Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma.
Five osteosarcoma (OS) cell lines, 37 OS tumors and 9 corresponding non-neoplastic samples were genotyped by Affymetrix 10 K 2.0 SNP array. Regions of high level amplification and homozygous deletion were identified and validated by quantitative PCR and FISH. Certain recurrent cytogenetic alterations were more frequent in recurrent/metastatic than in primary OS. These included deletion of 6q14.1, 6q16.2-q22.31, and 8p23.2-p12, amplification of 8q21.12, 8q22.3-q24.3 and 17p12, and loss of heterozygosity (LOH) at 2q24.3-q31.2, 5q11.2, 6p21.31-p21.1, 6q14.1-q16.2, 8p22-p12, 9q22.1, 10q21.1-q22.1, 10q23.31-q24.1, 12q15-q21.1 and 21q21.2-q21.3. Most of the LOH calls were associated with deletion, but a subset of them was associated with normal or increased copy number (CN). A consensus 3q13.31 deletion localized to a region within the limbic system-associated membrane protein (LSAMP) gene was also identified. The FISH evaluations demonstrated highly-localized homozygous or heterozygous LSAMP deletions in 6 of 11 primary OS. qRT-PCR evaluations of the two major alternative LSAMP transcripts demonstrated reduced expression of 1b isoform transcript in each of three OS with LSAMP exon 1b deletion. Further, the 1a isoform transcripts in these same OS had either reduced expression or a premature termination codon in LSAMP exon 2. This SNP genotyping study identified chromosomal aberrations associated with disease progression in OS and disclosed LSAMP as a novel tumor suppressor gene in OS. The study also demonstrated that CN and LOH analyses were able to detect distinct subsets of genetic abnormalities in OS.
Yen
Chueh-Chuan
CC
Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA. ccyen@vghtpe.gov.tw
Chen
Wei-Ming
WM
Chen
Tain-Hsiung
TH
Chen
Winby York-Kwan
WY
Chen
Paul Chih-Hsueh
PC
Chiou
Hong-Jen
HJ
Hung
Giun-Yi
GY
Wu
Hung-Ta Hondar
HT
Wei
Chao-Jung
CJ
Shiau
Cheng-Ying
CY
Wu
Yu-Chung
YC
Chao
Ta-Chung
TC
Tzeng
Cheng-Hwai
CH
Chen
Po-Min
PM
Lin
Chi-Hung
CH
Chen
Yann-Jang
YJ
Fletcher
Jonathan A
JA
D000293:Adolescent; D000328:Adult; D000368:Aged; D001483:Base Sequence; D015816:Cell Adhesion Molecules, Neuronal / Q000235:genetics*; D045744:Cell Line, Tumor; D002648:Child; D002872:Chromosome Deletion; D002893:Chromosomes, Human, Pair 3; D018389:Codon, Nonsense; D005260:Female; D058851:GPI-Linked Proteins; D005784:Gene Amplification; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D016147:Genes, Tumor Suppressor; D020022:Genetic Predisposition to Disease; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D019656:Loss of Heterozygosity; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009364:Neoplasm Recurrence, Local; D020411:Oligonucleotide Array Sequence Analysis; D012516:Osteosarcoma / Q000235:genetics* / Q000556:secondary; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D012333:RNA, Messenger / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D055815:Young Adult
D015816:Cell Adhesion Molecules, Neuronal; D018389:Codon, Nonsense; D058851:GPI-Linked Proteins; D012333:RNA, Messenger; C095362:limbic system-associated membrane protein