title: DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up.
abstract: BACKGROUND
  DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study.
  
  
  METHODS
  Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes. Correlations between these genomic and transcriptomic changes and their associations with clinical and histopathological parameters were assessed with the aim to identify molecular signatures associated with disease-free survival of the CRC patients during a 10 year follow-up.
  
  
  RESULTS
  DNA copy number gains were frequently detected in chromosomes 7, 8q, 13, 19, 20q and X, whereas DNA copy number losses were frequently detected in chromosomes 1p, 4, 8p, 15, 17p, 18, 19 and 22q. None of these alterations were observed in all samples. In addition, we found that 2,498 genes were up- and that 1,094 genes were down-regulated in the tumor samples compared to their corresponding normal mucosa (p < 0.01). The expression of 65 genes was found to be significantly associated with prognosis (p < 0.01). Specifically, we found that up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, were strongly associated with a poor survival. Subsequent integrated analyses revealed that increased expression levels of the MMP9, BMP7, UBE2C, I-CAM, NOTCH3, NOTCH1, PTGES2, HMGB1 and ERBB3 genes were associated with copy number gains, whereas decreased expression levels of the MUC1, E2F2, HRAS and SIRT3 genes were associated with copy number losses. Pathways related to cell cycle progression, eicosanoid metabolism, and TGF-β and apoptosis signaling, were found to be most significantly affected.
  
  
  CONCLUSIONS
  Our results suggest that CNAs in CRC tumor tissues are associated with concomitant changes in the expression of cancer-related genes. In other genes epigenetic mechanism may be at work. Up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, appear to be associated with a poor survival. These alterations may, in addition to Dukes' staging, be employed as new prognostic biomarkers for the prediction of clinical outcome in CRC patients.
authors.affiliation: Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini 6, 50139, Florence, Italy. elisabetta.bigagli@unifi.it.
authors.forename: Elisabetta
authors.identifier: http://orcid.org/0000-0003-1892-4343
authors.initials: E
authors.lastname: Bigagli
authors.affiliation: Institute of Biometeorology (IBIMET), National Research Council (CNR), Florence, Italy.
authors.forename: Carlotta
authors.initials: C
authors.lastname: De Filippo
authors.affiliation: Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini 6, 50139, Florence, Italy.
authors.forename: Cinzia
authors.initials: C
authors.lastname: Castagnini
authors.affiliation: ISTAT, Rome, Italy.
authors.forename: Simona
authors.initials: S
authors.lastname: Toti
authors.affiliation: Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre-CNIO, Madrid, Spain.
authors.forename: Francesco
authors.initials: F
authors.lastname: Acquadro
authors.affiliation: Department of Surgery and Translational Medicine, University of Florence, Florence, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Giudici
authors.affiliation: Department of Surgery and Translational Medicine, University of Florence, Florence, Italy.
authors.forename: Marilena
authors.initials: M
authors.lastname: Fazi
authors.affiliation: Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini 6, 50139, Florence, Italy.
authors.forename: Piero
authors.initials: P
authors.lastname: Dolara
authors.affiliation: Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Messerini
authors.affiliation: Department of Surgery and Translational Medicine, University of Florence, Florence, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Tonelli
authors.affiliation: Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini 6, 50139, Florence, Italy.
authors.forename: Cristina
authors.initials: C
authors.lastname: Luceri
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000401:mortality; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations / Q000235:genetics*; D018572:Disease-Free Survival; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008875:Middle Aged; D000089762:Multidrug Resistance-Associated Protein 2; D020411:Oligonucleotide Array Sequence Analysis; D059467:Transcriptome / Q000235:genetics*
keywords: Colorectal cancer; Comparative genomic hybridization (CGH); DNA copy number alterations; Disease-free survival; Gene expression alterations