title: Merging transcriptomics and metabolomics--advances in breast cancer profiling.
abstract: BACKGROUND
  Combining gene expression microarrays and high resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) of the same tissue samples enables comparison of the transcriptional and metabolic profiles of breast cancer. The aim of this study was to explore the potential of combining these two different types of information.
  
  
  METHODS
  Breast cancer tissue from 46 patients was analyzed by HR MAS MRS followed by gene expression microarrays. Two strategies were used to combine the gene expression and metabolic data; first using multivariate analyses to identify different groups based on gene expression and metabolic data; second correlating levels of specific metabolites to transcripts to suggest new hypotheses of connections between metabolite levels and the underlying biological processes. A parallel study was designed to address experimental issues of combining microarrays and HR MAS MRS.
  
  
  RESULTS
  In the first strategy, using the microarray data and previously reported molecular classification methods, the majority of samples were classified as luminal A. Three subgroups of luminal A tumors were identified based on hierarchical clustering of the HR MAS MR spectra. The samples in one of the subgroups, designated A2, showed significantly lower glucose and higher alanine levels than the other luminal A samples, suggesting a higher glycolytic activity in these tumors. This group was also enriched for genes annotated with Gene Ontology (GO) terms related to cell cycle and DNA repair. In the second strategy, the correlations between concentrations of myo-inositol, glycine, taurine, glycerophosphocholine, phosphocholine, choline and creatine and all transcripts in the filtered microarray data were investigated. GO-terms related to the extracellular matrix were enriched among the genes that correlated the most to myo-inositol and taurine, while cell cycle related GO-terms were enriched for the genes that correlated the most to choline. Additionally, a subset of transcripts was identified to have slightly altered expression after HR MAS MRS and was therefore removed from all other analyses.
  
  
  CONCLUSIONS
  Combining transcriptional and metabolic data from the same breast carcinoma sample is feasible and may contribute to a more refined subclassification of breast cancers as well as reveal relations between metabolic and transcriptional levels. See Commentary: http://www.biomedcentral.com/1741-7015/8/73.
authors.affiliation: Department of Genetics, Institute for Cancer Research, Division of Surgery and Cancer, Oslo University Hospital Radiumhospitalet, Oslo, Norway.
authors.forename: Eldrid
authors.initials: E
authors.lastname: Borgan
authors.forename: Beathe
authors.initials: B
authors.lastname: Sitter
authors.forename: Ole Christian
authors.initials: OC
authors.lastname: Lingjærde
authors.forename: Hilde
authors.initials: H
authors.lastname: Johnsen
authors.forename: Steinar
authors.initials: S
authors.lastname: Lundgren
authors.forename: Tone F
authors.initials: TF
authors.lastname: Bathen
authors.forename: Therese
authors.initials: T
authors.lastname: Sørlie
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
authors.forename: Ingrid S
authors.initials: IS
authors.lastname: Gribbestad
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000175:diagnosis / Q000378:metabolism*; D045744:Cell Line, Tumor; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D055432:Metabolomics / Q000379:methods*; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D014158:Transcription, Genetic