Array comparative genomic hybridization reveals frequent alterations of G1/S checkpoint genes in undifferentiated pleomorphic sarcoma of bone

Abstract

Undifferentiated pleomorphic sarcoma of bone (UPSb) is a rare tumor often difficult to differentiate from fibrosarcoma of bone (FSb), diagnostically. We applied array comparative genomic hybridization (array CGH) to screen for genes with potential importance in the tumor and compared the results with alterations seen in FSb. Twenty-two fresh frozen tissue specimens from 20 patients (18 primary tumors and 4 local recurrences) with UPSb were studied. DNA was isolated and hybridized onto Agilent 244K CGH oligoarrays. The hybridization data were analyzed using Agilent DNA Analytics Software. The number of changes ranged from 2 to 168 (average = 66). Losses were most frequently seen at 8p, 9p, 10, 13q, and 18q, and gains at 4q, 5p, 6p, 7p, 8q, 12p, 14q, 17q, 19p, 20q, 22q, and X. Homozygous deletions of CDKN2A, RB1, TP53, and ING1 were seen in 8/20, 7/20, 3/20, and 2/20 cases, respectively. Hypermethylation of both p16(INK4a) and p14(ARF) was found in two cases with loss at CDKN2A. Inactivation either of CDKN2A, RB1, or TP53 was detected in 18/20 cases. One case showed high level gains of CDK4 and MDM2. Frequent gains were seen at MYC, PDGFRA, KIT, and KDR. Immunohistochemical positivity of KIT, PDGFRA, KDR, and PDGFRB was found in 8/14, 5/14, 4/14, and 4/14 cases, respectively. The regions most significantly discriminating between UPSb and FSb included RB1 and MYC. No homozygous deletions of RB1 were found in FSb. In conclusion, our analysis showed the disruption of G1/S checkpoint regulation to be crucial for the oncogenesis of UPSb.

Genetic and molecular characterization of the human Osteosarcoma 3AB‐OS cancer stem cell line: A possible model for studying osteosarcoma origin and stemness

“…3AB‐OS cells also showed monosomies, trisomies and nullisomies, together with 32 unidentifiable marker chromosomes, and they exhibited 49 CNVs (gains/losses), spanning almost all the chromosomes. Remarkably, the abnormalities evidenced in 3AB‐OS cells appear to be strongly congruent with abnormalities described in the literature in a large number of pediatric and adult osteosarcomas (Bridge et al, 1997; Batanian et al, 2002; Niini et al, 2011), which have shown a karyotype ranging from haploid to near hexaploid, with structural abnormalities involving the chromosomal regions 1p11–13, 4q27–33, 6p23–25, 6q16–25, 7q11–36, 11p10–15, 11q23, and 17p11.2–13. Moreover, 3AB‐OS cells showed losses/gains in agreement with those seen in osteosarcoma patients (Bridge et al, 1997; Batanian et al, 2002; Niini et al, 2011), such as losses at chromosome arms 8p, 9p, 16p, 3q, 13q, and gains at chromosome arms 6p, 8q, 12p, 14q, 17p, and 20q.…”

“…Osteosarcoma, the most common of primary bone malignancies, is a highly aggressive tumor exhibiting clinical, histologic, and molecular heterogeneity (Tang et al, 2008). Classic cytogenetic studies and array CGH analysis in pediatric and adult osteosarcoma patients have demonstrated that the majority of osteosarcomas are characterized by complex chromosomal abnormalities, with specimens varying from haploid to near‐hexaploid, and frequent chromosomal gains and losses, indicating the highly unstable nature of the osteosarcoma cell genome (Bridge et al, 1997; Batanian et al, 2002; Niini et al, 2011). The tumor, which in about 80% of cases occurs at sites of rapid bone growth (e.g., the metaphyses of long bones), has an initial peak incidence in the pediatric and early adult population and a second peak incidence in later adult life (Tang et al, 2008).…”

Mutant p53 gain of function can be at the root of dedifferentiation of human osteosarcoma MG63 cells into 3AB-OS cancer stem cells

“…Moreover, bioinformatic analyses selected 196 genes and 46 anticorrelated miRNAs involved in carcinogenesis and stemness [14]. Remarkably, the abnormalities evidenced in 3AB-OS cells appear to be strongly congruent with abnormalities described in a large number of pediatric and adult OS patients, where karyotype ranging from haploid to near hexaploid with chromosome number ranging from 15 to 120 were described; in addition, a great number of chromosomal regions with structural abnormalities among which 17p11.2-13 that contains TP53 gene were found [15][16][17].…”

A short story of 3AB-OS Cancer Stem Cells, a possible model for studying cancer stemness

“…Moreover, 3AB-OS cells show monosomies, trisomies and nullisomies, have 32 unidentifiable marker chromosomes, and exhibit -with respect to parental MG63 cells-49 copy number variations (gains/losses) affecting almost all the chromosomes [22] . Intriguingly, the abnormalities evidenced in 3AB-OS cells are very similar to those described in a large number of pediatric and adult osteosarcomas, where karyotypes ranging from haploid to near hexaploid have been shown [23][24][25] . Moreover, 3AB-OS cells showed losses/gains in agreement with those seen in osteosarcoma patients [23][24][25] .…”

“…Intriguingly, the abnormalities evidenced in 3AB-OS cells are very similar to those described in a large number of pediatric and adult osteosarcomas, where karyotypes ranging from haploid to near hexaploid have been shown [23][24][25] . Moreover, 3AB-OS cells showed losses/gains in agreement with those seen in osteosarcoma patients [23][24][25] . Comparing 3AB-OS cells to MG63 cells we reported the gene expression profile of 3AB-OS cells.…”