title: Analysis of SEMA6B gene expression in breast cancer: identification of a new isoform.
abstract: BACKGROUND
  SEMA6B is a member of the semaphorins axon-guidance family. A growing body of evidence has been accumulated describing the role of semaphorin molecules in cancer development and the involvement of SEMA6B in cancer progression has recently been proposed.
  
  
  METHODS
  Our analysis, based on real-time PCR, focused on the expression of SEMA6B in a panel of breast cancer tissues, compared to the normal counterpart.
  
  
  RESULTS
  In cancer tissues we found a significantly strong down-modulation of this transcript. Moreover we identified and characterized a novel SEMA6B isoform, named SEMA6Ba. This isoform has a novel splice junction, created by the usage of alternative donor and acceptor splice sites internal to the exon 17. By in silico analysis we found that the new transcript 3' UTR lacks some highly-conserved miRNA binding sites, suggesting possible consequences on both spatial and temporal expression of SEMA6Ba. The translated sequence of SEMA6Ba lacks the cytoplasmic tail, crucial for triggering the reverse signaling described for the transmembrane semaphorins. We also demonstrated, by immunofluorescence analysis of endogenous and overexpressed SEMA6Ba, that the protein clearly localized to the endoplasmic reticulum and plasma membrane. In conclusion, SEMA6B gene products are strongly down modulated in breast cancer tissues and a new isoform named SEMA6Ba has been described and characterized.
  
  
  CONCLUSIONS
  Our work states a clear relation among breast cancer and SEMA6B expression; moreover we describe for the first time the SEMA6Ba protein and report here the analysis of SEMA6Ba RNA messenger, the protein expression and the cellular localization.
authors.affiliation: Institute of Protein Biochemistry, National Council of Research, Naples, Italy. l.dapice@ibp.cnr.it
authors.forename: Luciana
authors.initials: L
authors.lastname: D'Apice
authors.forename: Valerio
authors.initials: V
authors.lastname: Costa
authors.forename: Carmen
authors.initials: C
authors.lastname: Valente
authors.forename: Maria
authors.initials: M
authors.lastname: Trovato
authors.forename: Anna
authors.initials: A
authors.lastname: Pagani
authors.forename: Stefania
authors.initials: S
authors.lastname: Manera
authors.forename: Lea
authors.initials: L
authors.lastname: Regolo
authors.forename: Alberto
authors.initials: A
authors.lastname: Zambelli
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ciccodicola
authors.forename: Piergiuseppe
authors.initials: P
authors.lastname: De Berardinis
mesh_terms: D020413:3' Untranslated Regions; D000595:Amino Acid Sequence; D000818:Animals; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D005260:Female; D006801:Humans; D008969:Molecular Sequence Data; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D039961:Semaphorins / Q000737:chemistry / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D020413:3' Untranslated Regions; D020033:Protein Isoforms; D012333:RNA, Messenger; C504081:SEMA6B protein, human; D039961:Semaphorins
keywords: Alternative splicing; Breast cancer; Semaphorin; Subcellular localization