Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core needle biopsy samples of breast carcinoma
Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core needle biopsy samples of breast carcinoma
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DOI：
10.1002/cncr.11435
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发表时间：
2003-06-15
期刊：
影响因子：
6.2
通讯作者：
Pusztai, L
中科院分区：
文献类型：
--
作者：
Symmans, WF;Ayers, M;Pusztai, L
背景资料。如果微阵列技术要在乳腺癌的临床研究或管理中变得实用，基因表达谱分析应该适用于针刺活检样本。本研究比较了细针活检(FNAB)和芯针活检(CBX)的基因表达谱。方法从单个FNAB和CBX样本中提取总RNA。使用包含30,721个人类序列的cDNA微阵列分析相应的FNAb和CBX对基因表达谱的相似性。一个区分CBX样本和FNAB样本的基因子集在一个更大的针刺活检样本组和一个已发表的基因组数据库中被评估，该基因组数据库来自78个已知临床结果的散发性乳腺癌。结果：68名新诊断的乳腺癌患者被纳入本研究。65例患者接受FNAB治疗(17例同时接受FNAB和CBX治疗)，3例仅接受CBX治疗。提取的RNA在46个(71%)FNAB和15个(75%)CBX中具有良好的杂交质量。这些样本的总RNA产量与单次FNAb(平均3.6杯，中位数=2.2杯；n=46)和CBX(平均=2.8杯，中位数=2.0杯；n=15)相似，所有病例的总RNA均为1杯或更多。在总共50个样本(38个FNAB和12个CBX)中，包括来自10名患者的匹配的FNAB和CBX样本，在所有尝试时，所有病例都成功地进行了转录图谱分析。在10对匹配的FNAb和CBX样本中，基因表达谱存在差异。与FNAB样本相比，CBX样本中表达不同的基因被认为主要来自内皮细胞、成纤维细胞、肌纤维母细胞或平滑肌细胞以及组织细胞。FNAB的相应显微镜细胞计数显示平均80%的肿瘤细胞，15%的淋巴细胞和5%的基质细胞，而CBX含有50%的肿瘤细胞，20%的淋巴细胞和30%的基质细胞。考虑到CBX在非淋巴间质细胞中的含量大约是FNAB的6倍，并且CBX差异表达一组已知的间质基因，作者使用这些活检来定义乳腺癌间质的转录图谱。在已发表的乳腺癌基因组数据库中，对一组在CBX中差异表达的120个基因进行了独立评估，以根据基质基因表达对乳腺癌进行分类。有间质信号低或高的肿瘤亚型被发现，但与5年内全身转移的发展无关。FNAB和CBX产生的总结缔组织的质量和数量相似。RNA，并适用于约70-75%的单程样品的cDNA微阵列分析。同一肿瘤的FNAB和CBX的转录图谱通常是相似的，并由肿瘤细胞群驱动。作者总结说，每种技术都有相对的优势。FNAB提供的转录图谱更纯粹地代表了肿瘤细胞群体，而CBX的转录图谱包括更多来自非淋巴基质成分的表达。乳腺癌基因组研究首选的针吸活检取样技术的选择应取决于样本中是否需要可变间质基因的表达。(C)2003年美国癌症协会。
BACKGROUND. Gene expression profiling should be applicable to needle biopsy samples if microarray technology is to become practically useful for clinical research or management of breast carcinoma. This study compared gene expression profiles derived from fine-needle aspiration biopsy (FNAB) and from core needle biopsy (CBX).METHODS. Total RNA was extracted from single FNAB and CBX samples. Corresponding pairs of FNAB and CBX were analyzed for similarity of gene expression profiles using cDNA microarrays that contain 30,721 human sequences. A subset of genes that distinguished CBX samples from FNAB samples was evaluated in a larger group of needle biopsy samples and in a published genomic database derived from 78 sporadic breast carcinomas with known clinical outcome.RESULTS. Sixty-eight patients with newly diagnosed breast carcinoma were included in the current study. Sixty-five patients underwent FNAB (17 had both FNAB and CBX) and 3 underwent CBX only. Extracted RNA was of suitable quality for hybridization in 46 (71%) FNABs and 15 (75%) CBXs. Total RNA yield in those samples was similar for single-pass FNAB (mean = 3.6 mug and median = 2.2 mug; n = 46) and CBX (mean = 2.8 mug and median = 2.0 mug; n = 15), with I mug or more of total RNA in all cases. Transcriptional profiling was performed successfully in all cases when it was attempted, in a total of 50 samples (38 FNABs and 12 CBXs), including matched FNAB and CBX samples from 10 patients. There were differences in gene expression profiles in 10 matched FNAB and CBX sample pairs. Genes that were expressed differently in CBX samples, compared with FNAB samples, were recognized as being predominantly from the endothelium, fibroblasts, myofibroblasts or smooth muscle, and histiocytes. Corresponding microscopic cell counts from FNABs demonstrated means of 80% tumor cells, 15% lymphocytes, and 5% stromal cells, whereas CBXs contained 50% tumor cells, 20% lymphocytes, and 30% stromal cells. Considering that CBXs are approximately six-fold richer in nonlymphoid stromal cells than FNABs and that CBXs differentially express a set of recognized stromal genes, the authors used these biopsies to define a transcriptional profile of breast carcinoma stroma. A set of 120 genes differentially expressed in CBXs was assessed independently in a published breast carcinoma genomic database to classify breast carcinomas based on stromal gene expression. Subgroups of tumors with low or high stromal signal were identified, but there was no correlation with the development of systemic metastases within 5 years. Both FNAB and CBX yield a similar quality and quantity of totalCONCLUSIONS. RNA and are suitable for cDNA microarray analyses in approximately 70-75% of single-pass samples. Transcriptional profiles from FNAB and CBX of the same tumor generally are similar and are driven by the tumor cell population. The authors concluded that each technique has relative advantages. The FNABs provide transcriptional profiles that are a purer representation of the tumor cell population, whereas transcriptional profiles from CBXs include more representation from nonlymphoid stromal elements. Selection of the preferred needle biopsy sampling technique for genomic studies of breast carcinomas should depend on whether variable stromal gene expression is desirable in the samples. (C) 2003 American Cancer Society.