Discretization of Gene Expression Data Unmasks Molecular Subgroups Recurring in Different Human Cancer Types

PLoS One. 2016 Aug 18;11(8):e0161514. doi: 10.1371/journal.pone.0161514. eCollection 2016.

Abstract

Despite the individually different molecular alterations in tumors, the malignancy associated biological traits are strikingly similar. Results of a previous study using renal cell carcinoma (RCC) as a model pointed towards cancer-related features, which could be visualized as three groups by microarray based gene expression analysis. In this study, we used a mathematic model to verify the presence of these groups in RCC as well as in other cancer types. We developed an algorithm for gene-expression deviation profiling for analyzing gene expression data of a total of 8397 patients with 13 different cancer types and normal tissues. We revealed three common Cancer Transcriptomic Profiles (CTPs) which recurred in all investigated tumors. Additionally, CTPs remained robust regardless of the functions or numbers of genes analyzed. CTPs may represent common genetic fingerprints, which potentially reflect the closely related biological traits of human cancers.

MeSH terms

  • Algorithms
  • Carcinoma, Renal Cell / classification
  • Carcinoma, Renal Cell / genetics
  • Carcinoma, Renal Cell / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic / genetics*
  • Genes, Neoplasm / genetics
  • Genome-Wide Association Study
  • Humans
  • Kidney Neoplasms / classification
  • Kidney Neoplasms / genetics
  • Kidney Neoplasms / metabolism
  • Models, Theoretical
  • Neoplasms / classification
  • Neoplasms / genetics*
  • Neoplasms / metabolism
  • Oligonucleotide Array Sequence Analysis

Grant support

Authors MB, RS, ME, RG, CM, KH are employed by the Qlaym Healthcare AG. The specific roles of individual authors are articulated in the "author contributions" section. The funders provided support in the form of salaries but did not have any additional role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This project was also sponsored by a grant of the Swiss National Science Foundation (grant number: 3238BO-10314) to HM. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.