Genomic signatures of chromosomal instability and osteosarcoma progression detected by high resolution array CGH and interphase FISH

Background: Osteosarcoma (OS) tumors and derived cell lines are characterized by complex chromosomal abnormalities. The availability of molecular genome profiling techniques such as array CGH have markedly enabled the high-resolution genome analysis of tumor genomes, as well as helped elucidate the mechanisms leading to their complexity. The identification of tumor-specific genomic profiles is currently the focus of many array CGH studies, but there have been no analyses to date documenting the genomic signatures consistent with chromosomal instability mechanisms in OS. Results: In this study we utilized high-resolution oligonucleotide array CGH to interrogate recurrent signatures of genomic imbalance in 10 OS tumors that were consistent with the breakage fusion bridge(BFB) mechanism. Comparative analysis of the tumors showed that they exhibited varying levels of genomic imbalance. The analysis also highlighted three chromosomal regions (6p21 ~ p22, 8q24 and 17p11.2 ~ p12) that were consistently involved in high level gain or amplification events. These three regions have been previously shown by us to be not only involved in high-level imbalance in OS-derived cell lines, but also to exhibit similar imbalance profiles consistent with BFB-related events. Karyotype and dual-color FISH analysis showed that repeated rearrangements of these unstable chromosomes through BFB cycles may create a heterogeneous pattern of copy number alterations. Conclusions: This genome-wide analysis is the first to utilize oligonucleotide array CGH and FISH analysis to derive possible genomic signatures of chromosomal instability in OS tumors. Perpetuation of the BFB cycle will create a heterogeneous pattern of copy number alterations by repeated rearrangement of the unstable tumor genome., thereby generating diverse phenotypes The resulting phenotypic diversity can generate tumors with a propensity for an aggressive disease course. A better understanding of the underlying mechanisms events leading to tumor development could result in the identification of prognostic markers and therapeutic targets. Keywords: osteosarcoma, chromosomal instability, gene amplification, breakage-fusion-bridge cycle, oligonucleotide array comparative genomic hybridization 10 OS tumor samples were used; fluor-flip was performed with normal human DNA as control

背景：骨肉瘤（Osteosarcoma, OS）肿瘤及其衍生细胞系以复杂的染色体异常为典型特征。诸如阵列比较基因组杂交（array CGH）这类分子基因组谱分析技术的问世，不仅显著推动了肿瘤基因组的高分辨率分析，同时也助力阐明了导致其基因组复杂性的内在机制。目前诸多阵列比较基因组杂交研究均聚焦于肿瘤特异性基因组谱的鉴定，但迄今为止尚无分析明确证实骨肉瘤中与染色体不稳定机制相符的基因组特征。
结果：本研究采用高分辨率寡核苷酸阵列比较基因组杂交（oligonucleotide array CGH），对10例符合断裂-融合-桥（breakage fusion bridge, BFB）机制的骨肉瘤肿瘤的复发性基因组失衡特征进行了检测。对这些肿瘤的比较分析显示，它们呈现出不同程度的基因组失衡。该分析还明确了三个染色体区域（6p21~p22、8q24以及17p11.2~p12），这些区域始终存在高水平拷贝数增加或扩增事件。我们此前的研究已证实，这三个区域不仅在骨肉瘤衍生细胞系中存在高水平失衡，还呈现出与BFB相关事件相符的相似失衡特征。核型分析与双色荧光原位杂交（FISH）结果显示，通过BFB循环对这些不稳定染色体进行的反复重排，可能会产生拷贝数改变的异质性模式。
结论：本项全基因组分析首次利用寡核苷酸阵列比较基因组杂交与荧光原位杂交技术，推导得出骨肉瘤肿瘤中染色体不稳定的潜在基因组特征。BFB循环的持续进行会通过对不稳定肿瘤基因组的反复重排，产生拷贝数改变的异质性模式，进而催生多样化的表型。由此产生的表型多样性可生成具有侵袭性疾病进程倾向的肿瘤。对驱动肿瘤发生的潜在机制事件的深入解析，有望助力预后标志物与治疗靶点的鉴定。
关键词：骨肉瘤、染色体不稳定、基因扩增、断裂-融合-桥循环、寡核苷酸阵列比较基因组杂交。本研究使用10例OS肿瘤样本；以正常人类DNA作为对照开展fluor-flip实验。