title: The GALNT9, BNC1 and CCDC8 genes are frequently epigenetically dysregulated in breast tumours that metastasise to the brain.
abstract: BACKGROUND
  Tumour metastasis to the brain is a common and deadly development in certain cancers; 18-30 % of breast tumours metastasise to the brain. The contribution that gene silencing through epigenetic mechanisms plays in these metastatic tumours is not well understood.
  
  
  RESULTS
  We have carried out a bioinformatic screen of genome-wide breast tumour methylation data available at The Cancer Genome Atlas (TCGA) and a broad literature review to identify candidate genes that may contribute to breast to brain metastasis (BBM). This analysis identified 82 candidates. We investigated the methylation status of these genes using Combined Bisulfite and Restriction Analysis (CoBRA) and identified 21 genes frequently methylated in BBM. We have identified three genes, GALNT9, CCDC8 and BNC1, that were frequently methylated (55, 73 and 71 %, respectively) and silenced in BBM and infrequently methylated in primary breast tumours. CCDC8 was commonly methylated in brain metastases and their associated primary tumours whereas GALNT9 and BNC1 were methylated and silenced only in brain metastases, but not in the associated primary breast tumours from individual patients. This suggests differing roles for these genes in the evolution of metastatic tumours; CCDC8 methylation occurs at an early stage of metastatic evolution whereas methylation of GANLT9 and BNC1 occurs at a later stage of tumour evolution. Knockdown of these genes by RNAi resulted in a significant increase in the migratory and invasive potential of breast cancer cell lines.
  
  
  CONCLUSIONS
  These findings indicate that GALNT9 (an initiator of O-glycosylation), CCDC8 (a regulator of microtubule dynamics) and BNC1 (a transcription factor with a broad range of targets) may play a role in the progression of primary breast tumours to brain metastases. These genes may be useful as prognostic markers and their products may provide novel therapeutic targets.
authors.affiliation: Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Rajendra P
authors.initials: RP
authors.lastname: Pangeni
authors.affiliation: Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Prasanna
authors.initials: P
authors.lastname: Channathodiyil
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: David S
authors.initials: DS
authors.lastname: Huen
authors.affiliation: Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Lawrence W
authors.initials: LW
authors.lastname: Eagles
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Balraj K
authors.initials: BK
authors.lastname: Johal
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Dawar
authors.initials: D
authors.lastname: Pasha
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Natasa
authors.initials: N
authors.lastname: Hadjistephanou
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Oliver
authors.initials: O
authors.lastname: Nevell
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Claire L
authors.initials: CL
authors.lastname: Davies
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Ayobami I
authors.initials: AI
authors.lastname: Adewumi
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Hamida
authors.initials: H
authors.lastname: Khanom
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Ikroop S
authors.initials: IS
authors.lastname: Samra
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Vanessa C
authors.initials: VC
authors.lastname: Buzatto
authors.affiliation: School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Preethi
authors.initials: P
authors.lastname: Chandrasekaran
authors.affiliation: Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK.
authors.forename: Thoraia
authors.initials: T
authors.lastname: Shinawi
authors.affiliation: Department of Neurosciences, Lancashire Teaching Hospitals NHS Foundation Trust, Royal Preston Hospital, Fulwood, Preston, UK.
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Dawson
authors.affiliation: Department of Neurosciences, Lancashire Teaching Hospitals NHS Foundation Trust, Royal Preston Hospital, Fulwood, Preston, UK.
authors.forename: Katherine M
authors.initials: KM
authors.lastname: Ashton
authors.affiliation: Department of Neurosciences, Lancashire Teaching Hospitals NHS Foundation Trust, Royal Preston Hospital, Fulwood, Preston, UK.
authors.forename: Charles
authors.initials: C
authors.lastname: Davis
authors.affiliation: The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Brodbelt
authors.affiliation: The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool, UK.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Jenkinson
authors.affiliation: Department of Genetics, Institute Curie, Paris, France.
authors.forename: Ivan
authors.initials: I
authors.lastname: Bièche
authors.affiliation: Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK.
authors.forename: Farida
authors.initials: F
authors.lastname: Latif
authors.affiliation: Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK.
authors.forename: John L
authors.initials: JL
authors.lastname: Darling
authors.affiliation: Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK.
authors.forename: Tracy J
authors.initials: TJ
authors.lastname: Warr
authors.affiliation: Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK ; School of Biology, Chemistry and Forensic Sciences, University of Wolverhampton, Wolverhampton, UK ; Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Morris
keywords: Brain; Breast; DNA methylation; Epigenetic; Metastasis; Tumour suppressor