QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis

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.