Mitochondrial and nuclear genomic responses to loss of LRPPRC expression.
Mitochondrial and nuclear genomic responses to loss of LRPPRC expression.
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DOI：
10.1074/jbc.m109.098400
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发表时间：
2010-04-30
期刊：
影响因子：
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通讯作者：
Mootha VK
中科院分区：
文献类型：
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作者：
Gohil VM;Nilsson R;Belcher-Timme CA;Luo B;Root DE;Mootha VK
基因分型和测序技术的快速发展大大加快了人类疾病基因的发现。然而，阐明这些基因的功能并了解它们在发病机制中的作用仍然具有挑战性。在这里，我们介绍了一种基因组策略，以功能上的特点，这样的基因，我们将其应用到LRPPRC，一个研究不足的基因，是突变的利综合征，法国-加拿大型（LSFC）。我们利用RNA干扰工程的等位基因系列的细胞模型，其中LRPPRC已被稳定沉默到不同水平的敲低效率。然后，我们将联合收割机全基因组表达谱与基因集富集分析相结合，以鉴定与LRPPRC缺失相关的细胞反应。使用这种策略，我们发现了LRPPRC在所有线粒体DNA编码的mRNA表达中的特定作用，但不是rRNA，为疾病中观察到的酶缺陷提供了机制见解。我们的分析表明，核基因编码的线粒体蛋白不集体LRPPRC的损失的影响。我们确实观察到与己糖代谢、前列腺素合成和鞘糖脂生物学相关的基因的表达改变，这些基因可能在细胞存活中起适应性作用或促成发病机制。遗传扰动、基因组分析和途径分析的组合代表了理解疾病发病机制的通用策略。
Rapid advances in genotyping and sequencing technology have dramatically accelerated the discovery of genes underlying human disease. Elucidating the function of such genes and understanding their role in pathogenesis, however, remain challenging. Here, we introduce a genomic strategy to characterize such genes functionally, and we apply it to LRPPRC, a poorly studied gene that is mutated in Leigh syndrome, French-Canadian type (LSFC). We utilize RNA interference to engineer an allelic series of cellular models in which LRPPRC has been stably silenced to different levels of knockdown efficiency. We then combine genome-wide expression profiling with gene set enrichment analysis to identify cellular responses that correlate with the loss of LRPPRC. Using this strategy, we discovered a specific role for LRPPRC in the expression of all mitochondrial DNA-encoded mRNAs, but not the rRNAs, providing mechanistic insights into the enzymatic defects observed in the disease. Our analysis shows that nuclear genes encoding mitochondrial proteins are not collectively affected by the loss of LRPPRC. We do observe altered expression of genes related to hexose metabolism, prostaglandin synthesis, and glycosphingolipid biology that may either play an adaptive role in cell survival or contribute to pathogenesis. The combination of genetic perturbation, genomic profiling, and pathway analysis represents a generic strategy for understanding disease pathogenesis.