Identification of Tissue-Specific Genes in Nasopharyngeal Epithelial Tissue and Differentially Expressed Genes in Nasopharyngeal Carcinoma by Suppression Subtractive Hybridization and cDNA Microarray

Genes Chromosomes Cancer. 2003 Sep;38(1):80-90. doi: 10.1002/gcc.10247.


Suppression subtractive hybridization (SSH) was performed for isolation of tissue-specific genes in nasopharyngeal epithelial tissue, by use of cDNAs from human adult nasopharyngeal epithelial tissue as tester and mixed cDNAs from esophagus, lung, liver, heart, stomach, spleen, skeletal muscle, kidney, and skin as drivers. Fourteen differentially expressed genes in nasopharyngeal epithelial tissue were obtained. Among these genes, LPLUNC1 and SPLUNC1 were confirmed to be specifically expressed in nasopharyngeal epithelial tissue and the trachea. A novel transcript of SPLUNC1, which we designate NASG, was found. We also combined SSH and cDNA microarray hybridization to identify genes whose expressions were altered in nasopharyngeal carcinoma (NPC). We used NPC cell line HNE1 and primary human embryo nasopharyngeal epithelial cells in one SSH experiment, and NPC biopsies and normal adult nasopharyngeal epithelial tissue in another. Some 1,200 SSH inserts from four subtractive cDNA libraries were arrayed onto nylon membranes by use of robotic printing. Differential gene expression was verified by hybridizing of the membranes with radioactively labeled first-strand cDNA from NPC cell line HNE1, primary human embryo nasopharyngeal epithelial cells, NPC biopsies, and normal adult nasopharyngeal epithelial tissue. Seventeen differentially expressed genes in NPC were obtained. Among these genes, we identified SPLUNC1 and LPLUNC1 to be down-expressed in NPC biopsies (34/48, 33/48).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Alternative Splicing
  • Base Sequence
  • DNA, Complementary / analysis*
  • Down-Regulation / genetics
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Neoplastic / genetics*
  • Humans
  • Molecular Sequence Data
  • Nasal Mucosa / chemistry
  • Nasal Mucosa / metabolism*
  • Nasal Mucosa / pathology
  • Nasopharyngeal Neoplasms / chemistry
  • Nasopharyngeal Neoplasms / genetics*
  • Nasopharynx / chemistry
  • Nasopharynx / metabolism*
  • Nucleic Acid Hybridization / methods
  • Oligonucleotide Array Sequence Analysis / methods*
  • Organ Specificity / genetics
  • Tumor Cells, Cultured


  • DNA, Complementary