Abstract #1413: Allele-specific copy number analysis of human osteosarcoma by single nucleotide polymorphism (SNP) array identifies several monoallelic amplicons independent of MYC in chromosome 8 q-arm (8q)

Abstract

In an attempt to fully characterize the complex chromosomal changes of osteosarcoma (OS), 58 human OS samples including 40 primary OS tumors, 11 OS explants, and 7 OS cell lines were subjected to Affymetrix 50K and 250K single nucleotide polymorphism (SNP) array analysis. Allele-specific copy number (CN) analysis using anonymous references (AsCNAR) algorithm revealed many allele-specific events previously undetectable by conventional analysis. Common regions of high CN amplifications were identified in 1q21.1-q24.1 (14% of the samples), 6p21.1-p12.1 (14%), 8q23.3-qter (16%), 14q11.2-q12 (17%), and 17p12-p11.2 (16%). Interestingly, many amplicons showed allele-specific amplification frequently accompanying deletion of the other allele. The most prominent allele-specific amplifications were found in 8q23.3-qter. 59 % of the samples showed various levels of CN gains in this region. All human OS cell lines (U2OS, G292, MG63, HT161, HOS, and SAOS2) except SJSA (86 % of the cell lines) showed high CN amplification in the region. Although amplification of chromosome 8 q-arm (8q) targeting MYC oncogene is frequently found in many cancers, Many amplicons identified in the region were MYC-independent. Fluoresence In-Situ Hybridization (FISH) using BAC clones verified the presence of MYC-independent amplicons as well as frequent fusion and translocation of the amplicons into other chromosomes. To check the possibility of new cancer-related genes other than MYC gene in 8q, we checked the mRNA expression levels of all known genes in the amplicons of 7 human OS cell lines by quantitative reverse transcription PCR (qRT-PCR). Gene expression levels were normalized to the expression level in normal human osteoblast cell line hFOB1.19. Many genes in the region showed increased mRNA expression level: TRPS1 (median value of 34-fold increased expression), RAD21 (5-fold), THRAP6 (6-fold), CCN3 (24-fold), ENPP2 (10-fold), DEPDC6 (7-fold), SNTB1 (8-fold), FBXO32 (5-fold), ADCY8 (5-fold), CCN4 (12-fold), and PTK2 (4-fold) showed more than 10-fold increase in two or more cell lines. Common regions of homozygous deletions were also identified: 3q13.31 (16% of the samples), 7q35-q36.3 (9%), 9p21.3 (7%), and Xp21 (7%) were frequently deleted. Interestingly, many deletions targeted membrane associated guanylate kinase (MAGUK) family genes such as MAGI2, DLG2, and DLGAP2. In conclusion, our results suggest that there are several possible cancer-related genes in 8q regions as well as in homozygously deleted regions in OS. These findings will help developing new diagnostic markers and therapeutic targets.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 1413.