title: Differential gene expression in human glioma cells: correlation with presence or absence of DNA-dependent protein kinase.
abstract: The human glioma cell line M059J is deficient in DNA-dependent protein kinase (DNA-PK) due to a frame-shift mutation in PRKDC, the gene for its catalytic subunit, while cell line M059K, isolated from the same malignant tumor, has normal DNA-PK activity. DNA-PK is required for double-strand DNA break repair, and its absence is responsible for increased radiosensitivity of M059J. We show that transcripts of several melanoma antigen subfamily A (MAGE-A) genes, the expression of which is restricted to tumor and germ-line cells,are present in M059K, but that their expression is strongly downregulated in M059J. Normal levels of MAGE-A expression are restored in the PRKDC-complemented cell line M059J/Fus1, suggesting that the presence of DNA-PK is required for MAGE-A gene transcription. We also show that the MAGE-A1 promoter is methylated in M059J, while the promoter is demethylated in M059K and M059J/Fus1. Other genes, including all three major histocompatibility class I (HLA) genes, BENE, and an unnamed gene related to CNIL(CORNICHON-like), display an opposite expression profile (i.e., they are upregulated in the DNA-PK-deficient cell line, but show low levels of expression in both M059K and in the PRKDC-complemented cell line). For these genes, differential expression does not correlate with DNA methylation in upstream promoter sequences. Our results suggest that the presence of DNA-PK can exert effects on gene expression by various mechanisms and pathways, thus affecting overall cell physiology even in the absence of DNA damage.
authors.affiliation: Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, CA 92121, USA.
authors.forename: Rong
authors.initials: R
authors.lastname: Ai
authors.forename: Ana
authors.initials: A
authors.lastname: Sandoval
authors.forename: Paul
authors.initials: P
authors.lastname: Labhart
mesh_terms: D000951:Antigens, Neoplasm; D001932:Brain Neoplasms / Q000201:enzymology* / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D051747:DNA-Activated Protein Kinase; D004268:DNA-Binding Proteins; D015536:Down-Regulation / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D005910:Glioma / Q000201:enzymology* / Q000235:genetics*; D015395:Histocompatibility Antigens Class I / Q000235:genetics / Q000378:metabolism; D006801:Humans; D058950:Melanoma-Specific Antigens; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D062806:Myelin and Lymphocyte-Associated Proteolipid Proteins; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D009687:Nuclear Proteins; D011401:Promoter Regions, Genetic / Q000235:genetics; D011494:Protein Kinases / Q000235:genetics* / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000235:genetics* / Q000378:metabolism*; D014407:Tumor Cells, Cultured
chemical_list: D000951:Antigens, Neoplasm; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D015395:Histocompatibility Antigens Class I; C110862:MALL protein, human; D058950:Melanoma-Specific Antigens; D008565:Membrane Proteins; D062806:Myelin and Lymphocyte-Associated Proteolipid Proteins; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D011494:Protein Kinases; D051747:DNA-Activated Protein Kinase; C497263:PRKDC protein, human; D017346:Protein Serine-Threonine Kinases