Bachtiary Barbara, Boutros Paul C, Pintilie Melania, Shi Willa, Bastianutto Carlo, Li Jian-Hua, Schwock Joerg, Zhang Wendy, Penn Linda Z, Jurisica Igor, Fyles Anthony, Liu Fei-Fei
Department of Radiation Oncology, Clinical Study Coordination and Biostatistics, Division of Cancer Genomics and Proteomics, Princess Margaret Hospital, Toronto, Ontario, Canada.
Clin Cancer Res. 2006 Oct 1;12(19):5632-40. doi: 10.1158/1078-0432.CCR-06-0357.
To explore intratumor heterogeneity in gene expression profiles from patients with cervical cancer.
A total of 33 biopsies were obtained from 11 patients, sampling between two and five different areas for each tumor. The extracted RNA was hybridized onto the Affymetrix U133 Plus 2.0 oligonucleotide chip. The variance of expression within a patient (W), between patients (B) and the total variance (T = W + B) were calculated for each ProbeSet, and the ratio W/T was used as a measure of intratumor heterogeneity. Gene Ontology functional analysis was done to assess the function of genes that had high W/T (top 10%) and low W/T (bottom 10%) values.
In total, 448 ProbeSets (2.2% of the total) had W/T < 0.10, indicating low intratumor heterogeneity, and 537 ProbeSets (2.7% of the total) had W/T > 0.90, indicating high intratumor heterogeneity. In total 14,473 ProbeSets (72.4%) had higher intertumor than intratumor heterogeneity (W/T < 0.5). Genes with low intratumor heterogeneity were characterized by a statistically significant enrichment of immune-related functions (P < 0.0001). Genes with high intratumor heterogeneity were characterized by a significant tendency towards nuclear localization and nucleic acid binding (both P < 0.0001). For genes with W/T > 0.5, more than six biopsies would be required to minimize the intratumoral heterogeneity to <0.15; if W/T is 0.3 to 0.4, four biopsies are required; and for low W/T of 0.16 to 0.3, only two to three biopsies would be needed.
Although the intratumor heterogeneity was low for the majority of the tested ProbeSets, for many genes, multiple biopsies are required to obtain a reliable estimate of gene expression.
探索宫颈癌患者基因表达谱中的肿瘤内异质性。
从11例患者中总共获取了33份活检样本，对每个肿瘤在两到五个不同区域进行采样。提取的RNA与Affymetrix U133 Plus 2.0寡核苷酸芯片杂交。针对每个探针集计算患者内部（W）、患者之间（B）的表达方差以及总方差（T = W + B），并将W/T比值用作肿瘤内异质性的度量。进行基因本体功能分析以评估W/T值高（前10%）和W/T值低（后10%）的基因的功能。
总共448个探针集（占总数的2.2%）的W/T < 0.10，表明肿瘤内异质性低；537个探针集（占总数的2.7%）的W/T > 0.90，表明肿瘤内异质性高。总共14473个探针集（72.4%）的肿瘤间异质性高于肿瘤内异质性（W/T < 0.5）。肿瘤内异质性低的基因具有免疫相关功能的统计学显著富集特征（P < 0.0001）。肿瘤内异质性高的基因具有明显的核定位和核酸结合倾向（P均 < 0.0001）。对于W/T > 0.5的基因，需要超过六份活检样本才能将肿瘤内异质性最小化至<0.15；如果W/T为0.3至0.4，则需要四份活检样本；对于W/T低至0.16至0.3的情况，仅需要两到三份活检样本。
尽管大多数测试探针集的肿瘤内异质性较低，但对于许多基因而言，需要多次活检才能获得可靠的基因表达估计值。
