title: A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer.
abstract: BACKGROUND
  Cancer development is accompanied by genetic phenomena like deletion and amplification of chromosome parts or alterations of chromatin structure. It is expected that these mechanisms have a strong effect on regional gene expression.
  
  
  RESULTS
  We investigated genome-wide gene expression in colorectal carcinoma (CRC) and normal epithelial tissues from 25 patients using oligonucleotide arrays. This allowed us to identify 81 distinct chromosomal islands with aberrant gene expression. Of these, 38 islands show a gain in expression and 43 a loss of expression. In total, 7.892 genes (25.3% of all human genes) are located in aberrantly expressed islands. Many chromosomal regions that are linked to hereditary colorectal cancer show deregulated expression. Also, many known tumor genes localize to chromosomal islands of misregulated expression in CRC.
  
  
  CONCLUSIONS
  An extensive comparison with published CGH data suggests that chromosomal regions known for frequent deletions in colon cancer tend to show reduced expression. In contrast, regions that are often amplified in colorectal tumors exhibit heterogeneous expression patterns: even show a decrease of mRNA expression. Because for several islands of deregulated expression chromosomal aberrations have never been observed, we speculate that additional mechanisms (like abnormal states of regional chromatin) also have a substantial impact on the formation of co-expression islands in colorectal carcinoma.
authors.affiliation: Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany. eike.staub@nucleolus.net
authors.forename: Eike
authors.initials: E
authors.lastname: Staub
authors.forename: Jörn
authors.initials: J
authors.lastname: Gröne
authors.forename: Detlev
authors.initials: D
authors.lastname: Mennerich
authors.forename: Stefan
authors.initials: S
authors.lastname: Röpcke
authors.forename: Irina
authors.initials: I
authors.lastname: Klamann
authors.forename: Bernd
authors.initials: B
authors.lastname: Hinzmann
authors.forename: Esmeralda
authors.initials: E
authors.lastname: Castanos-Velez
authors.forename: Benno
authors.initials: B
authors.lastname: Mann
authors.forename: Christian
authors.initials: C
authors.lastname: Pilarsky
authors.forename: Thomas
authors.initials: T
authors.lastname: Brümmendorf
authors.forename: Birgit
authors.initials: B
authors.lastname: Weber
authors.forename: Heinz-Johannes
authors.initials: HJ
authors.lastname: Buhr
authors.forename: André
authors.initials: A
authors.lastname: Rosenthal
mesh_terms: D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D015179:Colorectal Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D012333:RNA, Messenger