title: Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis.
abstract: BACKGROUND
  Approximately half of all human genes use alternative transcription start sites (TSSs) to control mRNA levels and broaden the transcriptional output in healthy tissues. Aberrant expression patterns promoting carcinogenesis, however, may arise from alternative promoter usage.
  
  
  RESULTS
  By profiling 108 colorectal samples using exon arrays, we identified nine genes (TCF12, OSBPL1A, TRAK1, ANK3, CHEK1, UGP2, LMO7, ACSL5, and SCIN) showing tumor-specific alternative TSS usage in both adenoma and cancer samples relative to normal mucosa. Analysis of independent exon array data sets corroborated these findings. Additionally, we confirmed the observed patterns for selected mRNAs using quantitative real-time reverse-transcription PCR. Interestingly, for some of the genes, the tumor-specific TSS usage was not restricted to colorectal cancer. A comprehensive survey of the nine genes in lung, bladder, liver, prostate, gastric, and brain cancer revealed significantly altered mRNA isoform ratios for CHEK1, OSBPL1A, and TCF12 in a subset of these cancer types.To identify the mechanism responsible for the shift in alternative TSS usage, we antagonized the Wnt-signaling pathway in DLD1 and Ls174T colorectal cancer cell lines, which remarkably led to a shift in the preferred TSS for both OSBPL1A and TRAK1. This indicated a regulatory role of the Wnt pathway in selecting TSS, possibly also involving TP53 and SOX9, as their transcription binding sites were enriched in the promoters of the tumor preferred isoforms together with their mRNA levels being increased in tumor samples. Finally, to evaluate the prognostic impact of the altered TSS usage, immunohistochemistry was used to show deregulation of the total protein levels of both TCF12 and OSBPL1A, corresponding to the mRNA levels observed. Furthermore, the level of nuclear TCF12 had a significant correlation to progression free survival in a cohort of 248 stage II colorectal cancer samples.
  
  
  CONCLUSIONS
  Alternative TSS usage in colorectal adenoma and cancer samples has been shown for nine genes, and OSBPL1A and TRAK1 were found to be regulated in vitro by Wnt signaling. TCF12 protein expression was upregulated in cancer samples and correlated with progression free survival.
authors: Department of Molecular Medicine, Aarhus University Hospital, Skejby, 8200 Aarhus N, Denmark.
authors: Kasper
authors: K
authors: Thorsen
authors: Troels
authors: T
authors: Schepeler
authors: Bodil
authors: B
authors: Øster
authors: Mads H
authors: MH
authors: Rasmussen
authors: Søren
authors: S
authors: Vang
authors: Kai
authors: K
authors: Wang
authors: Kristian Q
authors: KQ
authors: Hansen
authors: Philippe
authors: P
authors: Lamy
authors: Jakob Skou
authors: JS
authors: Pedersen
authors: Asger
authors: A
authors: Eller
authors: Francisco
authors: F
authors: Mansilla
authors: Kirsti
authors: K
authors: Laurila
authors: Carsten
authors: C
authors: Wiuf
authors: Søren
authors: S
authors: Laurberg
authors: Lars
authors: L
authors: Dyrskjøt
authors: Torben F
authors: TF
authors: Ørntoft
authors: Claus L
authors: CL
authors: Andersen
mesh_terms: D033942:Adaptor Proteins, Vesicular Transport / Q000235:genetics / Q000378:metabolism; D017398:Alternative Splicing; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D000071877:Checkpoint Kinase 1; D015331:Cohort Studies; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D005091:Exons; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D011494:Protein Kinases / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D011987:Receptors, Steroid; D024363:Transcription Initiation Site; D060449:Wnt Signaling Pathway; D000098825:Oxysterol Binding Proteins
chemical_list: D033942:Adaptor Proteins, Vesicular Transport; D051792:Basic Helix-Loop-Helix Proteins; D002352:Carrier Proteins; D000071877:Checkpoint Kinase 1; D020033:Protein Isoforms; D011494:Protein Kinases; D012333:RNA, Messenger; D011987:Receptors, Steroid; D000098825:Oxysterol Binding Proteins; C531552:TRAK1 protein, human; C073366:TCF12 protein, human; C000605867:CHEK1 protein, human