PTEN-dependent regulation of genome-wide transcription during metabolic stress [RNA-Seq]

PTEN is implicated in a wide variety of pathophysiological conditions and traditionally studied in the context of the PIK3-AKT-mTOR axis. Recent studies from our group and others have reported a novel role of PTEN in the regulation of transcription at the genome-wide scale. This emerging role of PTEN on global transcriptional regulation is providing a better understanding of various diseases, including cancer. Since cancer progression is an energy-demanding process and PTEN is known to regulate metabolic processes, we sought to understand the role of PTEN in transcriptional regulation under metabolic stress, a condition often developing in the tumor microenvironment. In the present study, we demonstrate that PTEN modulates genome-wide RNA Polymerase II (Pol II) occupancy in cells undergoing glucose deprivation. The glucose-deprived PTEN null cells were found to continue global gene transcription, which may activate a survival mode. However, cells with constitutive PTEN expression slow transcription, an evolutionary mechanism that may save cellular energy and activate programmed cell death pathways, in the absence of glucose. Interestingly, alternative exon usage by PTEN null cells is increased under metabolic stress compared to PTEN expressing cells. Overall, our study comprehensively demonstrates distinct mechanisms involved in PTEN-dependent genome-wide transcriptional control under metabolic stress. Our findings provide a new insight in understanding the tumor microenvironment and how PTEN loss of function, whether by genetic or non-genetic mechanisms, can contribute to a favorable transcriptional program employed by tumor cells to escape apoptosis, hence developing more aggressive and metastatic phenotypes. Overall design: RNA-seq was performed on BT-549 control and PTEN over-expressing BT-549_PTEN cell.

PTEN（磷酸酶及张力蛋白同源物，Phosphatase and tensin homolog）广泛参与多种病理生理过程，传统研究多围绕PI3K-AKT-mTOR信号轴展开。本团队及其他学者近期的研究揭示了PTEN在全基因组尺度转录调控中的全新功能。这一关于PTEN全局转录调控的新兴认知，为包括癌症在内的多种疾病的发病机制研究提供了更深入的理解视角。

由于肿瘤进展是一个高能量需求的过程，且PTEN已知可调控细胞代谢过程，我们旨在探究PTEN在代谢应激——肿瘤微环境中常见的状态——下的转录调控作用。在本研究中，我们证实PTEN可调控葡萄糖剥夺状态下细胞内的全基因组RNA聚合酶II（RNA Polymerase II, Pol II）结合占据情况。研究发现，PTEN敲除的葡萄糖剥夺细胞可维持全局基因转录，这可能激活细胞存活模式；而持续表达PTEN的细胞则会减慢转录速率，这一进化保守机制可在葡萄糖缺乏时节省细胞能量，并激活程序性细胞死亡通路。

有趣的是，与表达PTEN的细胞相比，PTEN敲除细胞在代谢应激条件下的可变外显子使用频率显著升高。

综上，本研究全面阐明了代谢应激条件下PTEN依赖的全基因组转录调控的独特分子机制。本研究结果为理解肿瘤微环境，以及PTEN功能缺失（无论是遗传还是非遗传机制）如何助力肿瘤细胞形成逃避凋亡的有利转录程序，进而发展为更具侵袭性和转移性表型提供了全新的研究视角。

实验整体设计：对BT-549对照细胞与过表达PTEN的BT-549_PTEN细胞开展RNA测序（RNA-seq）。