Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing.
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing.
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DOI：
10.1186/1755-8794-2-35
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发表时间：
2009-06-09
影响因子：
2.7
通讯作者：
Litman T
中科院分区：
文献类型：
--
作者：
Nygaard S;Jacobsen A;Lindow M;Eriksen J;Balslev E;Flyger H;Tolstrup N;Møller S;Krogh A;Litman T
miRNA在细胞控制和各种疾病状态如癌症中发挥重要作用，它们可以作为标记物甚至可能是治疗剂。因此，鉴定整个miRNAs库并了解它们的表达模式是一个重要的目标。在这里，我们描述了454焦磷酸测序的小RNA的分析，从四个不同的组织：乳腺癌，正常的相邻乳腺，和两个畸胎瘤细胞系。我们开发了一个用于识别新miRNAs的管道，强调从即使是嘈杂的测序数据中提取和保留尽可能多的数据。我们研究了miRNA在乳腺癌和正常相邻乳腺样本中的差异表达，并系统地检测了与非miRNA位点相比miRNA成熟序列末端的变异性。我们鉴定了五种新的miRNAs，以及已知miRNAs的两种推定的替代前体。几种miRNA在乳腺癌和正常乳腺样品之间差异表达。末端变异性在miRNA和非miRNA基因座之间显示出显著不同。小RNA的焦磷酸测序与计算管道一起可用于鉴定肿瘤和其他组织中的miRNA。miRNA末端变异性的测量可能在未来被纳入发现管道中作为区分特征。乳腺癌样本与正常相邻乳腺相比显示出不同的miRNA表达谱。
MiRNAs play important roles in cellular control and in various disease states such as cancers, where they may serve as markers or possibly even therapeutics. Identifying the whole repertoire of miRNAs and understanding their expression patterns is therefore an important goal. Here we describe the analysis of 454 pyrosequencing of small RNA from four different tissues: Breast cancer, normal adjacent breast, and two teratoma cell lines. We developed a pipeline for identifying new miRNAs, emphasizing extracting and retaining as much data as possible from even noisy sequencing data. We investigated differential expression of miRNAs in the breast cancer and normal adjacent breast samples, and systematically examined the mature sequence end variability of miRNA compared to non-miRNA loci. We identified five novel miRNAs, as well as two putative alternative precursors for known miRNAs. Several miRNAs were differentially expressed between the breast cancer and normal breast samples. The end variability was shown to be significantly different between miRNA and non-miRNA loci. Pyrosequencing of small RNAs, together with a computational pipeline, can be used to identify miRNAs in tumor and other tissues. Measures of miRNA end variability may in the future be incorporated into the discovery pipeline as a discriminatory feature. Breast cancer samples show a distinct miRNA expression profile compared to normal adjacent breast.
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影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
DOI：
10.1073/pnas.0800121105
发表时间：
2008-04-01
影响因子：
11.1
作者：
Calin, George A.;Cimmino, Amelia;Croce, Carlo M.
通讯作者：
Croce, Carlo M.
影响因子：
30.8
作者：
Bentwich, I;Avniel, A;Bentwich, Z
通讯作者：
Bentwich, Z
影响因子：
11.2
作者：
Hurteau, Gregory J.;Carlson, J. Andrew;Brock, Graham J.
通讯作者：
Brock, Graham J.