title: DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers.
abstract: OBJECTIVE
  About 15% of colorectal cancers harbor microsatellite instability (MSI). MSI-associated gene expression changes have been identified in colorectal cancers, but little overlap exists between signatures hindering an assessment of overall consistency. Little is known about the causes and downstream effects of differential gene expression.
  
  
  METHODS
  DNA microarray data on 89 MSI and 140 microsatellite-stable (MSS) colorectal cancers from this study and 58 MSI and 77 MSS cases from three published reports were randomly divided into test and training sets. MSI-associated gene expression changes were assessed for cross-study consistency using training samples and validated as MSI classifier using test samples. Differences in biological pathways were identified by functional category analysis. Causation of differential gene expression was investigated by comparison to DNA copy-number data.
  
  
  RESULTS
  MSI-associated gene expression changes in colorectal cancers were found to be highly consistent across multiple studies of primary tumors and cancer cell lines from patients of different ethnicities (P < 0.001). Clustering based on consistent changes separated additional test cases by MSI status, and classification of individual samples predicted MSI status with a sensitivity of 96% and specificity of 85%. Genes associated with immune response were up-regulated in MSI cancers, whereas genes associated with cell-cell adhesion, ion binding, and regulation of metabolism were down-regulated. Differential gene expression was shown to reflect systematic differences in DNA copy-number aberrations between MSI and MSS tumors (P < 0.001).
  
  
  CONCLUSIONS
  Our results show cross-study consistency of MSI-associated gene expression changes in colorectal cancers. DNA copy-number alterations partly cause the differences in gene expression between MSI and MSS cancers.
authors.affiliation: Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Parkville, Victoria, Australia.
authors.forename: Robert N
authors.initials: RN
authors.lastname: Jorissen
authors.forename: Lara
authors.initials: L
authors.lastname: Lipton
authors.forename: Peter
authors.initials: P
authors.lastname: Gibbs
authors.forename: Matthew
authors.initials: M
authors.lastname: Chapman
authors.forename: Jayesh
authors.initials: J
authors.lastname: Desai
authors.forename: Ian T
authors.initials: IT
authors.lastname: Jones
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Yeatman
authors.forename: Philip
authors.initials: P
authors.lastname: East
authors.forename: Ian P M
authors.initials: IP
authors.lastname: Tomlinson
authors.forename: Hein W
authors.initials: HW
authors.lastname: Verspaget
authors.forename: Lauri A
authors.initials: LA
authors.lastname: Aaltonen
authors.forename: Mogens
authors.initials: M
authors.lastname: Kruhøffer
authors.forename: Torben F
authors.initials: TF
authors.lastname: Orntoft
authors.forename: Claus Lindbjerg
authors.initials: CL
authors.lastname: Andersen
authors.forename: Oliver M
authors.initials: OM
authors.lastname: Sieber
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics*; D018628:Gene Dosage; D020869:Gene Expression Profiling; D006801:Humans; D053842:Microsatellite Instability; D008875:Middle Aged