title: Fine-mapping loss of gene architecture at the CDKN2B (p15INK4b), CDKN2A (p14ARF, p16INK4a), and MTAP genes in head and neck squamous cell carcinoma.
abstract: OBJECTIVE
  To identify the extent and the smallest region of loss for CDKN2B(INK4b), CDKN2A(ARF,INK4a), and MTAP. Homozygous deletions of human chromosome 9p21 occur frequently in malignant cell lines and are common in squamous cell carcinoma of the head and neck (HNSCC). This complex region encodes the tumor suppressor genes cyclin-dependent kinase 2B (CDKN2B) (p15(INK4b)) and CDKN2A (p14(ARF), p16(INK4a)) and the housekeeping gene methylthioadenosine phosphorylase (MTAP).
  
  
  METHODS
  A targeted probe panel designed to finely map the region of 9p21 loss comprised 3 probes for CDKN2B(INK4b), 7 for CDKN2A(ARF, INK4a), and 3 for MTAP and was interrogated using the multiplex ligation-dependent probe amplification assay (MLPA). The MLPA genomic copy number alterations for CDKN2A were validated using real-time polymerase chain reaction.
  
  
  METHODS
  Six HNSCC primary (A) and recurrent or metastatic (B) cell lines were examined: UMSCC-11A/11B, UMSCC-17A/17B, and UMSCC-81A/81B.
  
  
  RESULTS
  Cell line UMSCC-11B retained all 9p loci tested in the region. Cell lines UMSCC-17A/B indicated homozygous deletion of CDKN2A(ARF, INK4a) starting at p16(INK4) exon 1alpha to include exons 2 and 3. Homozygous loss was indicated for CDKN2B(INK4b) and CDKN2A(ARF,INK4a) in UMSCC-11A, and UMSCC-81A. Cell line UMSCC-81B indicated retention of all 9p loci except for exon 1alpha (p16(INK4a)). Selective loss of the 3' end of MTAP was observed in UMSCC-11A. Genomic alterations by fine-mapping MLPA were validated at the DNA level for CDKN2A.
  
  
  CONCLUSIONS
  We identified exon 1alpha (p16(INK4a)) as the smallest region of loss in the CDKN2A(ARF, INK4a) gene. The frequency and precise loss of CDKN2B(INK4b), CDKN2A(ARF, INK4a), and MTAP in the prognosis of 9p21-deleted HNSCC may provide impetus for use of these targets as therapeutic biomarkers in head and neck cancer.
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery and Research Division, Henry Ford Hospital, Detroit, MI 48202, USA. mworsha1@hfhs.org
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Worsham
authors.forename: Kang Mei
authors.initials: KM
authors.lastname: Chen
authors.forename: Nivedita
authors.initials: N
authors.lastname: Tiwari
authors.forename: Gerard
authors.initials: G
authors.lastname: Pals
authors.forename: Jan P
authors.initials: JP
authors.lastname: Schouten
authors.forename: Seema
authors.initials: S
authors.lastname: Sethi
authors.forename: Michael S
authors.initials: MS
authors.lastname: Benninger
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D050762:Cyclin-Dependent Kinase Inhibitor p15 / Q000235:genetics; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics; D004273:DNA, Neoplasm / Q000032:analysis; D017353:Gene Deletion; D020868:Gene Silencing; D016147:Genes, Tumor Suppressor; D019942:Genes, p16; D006258:Head and Neck Neoplasms / Q000235:genetics*; D006801:Humans; D011683:Purine-Nucleoside Phosphorylase / Q000235:genetics*; D025803:Tumor Suppressor Protein p14ARF / Q000235:genetics
chemical_list: C493966:CDKN2B protein, human; D050762:Cyclin-Dependent Kinase Inhibitor p15; D019941:Cyclin-Dependent Kinase Inhibitor p16; D004273:DNA, Neoplasm; D025803:Tumor Suppressor Protein p14ARF; D011683:Purine-Nucleoside Phosphorylase; C021784:5'-methylthioadenosine phosphorylase