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QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis
Science ( IF 56.9 ) Pub Date : 2020-12-31 , DOI: 10.1126/science.abb6896
Kwontae You 1 , Lingfei Wang 1 , Chih-Hung Chou 1 , Kai Liu 2, 3 , Toru Nakata 2, 3 , Alok Jaiswal 1 , Junmei Yao 2, 3 , Ariel Lefkovith 1 , Abdifatah Omar 2, 3 , Jacqueline G Perrigoue 4 , Jennifer E Towne 4 , Aviv Regev 5, 6 , Daniel B Graham 1, 2, 3 , Ramnik J Xavier 1, 2, 3
Affiliation  

Transcriptional control of proteostasis Tissue homeostasis requires the coordinated activity of multiple cell types to initiate and then resolve inflammation. Intrinsic cellular stress-response pathways facilitate adaptation to stress and tissue restitution. Among these stress pathways, the unfolded protein response can elicit two divergent outcomes: adaptation to endoplasmic reticulum (ER) stress or termination by programmed cell death. You et al. identified QRICH1 as a transcriptional regulator controlling adaptation to ER stress at the level of protein translation and secretion. The authors further demonstrate the role of the QRICH1 program in inflammatory diseases of the colon and liver. Science, this issue p. 45 A glutamine-rich protein regulates translation and secretory networks that are specifically up-regulated in inflammatory pathologies. INTRODUCTION Tissue homeostasis requires the coordinated activity of multiple cell types to initiate and then resolve inflammation. Endoplasmic reticulum (ER) stress is a hallmark of inflammation and exacerbates tissue pathology across a broad range of human diseases. Environmental stressors associated with inflammation and cell-intrinsic metabolic demands can elicit ER stress, protein misfolding, and cell death. To counteract these processes, stress response pathways, including the unfolded protein response (UPR), facilitate adaptation to stress and tissue restitution. Cells sense ER stress and initiate the UPR through three coordinated pathways mediated by the effector proteins inositol-requiring enzyme 1 (IRE1/ERN1), activating transcription factor 6 (ATF6), and protein kinase RNA-like ER kinase (PERK,EIF2AK3). Collectively, the UPR effector pathways fine-tune the rate of protein translation and induce transcriptional up-regulation of genes that promote ER function, such as those encoding chaperone proteins and secretory machinery. Although these functional responses to ER stress by the UPR pathways aim to restore cellular homeostasis, prolonged and unresolved ER stress can elicit programed cell death. In this context, the molecular mechanisms that dictate the outcome of ER stress are incompletely understood. RATIONALE Mismanagement of ER stress in intestinal epithelial cells can lead to disruption of barrier integrity, resulting in exposure of the host immune sysem to commensal microbes that trigger uncontrolled inflammation. With accumulating evidence highlighting the prominent role of ER stress in disease, it remains to be determined how the UPR directs divergent cell fate decisions. The UPR either induces an adaptive phase that promotes recovery of ER proteostasis and cell survival or induces a terminal phase that initiates the active engagement of programmed cell death pathways. RESULTS Toward the objective of defining mechanisms controlling the adaptive versus terminal UPR, we used single-cell RNA sequencing (scRNA-seq) in primary intestinal epithelial monolayers. Single-cell resolution enabled detailed kinetic profiling of dynamic transcriptional states that correspond to the early acute UPR followed by adaptive restoration of ER homeostasis or terminal cell death. In parallel, we performed a genome-wide CRISPR screen to identify regulatory nodes that control the terminal UPR. Integrative analysis of CRISPR screen results with single-cell transcriptional profiling identified QRICH1 as a critical determinant of cellular entry into the terminal versus adaptive UPR. We demonstrate that QRICH1 is a key effector of the PERK-eIF2α axis of the UPR and that its translation is regulated by an upstream open reading frame in the QRICH1 mRNA. Using a combination of RNA-seq and chromatin immunoprecipitation sequencing (ChIP-seq), we show that QRICH1 bound promoter regions to control a transcriptional module that regulates protein translation and secretory networks. QRICH1-mediated translational activation increased protein flux into the ER and proteotoxicity, whereas QRICH1 knockout protected intestinal epithelial cells from proteotoxicity. Finally, to assess the role of QRICH1 in human disease, we analyzed biopsies of patients with ulcerative colitis (UC) and found evidence of enrichment of the QRICH1 transcriptional signature in inflamed colon biopsies, particularly in secretory epithelial cells and enterocytes. The QRICH1 transcriptional signature was also up-regulated in biopsies of patients with nonalcoholic steatohepatitis and in inflamed and cirrhotic samples from liver biopsies. CONCLUSION Here, we identify a distinct arm of the PERK-eIF2α axis mediated by the transcriptional regulator QRICH1. Cells dynamically respond to ER stress by inducing up-regulation of QRICH1, which modulates translation and transit of proteins through the ER-Golgi secretory pathway. Thus, QRICH1 acts as a regulator of a distinct transcriptional module that coordinates cellular stress responses to regulate protein synthesis and secretion under homeostatic and pathological conditions. Taken together, these findings suggest a broadly conserved role for the QRICH1 transcriptional program in managing cell stress responses and acting as a gatekeeper for controlling cellular entry into the adaptive versus terminal UPR. Mechanistic characterization of QRICH1 within this context provides insight into how cells manage responses to stress and expands our understanding of the UPR pathway, broadening our understanding of the molecular mechanisms by which cellular stress responses are dynamically regulated. QRICH1 controls a distinct arm of the PERK-eIF2α axis to modulate proteostasis and dictate entry into the adaptive versus terminal UPR. In response to ER stress, PERK phosphorylates eIF2α, suppressing global translation while promoting ATF4 and QRICH1 translation by bypassing inhibitory upstream open reading frames (uORFs). QRICH1 localizes to the nucleus and positively regulates the transcription of genes that regulate protein secretion. Prolonged QRICH1 expression is associated with proteotoxicity and cell death during the terminal UPR, whereas its down-regulation is associated with restoration of ER homeostasis during the adaptive UPR. P, phosphorylation; p-PERK, phosphorylated PERK; p-eIF2α, phosphorylated eIF2α. Tissue homeostasis is perturbed in a diversity of inflammatory pathologies. These changes can elicit endoplasmic reticulum (ER) stress, protein misfolding, and cell death. ER stress triggers the unfolded protein response (UPR), which can promote recovery of ER proteostasis and cell survival or trigger programmed cell death. Here, we leveraged single-cell RNA sequencing to define dynamic transcriptional states associated with the adaptive versus terminal UPR in the mouse intestinal epithelium. We integrated these transcriptional programs with genome-scale CRISPR screening to dissect the UPR pathway functionally. We identified QRICH1 as a key effector of the PERK-eIF2α axis of the UPR. QRICH1 controlled a transcriptional program associated with translation and secretory networks that were specifically up-regulated in inflammatory pathologies. Thus, QRICH1 dictates cell fate in response to pathological ER stress.

中文翻译:

QRICH1 通过蛋白质稳态的转录控制来决定 ER 应激的结果

蛋白质稳态的转录控制组织稳态需要多种细胞类型的协调活动来启动然后解决炎症。内在的细胞应激反应途径有助于适应应激和组织恢复。在这些应激途径中,未折叠蛋白反应可以引发两种不同的结果:适应内质网 (ER) 应激或通过程序性细胞死亡终止。你等人。将 QRICH1 鉴定为在蛋白质翻译和分泌水平上控制对 ER 应激的适应的转录调节因子。作者进一步证明了 QRICH1 程序在结肠和肝脏炎症性疾病中的作用。科学,本期第 3 页。45 富含谷氨酰胺的蛋白质调节在炎症病理中特别上调的翻译和分泌网络。引言 组织稳态需要多种细胞类型的协调活动来启动和解决炎症。内质网 (ER) 应激是炎症的标志,会加剧多种人类疾病的组织病理学。与炎症和细胞内在代谢需求相关的环境压力源可引发 ER 应激、蛋白质错误折叠和细胞死亡。为了抵消这些过程,包括未折叠蛋白反应 (UPR) 在内的应激反应途径有助于适应压力和组织恢复。细胞通过由效应蛋白肌醇需要酶 1 (IRE1/ERN1)、激活转录因子 6 (ATF6) 和蛋白激酶 RNA 样 ER 激酶 (PERK、EIF2AK3) 介导的三个协调途径感知 ER 压力并启动 UPR。集体,UPR 效应通路微调蛋白质翻译速率并诱导促进 ER 功能的基因转录上调,例如编码伴侣蛋白和分泌机制的基因。尽管通过 UPR 途径对 ER 应激的这些功能性反应旨在恢复细胞稳态,但长期和未解决的 ER 应激可以引发程序性细胞死亡。在这种情况下,决定 ER 应激结果的分子机制尚不完全清楚。基本原理 肠上皮细胞中 ER 应激的管理不当会导致屏障完整性的破坏,导致宿主免疫系统暴露于引发不受控制的炎症的共生微生物。随着越来越多的证据表明 ER 应激在疾病中的重要作用,UPR 如何指导不同的细胞命运决定仍有待确定。UPR要么诱导促进ER蛋白稳态恢复和细胞存活的适应性阶段,要么诱导启动程序性细胞死亡途径的主动参与的终末期。结果 为了确定控制适应性和终末 UPR 的机制,我们在原代肠上皮单层中使用了单细胞 RNA 测序 (scRNA-seq)。单细胞分辨率能够对动态转录状态进行详细的动力学分析,这些状态对应于早期急性 UPR,然后是 ER 稳态或终末细胞死亡的适应性恢复。同时,我们进行了全基因组 CRISPR 筛选,以识别控制终端 UPR 的调节节点。CRISPR 筛选结果与单细胞转录谱的综合分析确定 QRICH1 是细胞进入终端与自适应 UPR 的关键决定因素。我们证明 QRICH1 是 UPR 的 PERK-eIF2α 轴的关键效应器,并且其翻译受 QRICH1 mRNA 中上游开放阅读框的调节。使用 RNA-seq 和染色质免疫沉淀测序 (ChIP-seq) 的组合,我们显示 QRICH1 结合启动子区域来控制调节蛋白质翻译和分泌网络的转录模块。QRICH1 介导的翻译激活增加了进入 ER 的蛋白质通量和蛋白毒性,而 QRICH1 敲除保护肠上皮细胞免受蛋白毒性。最后,为了评估 QRICH1 在人类疾病中的作用,我们分析了溃疡性结肠炎 (UC) 患者的活检,发现炎症结肠活检中 QRICH1 转录特征富集的证据,特别是在分泌性上皮细胞和肠细胞中。QRICH1 转录特征也在非酒精性脂肪性肝炎患者的活检以及肝活检的发炎和肝硬化样本中上调。结论 在这里,我们确定了由转录调节因子 QRICH1 介导的 PERK-eIF2α 轴的一个独特臂。细胞通过诱导 QRICH1 的上调来动态响应 ER 应激,QRICH1 通过 ER-Golgi 分泌途径调节蛋白质的翻译和转运。因此,QRICH1 充当独特转录模块的调节剂,该模块协调细胞应激反应以调节稳态和病理条件下的蛋白质合成和分泌。总之,这些发现表明 QRICH1 转录程序在管理细胞应激反应和作为控制细胞进入适应性与终端 UPR 的看门人方面具有广泛保守的作用。在这种情况下,QRICH1 的机制表征提供了对细胞如何管理对压力的反应的洞察,并扩大了我们对 UPR 途径的理解,拓宽了我们对动态调节细胞应激反应的分子机制的理解。QRICH1 控制 PERK-eIF2α 轴的一个独特臂来调节蛋白质稳态并指示进入自适应与终末 UPR。响应 ER 应激,PERK 磷酸化 eIF2α,抑制全局翻译,同时通过绕过抑制性上游开放阅读框 (uORF) 促进 ATF4 和 QRICH1 翻译。QRICH1 定位于细胞核并正向调节调节蛋白质分泌的基因的转录。延长的 QRICH1 表达与终末 UPR 期间的蛋白毒性和细胞死亡有关,而其下调与适应性 UPR 期间内质网稳态的恢复有关。P,磷酸化;p-PERK,磷酸化 PERK;p-eIF2α,磷酸化的 eIF2α。组织稳态在多种炎症病理中受到干扰。这些变化会引发内质网 (ER) 应激、蛋白质错误折叠和细胞死亡。内质网应激触发未折叠蛋白反应(UPR),这可以促进 ER 蛋白质稳态的恢复和细胞存活或触发程序性细胞死亡。在这里,我们利用单细胞 RNA 测序来定义与小鼠肠上皮细胞中适应性与末端 UPR 相关的动态转录状态。我们将这些转录程序与基因组规模的 CRISPR 筛选相结合,以在功能上剖析 UPR 通路。我们将 QRICH1 确定为 UPR 的 PERK-eIF2α 轴的关键效应器。QRICH1 控制与翻译和分泌网络相关的转录程序,这些网络在炎症病理中被特异性上调。因此,QRICH1 决定细胞命运以响应病理性 ER 应激。我们利用单细胞 RNA 测序来定义与小鼠肠上皮细胞中适应性与终末 UPR 相关的动态转录状态。我们将这些转录程序与基因组规模的 CRISPR 筛选相结合,以在功能上剖析 UPR 通路。我们将 QRICH1 确定为 UPR 的 PERK-eIF2α 轴的关键效应器。QRICH1 控制与翻译和分泌网络相关的转录程序,这些网络在炎症病理中被特异性上调。因此,QRICH1 决定细胞命运以响应病理性 ER 应激。我们利用单细胞 RNA 测序来定义与小鼠肠上皮细胞中适应性与终末 UPR 相关的动态转录状态。我们将这些转录程序与基因组规模的 CRISPR 筛选相结合,以在功能上剖析 UPR 通路。我们将 QRICH1 确定为 UPR 的 PERK-eIF2α 轴的关键效应器。QRICH1 控制与翻译和分泌网络相关的转录程序,这些网络在炎症病理中被特异性上调。因此,QRICH1 决定细胞命运以响应病理性 ER 应激。QRICH1 控制与翻译和分泌网络相关的转录程序,这些网络在炎症病理中被特异性上调。因此,QRICH1 决定细胞命运以响应病理性 ER 应激。QRICH1 控制与翻译和分泌网络相关的转录程序,这些网络在炎症病理中被特异性上调。因此,QRICH1 决定细胞命运以响应病理性 ER 应激。
更新日期:2020-12-31
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