title: Copy number changes of target genes in chromosome 3q25.3-qter of esophageal squamous cell carcinoma: TP63 is amplified in early carcinogenesis but down-regulated as disease progressed.
abstract: OBJECTIVE
  By using comparative genomic hybridization, gain of 3q was found in 45-86% cases of esophageal squamous cell carcinoma (EC-SCC). Chromosome 3q25.3-qter is the minimal common region with several oncogenes found within this region. However, amplification patterns of these genes in EC-SCC have never been reported. The possible association of copy number changes of these genes with pathologic characteristics is still not clear.
  
  
  METHODS
  Real-time quantitative PCR (Q-PCR) was performed to analyze the copy number changes of 13 candidate genes within this region in 60 primary tumors of EC-SCC, and possible association of copy number changes with pathologic characteristics was analyzed by statistics. Immunohistochemistry (IHC) study was also performed on another set of 111 primary tumors of EC-SCC to verify the association between TP63 expression change and lymph node metastasis status.
  
  
  RESULTS
  The average copy numbers (+/-SE) per haploid genome of individual genes in 60 samples were (from centromere to telomere): SSR3: 4.19 (+/-0.69); CCNL1: 5.24 (+/-0.67); SMC4L1: 2.01 (+/-0.16); EVI1: 2.02 (+/-0.12); hTERC: 5.28 (+/-0.54); SKIL: 2.71 (+/-0.14); EIF5A2: 1.95 (+/-0.12); ECT2: 9.18 (+/-1.68); PIK3CA: 8.13 (+/-1.17); EIF4G1: 1.07 (+/-0.05); SST: 3.07 (+/-0.25); TP63: 2.51 (+/-0.22); TFRC: 2.42 (+/-0.19). Four clusters of amplification were found: SSR3 and CCLN1 at 3q25.31; hTERC and SKIL at 3q26.2; ECT2 and PIK3CA at 3q26.31-q26.32; and SST, TP63 and TFRC at 3q27.3-q29. Patients with lymph node metastasis had significantly lower copy number of TP63 in the primary tumor than those without lymph node metastasis. IHC study on tissue arrays also showed that patients with lymph node metastasis have significantly lower TP63 staining score in the primary tumor than those without lymph node metastasis.
  
  
  CONCLUSIONS
  This study showed that different amplification patterns were seen among different genes within 3q25.3-qter in EC-SCC, and several novel candidate oncogenes (SSR3, SMC4L1, ECT2, and SST) were identified. TP63 is amplified in early stage of EC-SCC carcinogenesis but down-regulated in advanced stage of disease.
authors.affiliation: Division of Medical Oncology, Department of Medicine, Taipei Veterans General Hospital and National Yang-Ming University School of Medicine, Taipei, Taiwan, China.
authors.forename: Chueh-Chuan
authors.initials: CC
authors.lastname: Yen
authors.forename: Yann-Jang
authors.initials: YJ
authors.lastname: Chen
authors.forename: Chin-Chen
authors.initials: CC
authors.lastname: Pan
authors.forename: Kai-Hsi
authors.initials: KH
authors.lastname: Lu
authors.forename: Paul Chih-Hsueh
authors.initials: PC
authors.lastname: Chen
authors.forename: Jiun-Yi
authors.initials: JY
authors.lastname: Hsia
authors.forename: Jung-Ta
authors.initials: JT
authors.lastname: Chen
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Wu
authors.forename: Wen-Hu
authors.initials: WH
authors.lastname: Hsu
authors.forename: Liang-Shun
authors.initials: LS
authors.lastname: Wang
authors.forename: Min-Hsiung
authors.initials: MH
authors.lastname: Huang
authors.forename: Biing-Shiung
authors.initials: BS
authors.lastname: Huang
authors.forename: Cheng-Po
authors.initials: CP
authors.lastname: Hu
authors.forename: Po-Min
authors.initials: PM
authors.lastname: Chen
authors.forename: Chi-Hung
authors.initials: CH
authors.lastname: Lin
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000556:secondary; D002454:Cell Differentiation; D002869:Chromosome Aberrations; D002893:Chromosomes, Human, Pair 3; D004268:DNA-Binding Proteins; D015536:Down-Regulation; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000473:pathology; D018628:Gene Dosage; D015972:Gene Expression Regulation, Neoplastic; D016147:Genes, Tumor Suppressor; D006801:Humans; D008207:Lymphatic Metastasis; D009367:Neoplasm Staging; D010750:Phosphoproteins / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000592:standards; D015203:Reproducibility of Results; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins
chemical_list: D004268:DNA-Binding Proteins; D010750:Phosphoproteins; C115051:TP63 protein, human; D015534:Trans-Activators; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins