Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues.
Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues.
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DOI：
10.1186/1471-2407-11-244
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发表时间：
2011-06-13
期刊：
影响因子：
3.8
通讯作者：
Perego RA
中科院分区：
文献类型：
--
作者：
Cifola I;Bianchi C;Mangano E;Bombelli S;Frascati F;Fasoli E;Ferrero S;Di Stefano V;Zipeto MA;Magni F;Signorini S;Battaglia C;Perego RA
透明细胞肾细胞癌（ccRCC）的特点是反复出现拷贝数改变（CNA）和杂合性丢失（LOH），这可能具有潜在的诊断和预后应用。在这里，我们探讨了从手术肿瘤标本建立的 ccRCC 原代培养物是否保持亲代肿瘤组织的 DNA 图谱，从而能够对原始组织进行更可靠的 CNA 和 LOH 区分。我们建立了 9 种表型特征良好的 ccRCC 原代细胞培养物的集合。使用 Affymetrix SNP 阵列技术，我们对两种培养物和相应的肿瘤组织进行了全基因组拷贝数 (CN) 分析。对每个培养物/组织对的全局一致性进行了分析，评估全基因组 CN 图谱和 SNP 等位基因调用之间的相关性。使用 CNAG v3.0 和 Partek 两种软件进行 CN 分析，并比较两种不同算法（隐马尔可夫模型和基因组分割）返回的结果。观察到每种培养物的 CNA 和相应组织之间有很好的重叠。这一发现得到了高度全基因组 CN 相关性和 SNP 一致性的强化，提供了证据表明每种培养物均源自其相应的组织，并维持了亲代肿瘤的基因组改变。此外，原代培养物 DNA 谱保持稳定至少 3 周，直至第三代。这些培养物显示出比原始组织更高的细胞同质性和肿瘤成分的富集性，从而能够更好地区分 CNA 和 LOH。特别是对于半合子缺失，原代培养物表现出更明显的 CN 丢失，通常伴有 LOH；不同的是，在原始组织中，这些缺失的强度因正常细胞污染而减弱，并且 LOH 调用被遗漏。 ccRCC 原代培养物是一种可靠的体外模型，可以很好地再现原始肿瘤遗传学和表型，对于未来旨在研究参与 ccRCC 发病机制的基因或途径以及识别新的临床标志物或治疗靶点的功能方法可能有用。此外，SNP 阵列技术被证明是一个强大的工具，可以更好地确定 RCC 原代培养物的细胞组成和同质性。
Clear cell renal cell carcinoma (ccRCC) is characterized by recurrent copy number alterations (CNAs) and loss of heterozygosity (LOH), which may have potential diagnostic and prognostic applications. Here, we explored whether ccRCC primary cultures, established from surgical tumor specimens, maintain the DNA profile of parental tumor tissues allowing a more confident CNAs and LOH discrimination with respect to the original tissues. We established a collection of 9 phenotypically well-characterized ccRCC primary cell cultures. Using the Affymetrix SNP array technology, we performed the genome-wide copy number (CN) profiling of both cultures and corresponding tumor tissues. Global concordance for each culture/tissue pair was assayed evaluating the correlations between whole-genome CN profiles and SNP allelic calls. CN analysis was performed using the two CNAG v3.0 and Partek software, and comparing results returned by two different algorithms (Hidden Markov Model and Genomic Segmentation). A very good overlap between the CNAs of each culture and corresponding tissue was observed. The finding, reinforced by high whole-genome CN correlations and SNP call concordances, provided evidence that each culture was derived from its corresponding tissue and maintained the genomic alterations of parental tumor. In addition, primary culture DNA profile remained stable for at least 3 weeks, till to third passage. These cultures showed a greater cell homogeneity and enrichment in tumor component than original tissues, thus enabling a better discrimination of CNAs and LOH. Especially for hemizygous deletions, primary cultures presented more evident CN losses, typically accompanied by LOH; differently, in original tissues the intensity of these deletions was weaken by normal cell contamination and LOH calls were missed. ccRCC primary cultures are a reliable in vitro model, well-reproducing original tumor genetics and phenotype, potentially useful for future functional approaches aimed to study genes or pathways involved in ccRCC etiopathogenesis and to identify novel clinical markers or therapeutic targets. Moreover, SNP array technology proved to be a powerful tool to better define the cell composition and homogeneity of RCC primary cultures.
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影响因子：
11.2
作者：
Bacolod MD;Schemmann GS;Giardina SF;Paty P;Notterman DA;Barany F
通讯作者：
Barany F
影响因子：
6.4
作者：
KOVACS, G;SZUCS, S;BAUMGARTEL, H
通讯作者：
BAUMGARTEL, H
影响因子：
23.4
作者：
Li, GR;Cuilleron, M;Tostain, J
通讯作者：
Tostain, J
影响因子：
4.4
作者：
Perego, RA;Bianchi, C;Mocarelli, P
通讯作者：
Mocarelli, P
影响因子：
4.5
作者：
Heinzman, Jamie M.;Brower, Stacey L.;Silverman, Jan F.
通讯作者：
Silverman, Jan F.