict disease control in metastatic colorectal cancer patients treated with cetuximab.

Authors:  Shirin Khambata-Ford; Christopher R Garrett; Neal J Meropol; Mark Basik; Christopher T Harbison; Shujian Wu; Tai W Wong; Xin Huang; Chris H Takimoto; Andrew K Godwin; Benjamin R Tan; Smitha S Krishnamurthi; Howard A Burris; Elizabeth A Poplin; Manuel Hidalgo; Jose Baselga; Edwin A Clark; David J Mauro
Journal:  J Clin Oncol       Date:  2007-08-01       Impact factor: 44.544

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  29 in total

Review 1.  Colorectal cancer: genetic abnormalities, tumor progression, tumor heterogeneity, clonal evolution and tumor-initiating cells.

Authors:  Ugo Testa; Elvira Pelosi; Germana Castelli
Journal:  Med Sci (Basel)       Date:  2018-04-13

2.  Clinical Outcome From Oxaliplatin Treatment in Stage II/III Colon Cancer According to Intrinsic Subtypes: Secondary Analysis of NSABP C-07/NRG Oncology Randomized Clinical Trial.

Authors:  Nan Song; Katherine L Pogue-Geile; Patrick G Gavin; Greg Yothers; S Rim Kim; Nicole L Johnson; Corey Lipchik; Carmen J Allegra; Nicholas J Petrelli; Michael J O'Connell; Norman Wolmark; Soonmyung Paik
Journal:  JAMA Oncol       Date:  2016-09-01       Impact factor: 31.777

3.  Reply to Colorectal cancer classification based on gene expression is not associated with FOLFIRI response.

Authors:  Anguraj Sadanandam; Joe Gray; Douglas Hanahan
Journal:  Nat Med       Date:  2014-11       Impact factor: 53.440

4.  Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.

Authors:  Huipeng Li; Elise T Courtois; Debarka Sengupta; Yuliana Tan; Kok Hao Chen; Jolene Jie Lin Goh; Say Li Kong; Clarinda Chua; Lim Kiat Hon; Wah Siew Tan; Mark Wong; Paul Jongjoon Choi; Lawrence J K Wee; Axel M Hillmer; Iain Beehuat Tan; Paul Robson; Shyam Prabhakar
Journal:  Nat Genet       Date:  2017-03-20       Impact factor: 38.330

Review 5.  From tumour heterogeneity to advances in precision treatment of colorectal cancer.

Authors:  Cornelis J A Punt; Miriam Koopman; Louis Vermeulen
Journal:  Nat Rev Clin Oncol       Date:  2016-12-06       Impact factor: 66.675

Review 6.  Pathophysiological role of guanylate-binding proteins in gastrointestinal diseases.

Authors:  Nathalie Britzen-Laurent; Christian Herrmann; Elisabeth Naschberger; Roland S Croner; Michael Stürzl
Journal:  World J Gastroenterol       Date:  2016-07-28       Impact factor: 5.742

7.  Gene Copy Number and Post-Transductional Mechanisms Regulate TRAP1 Expression in Human Colorectal Carcinomas.

Authors:  Michele Pietrafesa; Francesca Maddalena; Luciana Possidente; Valentina Condelli; Pietro Zoppoli; Valeria Li Bergolis; Maria Grazia Rodriquenz; Michele Aieta; Giulia Vita; Franca Esposito; Matteo Landriscina
Journal:  Int J Mol Sci       Date:  2019-12-24       Impact factor: 5.923

8.  Collagen-rich stroma in aggressive colon tumors induces mesenchymal gene expression and tumor cell invasion.

Authors:  T T Vellinga; S den Uil; I H B Rinkes; D Marvin; B Ponsioen; A Alvarez-Varela; S Fatrai; C Scheele; D A Zwijnenburg; H Snippert; L Vermeulen; J P Medema; H B Stockmann; J Koster; R J A Fijneman; J de Rooij; O Kranenburg
Journal:  Oncogene       Date:  2016-03-21       Impact factor: 9.867

9.  Genes associated with metabolic syndrome predict disease-free survival in stage II colorectal cancer patients. A novel link between metabolic dysregulation and colorectal cancer.

Authors:  Teodoro Vargas; Juan Moreno-Rubio; Jesús Herranz; Paloma Cejas; Susana Molina; Margarita González-Vallinas; Ricardo Ramos; Emilio Burgos; Cristina Aguayo; Ana B Custodio; Guillermo Reglero; Jaime Feliu; Ana Ramírez de Molina
Journal:  Mol Oncol       Date:  2014-06-10       Impact factor: 6.603

Review 10.  Molecular subtyping of colorectal cancer: Recent progress, new challenges and emerging opportunities.

Authors:  Wei Wang; Raju Kandimalla; Hao Huang; Lina Zhu; Ying Li; Feng Gao; Ajay Goel; Xin Wang
Journal:  Semin Cancer Biol       Date:  2018-05-18       Impact factor: 15.707

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