title: Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.
abstract: BACKGROUND
  CYYR1 is a recently identified gene located on human chromosome 21 whose product has no similarity to any known protein and is of unknown function. Analysis of expressed sequence tags (ESTs) have revealed high human CYYR1 expression in cells belonging to the diffuse neuroendocrine system (DNES). These cells may be the origin of neuroendocrine (NE) tumors. The aim of this study was to conduct an initial analysis of sequence, splicing and expression of the CYYR1 mRNA in human NE tumors.
  
  
  METHODS
  The CYYR1 mRNA coding sequence (CDS) was studied in 32 NE tumors by RT-PCR and sequence analysis. A subtle alternative splicing was identified generating two isoforms of CYYR1 mRNA differing in terms of the absence (CAG- isoform, the first described mRNA for CYYR1 locus) or the presence (CAG+ isoform) of a CAG codon. When present, this specific codon determines the presence of an alanine residue, at the exon 3/exon 4 junction of the CYYR1 mRNA. The two mRNA isoform amounts were determined by quantitative relative RT-PCR in 29 NE tumors, 2 non-neuroendocrine tumors and 10 normal tissues. A bioinformatic analysis was performed to search for the existence of the two CYYR1 isoforms in other species.
  
  
  RESULTS
  The CYYR1 CDS did not show differences compared to the reference sequence in any of the samples, with the exception of an NE tumor arising in the neck region. Sequence analysis of this tumor identified a change in the CDS 333 position (T instead of C), leading to the amino acid mutation P111S. NE tumor samples showed no significant difference in either CYYR1 CAG- or CAG+ isoform expression compared to control tissues. CYYR1 CAG- isoform was significantly more expressed than CAG+ isoform in NE tumors as well as in control samples investigated. Bioinformatic analysis revealed that only the genomic sequence of Pan troglodytes CYYR1 is consistent with the possible existence of the two described mRNA isoforms.
  
  
  CONCLUSIONS
  A new "subtle" splicing isoform (CAG+) of CYYR1 mRNA, the sequence and the expression of this gene were defined in a large series of NE tumors.
authors: Department of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy. vitale@alma.unibo.it <vitale@alma.unibo.it>
authors: Lorenza
authors: L
authors: Vitale
authors: Flavia
authors: F
authors: Frabetti
authors: Shane A
authors: SA
authors: Huntsman
authors: Silvia
authors: S
authors: Canaider
authors: Raffaella
authors: R
authors: Casadei
authors: Luca
authors: L
authors: Lenzi
authors: Federica
authors: F
authors: Facchin
authors: Paolo
authors: P
authors: Carinci
authors: Maria
authors: M
authors: Zannotti
authors: Domenico
authors: D
authors: Coppola
authors: Pierluigi
authors: P
authors: Strippoli
mesh_terms: D000328:Adult; D000368:Aged; D000409:Alanine / Q000032:analysis; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D004067:Digestive System Neoplasms / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D008875:Middle Aged; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000235:genetics; D018358:Neuroendocrine Tumors / Q000235:genetics*; D002679:Pan troglodytes / Q000235:genetics; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017385:Sequence Homology; D013045:Species Specificity
chemical_list: C464455:CYYR1 protein, human; D003062:Codon; D008565:Membrane Proteins; D020033:Protein Isoforms; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D000409:Alanine