Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.
Hum Mol Genet. 2011 Oct 1;20(19):3852-66. doi: 10.1093/hmg/ddr306. Epub 2011 Jul 13.
In metazoans, lysosomes are the center for the degradation of macromolecules and play a key role in a variety of cellular processes, such as autophagy, exocytosis and membrane repair. Defects of lysosomal pathways are associated with lysosomal storage disorders and with several late onset neurodegenerative diseases. We recently discovered the CLEAR (Coordinated Lysosomal Expression and Regulation) gene network and its master gene transcription factor EB (TFEB), which regulates lysosomal biogenesis and function. Here, we used a combination of genomic approaches, including ChIP-seq (sequencing of chromatin immunoprecipitate) analysis, profiling of TFEB-mediated transcriptional induction, genome-wide mapping of TFEB target sites and recursive expression meta-analysis of TFEB targets, to identify 471 TFEB direct targets that represent essential components of the CLEAR network. This analysis revealed a comprehensive system regulating the expression, import and activity of lysosomal enzymes that control the degradation of proteins, glycosaminoglycans, sphingolipids and glycogen. Interestingly, the CLEAR network appears to be involved in the regulation of additional lysosome-associated processes, including autophagy, exo- and endocytosis, phagocytosis and immune response. Furthermore, non-lysosomal enzymes involved in the degradation of essential proteins such as hemoglobin and chitin are also part of the CLEAR network. Finally, we identified nine novel lysosomal proteins by using the CLEAR network as a tool for prioritizing candidates. This study provides potential therapeutic targets to modulate cellular clearance in a variety of disease conditions.
在后生动物中，溶酶体是降解大分子的中心，在多种细胞过程中发挥关键作用，如自噬、胞吐和膜修复。溶酶体途径的缺陷与溶酶体贮积症和几种迟发性神经退行性疾病有关。我们最近发现了 CLEAR（协调溶酶体表达和调节）基因网络及其主基因转录因子 EB（TFEB），它调节溶酶体的生物发生和功能。在这里，我们使用了基因组学方法的组合，包括 ChIP-seq（染色质免疫沉淀测序）分析、TFEB 介导的转录诱导分析、TFEB 靶位点的全基因组图谱和 TFEB 靶基因的递归表达元分析，来鉴定 471 个 TFEB 的直接靶基因，这些基因代表了 CLEAR 网络的基本组成部分。这项分析揭示了一个全面的系统，该系统调节溶酶体酶的表达、导入和活性，控制蛋白质、糖胺聚糖、鞘脂和糖原的降解。有趣的是，CLEAR 网络似乎参与了其他与溶酶体相关过程的调节，包括自噬、胞吐和胞吞、吞噬和免疫反应。此外，参与降解血红蛋白和几丁质等重要蛋白质的非溶酶体酶也属于 CLEAR 网络。最后，我们使用 CLEAR 网络作为优先考虑候选物的工具，鉴定了 9 种新的溶酶体蛋白。这项研究为在各种疾病条件下调节细胞清除提供了潜在的治疗靶点。
