A web-accessible complete transcriptome of normal human and DMD muscle
A web-accessible complete transcriptome of normal human and DMD muscle
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DOI：
10.1016/s0960-8966(02)00093-7
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发表时间：
2002-10-01
影响因子：
2.8
通讯作者：
Hoffman, EP
中科院分区：
文献类型：
--
作者：
Bakay, M;Zhao, P;Hoffman, EP
我们评估了Duchenne肌营养不良患者和非营养不良对照的人骨骼肌的完整转录组（从10个Duchenne肌营养不良和8个对照中分析了36个RNA;类似于在U95五基因芯片系列和MuscleChip上查询的65，000个基因/表达序列标签/探针集）。多种芯片类型的使用使我们能够比较同一基因的不同探针组的结果：我们发现不同微阵列上不同探针组之间具有极好的一致性。我们发现30%的人类基因在肌肉中以可检测的水平表达。其中3%的人在肌营养不良蛋白缺乏症中表现出差异调节。在1882个失调探针组中，1324个对应于表征的基因/蛋白质（891个非冗余转录单位），588个对应于表达的序列标签或预测的基因。数据解释仅限于胰岛素样生长因子途径成员，对心脏谱系可能的失调的调查，以及男性和女性特异性转录本的鉴定。我们发现营养不良肌肉中IGF-I和IGF-II的转录上调，然而生长因子的可能有益作用似乎被抑制性IGF结合蛋白和调节剂（IGFBP-2、-4、-6和-7;和PRSS 11 [IGFBP-5蛋白酶]）的转录上调抵消。我们推测，IGF-I或IGF-II补充营养不良肌肉的有益作用可能是抑制性IGF结合蛋白的剂量依赖性螯合的结果。我们还关注了在肌肉中表达的六个“心脏”基因（α-心脏肌动蛋白、CARP、CASQ 2、心脏肌钙蛋白T2 [TNNT 2]、CUGBP 2和连接蛋白43）。与27个时间点的鼠肌肉再生系列和mdx肌肉谱的比较显示，CARP和Cx43与巨噬细胞相关，并且与TNNT 2活化的成肌细胞相关。心肌肌动蛋白和CUGBP 2的上调与肌肉再生谱无关，表明肌营养不良蛋白缺乏引起的更特异性的失调。我们发现两个Y连锁基因（RPS 4 Y、DDX 3 Y）仅在男性肌肉中表达，而两个常染色体基因（GRO 2、ZNF 91）在女性肌肉中表达更高（所有比较P < 0.01）。最后，我们提出了第一个网络可访问的表达谱数据库的所有数据，包括图像文件（.dat），处理后的图像文件（.cel），和完整的比较文件，这是公开的，通过一个新的可查询的网站，允许查询的基因在所有的配置文件（http：//microarray.cnmcresearch.org/pga）。这些数据列举了与肌营养不良蛋白缺乏下游相关的全方位分子变化，并提供了一个网络访问平台来研究肌肉疾病中转录途径改变的特异性。(C)出版社：Elsevier Science B. V.
We present an assessment of the complete transcriptome of human skeletal muscle in Duchenne muscular dystrophy patient muscle and non-dystrophic controls (36 RNAs analyzed from ten Duchenne dystrophy and eight controls; similar to65,000 gene/expressed sequence tag/probe sets queried on U95 five-GeneChip series and MuscleChip). The use of the multiple chip types allowed us to compare results from different probe sets for the same gene: we found excellent concordance between different probe sets on different microarrays. We found 30% of human genes expressed in muscle at detectable levels. Three percent of these showed differential regulation in dystrophin deficiency. Among 1882 dysregulated probe sets, 1324 corresponded to characterized genes/proteins (891 non-redundant transcript units), and 588 to expressed sequence tags or predicted genes. Data interpretation was limited to the insulin-like growth factor pathway members, an investigation of possible de-regulation towards a cardiac lineage, and identification of male- and female-specific transcripts. We found transcriptional upregulation of both IGF-I and IGF-II in dystrophic muscle, however the possible beneficial effects of the growth factors appear offset by transcriptional upregulation of inhibitory IGF-binding proteins and regulators (IGFBP-2, -4, -6 and -7; and PRSS11 [IGFBP-5 protease]). We hypothesize that the beneficial effects of IGF-I or IGF-II supplementation in dystrophic muscle may be the result of dose-dependent sequestration of inhibitory IGF-binding proteins. We also focused on six 'cardiac' genes expressed in muscle (alpha-cardiac actin, CARP, CASQ2, troponin T2 cardiac [TNNT2], CUGBP2, and connexin 43). Comparison to a 27 time point murine muscle regeneration series and mdx muscle profiles showed that CARP and Cx43 were macrophage-associated, and TNNT2 activated-myoblast-associated. Upregulation of cardiac actin and CUGBP2 was not associated with muscle regeneration profiles, suggesting a more specific dysregulation induced by dystrophin deficiency. We found two Y-linked genes expressed solely in male muscle (RPS4Y, DDX3Y), and two autosomal genes expressed much more highly in female muscle (GRO2, ZNF91) (all comparisons P < 0.01). Finally, we present the first web-accessible expression profiling database for all data, including image files (.dat), processed image files (.cel), and complete comparison files which are publicly available through a novel queriable web site, that permits query-by-gene across all profiles (http://microarray.cnmcresearch.org/pga). These data enumerate the full range of molecular changes associated downstream of dystrophin deficiency, and provide a web-accessible platform to study the specificity of transcriptional pathway alterations in muscle disease. (C) 2002 Published by Elsevier Science B.V.