干细胞多潜能性的新式生物信息学检测法（附原文）

tpwang

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多能干细胞是当前干细胞研究的热点和焦点。它可以分化成体内所有的细胞，进而形成身体的所有组织和器官。目前，斯克里普斯研究所的科学家们建立了一套质量控制诊断测试，使研究人员更方便确认其细胞系是否是正常的多能干细胞。; v5 D( p- o8 s! O1 `0 _; K

) M2 Y* G3 B9 c3 q- E- N" O: E该研究发表在2011年3月6日的《科学方法》(Nature Methods)上，斯克里普斯研究院的分子生物学科学家Jeanne Loring谈到，对于目前黄金标准（畸胎瘤法）的多能性测试，很多科学家表示不满。畸胎瘤法要求开展动物试验，并在科学家能证明他们拥有多能干细胞系之前，需要六到八周的时间。此外，这种方法具有技术上的挑战性，并很难规范化。
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新的测试，称为“多能测试”(PluriTest)，具有收效大、精准、无需动物展开的多能性测试特点。使用微阵列技术，能同时对数以千计不同的DNA序列进行分析。斯克里普斯研究小组开创了关于所有基因信息的大型数据库，这些基因活跃在正常的人体胚胎干细胞、诱导多能干细胞和许多的非多能细胞系中。对于多能测试，这个数据库对正常多能干细胞系建立了详细的分子模型。
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Loring说，与使用小的生物标志检测细胞的诊断测试不同，分子模型的方法使用了微阵列中的数千条信息。这个诊断测试的结果具有高度的灵敏度和特异性。科学家把直接来自微阵列分析中的原始数据上传到多能测试网站中，十分钟之内即可知道其细胞系是否具有多能性。
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多能诊断测试的另一个特点是，它能表明多能的细胞在某些方面是与正常模型的多能细胞系不同。例如由软件生成的新的得分反应了多能细胞存在基因变异，比如：基因或染色体的额外拷贝。这个特点提醒研究者对细胞做进一步的分析以确定引起变异的原因。
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该项研究的第一作者Franz-Josef Mueller说，科学家可在迅速建立多能干细胞系以了解人类的疾病，测试新药等。7 ]% \6 `- [& S1 B+ w0 n

: f; d2 C0 L2 z$ ]' {2 A, p"Pluripotent" stem cells—which have the potential to mature into almost any cell in the body—are being widely studied for their role in treating a vast array of human diseases and for generating cells and tissues for transplantation. Now, a team of Scripps Research Institute scientists has created a quality control diagnostic test that will make it much easier for researchers to determine whether their cell lines are normal pluripotent cells. * c7 Q6 f1 g. b& L- K3 S+ r

( y9 x! p2 Z8 i8 F+ ?8 l"Many scientists are unhappy with the current gold standard for testing for pluripotency, called the teratoma assay," said Scripps Research molecular biologist Jeanne Loring, principal investigator of the study. "The teratoma assay requires animal testing and a time span of six to eight weeks before scientists can prove that they have a pluripotent stem cell line. In addition, this method is technically challenging and difficult to standardize."
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The new test, called "PluriTest," meets the need for a cost-effective, accurate, animal-free alternative to the teratoma assay for assessing pluripotency. Using microarray technology, which enables the simultaneous analysis of thousands of different DNA sequences, the Scripps Research team created a large database of information about all the genes that are active in hundreds of normal human embryonic and induced pluripotent stem cells and a variety of non-pluripotent cell lines. For PluriTest, this database was used to create a detailed molecular model of a normal pluripotent stem cell line.
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"Unlike diagnostic tests that use small sets of biomarkers to examine cells, the molecular model approach uses all of the thousands of pieces of information in a microarray," Loring said. "This results in a diagnostic test with remarkable sensitivity and specificity." Scientists upload raw data straight from a single microarray analysis to the PluriTest website and learn within 10 minutes whether their cell line is pluripotent.% B+ Y9 F6 Q& r0 S6 m5 J

5 t0 V0 s+ R/ o& Q& WAn additional feature of the PluriTest diagnostic test is that it can show whether a cell that is pluripotent is different in some way from the normal model pluripotent cell line. For example, a "novelty score" generated by the software may indicate that the pluripotent cells have genomic aberrations such as extra copies of genes or chromosomes. This feature would alert the researcher to do additional analysis on the cells to determine what is causing the abnormality.
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A first author of the study, Franz-Josef Mueller, said, "Scientists are making new induced pluripotent stem cell lines at a rapid pace to understand human disease, test new drugs, and develop regenerative therapies. Thousands of induced pluripotent stem cell lines have already been generated and soon there will be many more thousands. PluriTest is designed to enable the growth of this technology."9 g) E0 K. h; I9 y8 j$ l
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Journal Reference:" x, d5 Q+ i: A* J$ e9 L
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1.Franz-Josef Müller, Bernhard M Schuldt, Roy Williams, Dylan Mason, Gulsah Altun, Eirini P Papapetrou, Sandra Danner, Johanna E Goldmann, Arne Herbst, Nils O Schmidt, Josef B Aldenhoff, Louise C Laurent & Jeanne F Loring. A bioinformatic assay for pluripotency in human cells. Nature Methods, 06 March 2011 DOI: 10.1038/nmeth.1580
- ]1 ^0 z, w$ f% f# X3 t英文链接：http://www.sciencedaily.com/releases/2011/03/110306141657.htm* a( Z- R' T  e, v) i' a
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5楼原文 感谢conquer87 提供

tpwang

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回复 tpwang 的帖子
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这种生物信息学方法与Nature上关于iPS的Scoreboard类似，不知在多大程度上能够取代传统的检测方法，未来在规模化应用中的意义如何。
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/ ?/ J; o" X# F更现实的问题是这类网络公开信息工具是否会很快由研究人员接受并将使用结果普遍纳入到成果发表中，成为一个规则。
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估计会有更多的类似技术出现。是否可以想象未来干细胞的各种状态都可以采用生物信息方法来评判。2 |0 Z' F/ D4 T& O* g" S$ }! Y
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哪位朋友能提供原文看看。

xiaoheilong

畸胎瘤比起芯片要便宜，许多文章两项都去做

lorey

谁能提供下原文？

conquer87

这是全文