Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA.
BMC Genomics. 2011 Jan 6;12:11. doi: 10.1186/1471-2164-12-11.
SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. SOX2 appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of SOX2 in GBM has not yet been defined.
We show that knockdown of the SOX2 gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the SOX2 response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing. Using ChIP-seq technology, we identified 4883 SOX2 binding regions in the GBM cancer genome. SOX2 binding regions contain the consensus sequence wwTGnwTw that occurred 3931 instances in 2312 SOX2 binding regions. Microarray analysis identified 489 genes whose expression altered in response to SOX2 knockdown. Interesting findings include that SOX2 regulates the expression of SOX family proteins SOX1 and SOX18, and that SOX2 down regulates BEX1 (brain expressed X-linked 1) and BEX2 (brain expressed X-linked 2), two genes with tumor suppressor activity in GBM. Using next generation sequencing, we identified 105 precursor microRNAs (corresponding to 95 mature miRNAs) regulated by SOX2, including down regulation of miR-143, -145, -253-5p and miR-452. We also show that miR-145 and SOX2 form a double negative feedback loop in GBM cells, potentially creating a bistable system in GBM cells.
We present an integrated dataset of ChIP-seq, expression microarrays and microRNA sequencing representing the SOX2 response program in LN229 GBM cells. The insights gained from our integrated analysis further our understanding of the potential actions of SOX2 in carcinogenesis and serves as a useful resource for the research community.
SOX2 是一个关键基因，涉及维持胚胎和成人干细胞的干性。SOX2 似乎在包括多形性胶质母细胞瘤（GBM）在内的几种人类癌症中重新激活，然而，SOX2 在 GBM 中的详细反应程序尚未确定。
我们表明，在 LN229 GBM 细胞中敲低 SOX2 基因可减少细胞增殖和集落形成。然后，我们通过使用几种先进的基因组技术（包括 ChIP-seq、微阵列分析和 microRNA 测序）进行综合分析，全面描绘了 SOX2 的反应程序。使用 ChIP-seq 技术，我们在 GBM 癌症基因组中鉴定出 4883 个 SOX2 结合区域。SOX2 结合区域包含 wwTGnwTw 共识序列，在 2312 个 SOX2 结合区域中出现 3931 次。微阵列分析确定了 489 个基因，其表达在 SOX2 敲低后发生改变。有趣的发现包括 SOX2 调节 SOX 家族蛋白 SOX1 和 SOX18 的表达，以及 SOX2 下调 BEX1（脑表达 X 连锁 1）和 BEX2（脑表达 X 连锁 2），这两个基因在 GBM 中具有肿瘤抑制活性。使用下一代测序，我们鉴定出 105 个受 SOX2 调节的前体 microRNAs（对应 95 个成熟 miRNAs），包括 miR-143、-145、-253-5p 和 miR-452 的下调。我们还表明，miR-145 和 SOX2 在 GBM 细胞中形成双负反馈环，可能在 GBM 细胞中创建双稳态系统。
我们展示了代表 LN229 GBM 细胞中 SOX2 反应程序的 ChIP-seq、表达微阵列和 microRNA 测序的综合数据集。我们综合分析获得的见解进一步加深了我们对 SOX2 在致癌作用中的潜在作用的理解，并为研究社区提供了有用的资源。
