bims-ershed Biomed News
on ER Stress in Health and Diseases
Issue of 2021–10–10
seven papers selected by
Matías Eduardo González Quiroz, Worker’s Hospital
  1. Epithelial XBP1 coordinates TP53-driven DNA damage responses and suppression of intestinal carcinogenesis.
  2. The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction in Drosophila.
  3. Ubiquitination of ATF6 by disease-associated RNF186 promotes the innate receptor-induced unfolded protein response.
  4. Sevoflurane post-conditioning alleviated hypoxic-ischemic brain injury in neonatal rats by inhibiting endoplasmic reticulum stress-mediated autophagy via IRE1 signalings.
  5. Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells.
  6. Cell survival after DNA damage in the comet assay.
  7. An atlas of gene regulatory elements in adult mouse cerebrum.
  1. Gastroenterology. 2021 Sep 29. pii: S0016-5085(21)03606-4. [Epub ahead of print]
    Epithelial XBP1 coordinates TP53-driven DNA damage responses and suppression of intestinal carcinogenesis.
    Lina Welz, Nassim Kakavand, Xiang Hang, Georg Laue, Go Ito, Miguel Gomes Silva, Christina Plattner, Neha Mishra, Felicitas Tengen, Christoph Ogris, Moritz Jesinghaus, Felix Wottawa, Philipp Arnold, Leena Kaikkonen, Stefanie Stengel, Florian Tran, Saumya Das, Arthur Kaser, Zlatko Trajanoski, Richard Blumberg, Christoph Roecken, Dieter Saur, Markus Tschurtschenthaler, Stefan Schreiber, Philip Rosenstiel, Konrad Aden.
       BACKGROUND AIMS: Throughout life, the intestinal epithelium undergoes constant self-renewal from intestinal stem cells. Together with genotoxic stressors and failing DNA repair, this self-renewal causes susceptibility towards malignant transformation. X-box binding protein 1 (XBP1) is a stress sensor involved in the unfolded protein response (UPR). We hypothesized that XBP1 acts as a signaling hub to regulate epithelial DNA damage responses.
    METHODS: Data from the TCGA were analyzed for association of XBP1 with CRC survival and molecular interactions between XBP1 andp53 pathway activity. The role of XBP1 in orchestrating p53-driven DNA damage response was tested in-vitro, in mouse models of chronic intestinal epithelial DNA damage (Xbp1/H2bfl/fl, Xbp1ΔIEC, H2bΔIEC, H2b/Xbp1ΔIEC) and via orthotopic tumor organoid transplantation. Transcriptome analysis of intestinal organoids was performed to identify molecular targets of Xbp1-mediated DNA damage response.
    RESULTS: In the TCGA dataset of CRC, low XBP1 expression was significantly associated with poor overall survival (OS) and reduced p53 pathway activity. In-vivo, H2b/Xbp1ΔIEC mice developed spontaneous intestinal carcinomas. Orthotopic tumor organoid transplantation revealed a metastatic potential of H2b/Xbp1ΔIEC-derived tumors. RNA sequencing of intestinal organoids (H2b/Xbp1fl/fl, H2bΔIEC, H2b/Xbp1ΔIEC, H2b/p53ΔIEC) identified a transcriptional program downstream of p53, in which XBP1 directs DNA damage-induced Ddit4l expression. DDIT4L inhibits mTOR-mediated phosphorylation of 4E-BP1. Pharmacological mTOR inhibition suppressed epithelial hyperproliferation via 4E-BP1.
    CONCLUSIONS: Our data suggest a crucial role for XBP1 in coordinating epithelial DNA damage responses and stem cell function via a p53-DDIT4L-dependent feedback mechanism.
    Keywords:  CRC; DNA damage; XBP1; intestinal epithelial cell; p53
    DOI:  https://doi.org/10.1053/j.gastro.2021.09.057
  2. Elife. 2021 Oct 04. pii: e74047. [Epub ahead of print]10
    The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction in Drosophila.
    Brian Brown, Sahana Mitra, Finnegan D Roach, Deepika Vasudevan, Hyung Don Ryoo.
      PERK is an endoplasmic reticulum (ER) transmembrane sensor that phosphorylates eIF2a to initiate the Unfolded Protein Response (UPR). eIF2a phosphorylation promotes stress-responsive gene expression most notably through the transcription factor ATF4 that contains a regulatory 5' leader. Possible PERK effectors other than ATF4 remain poorly understood. Here, we report that the bZIP transcription factor Xrp1 is required for ATF4-independent PERK signaling. Cell type-specific gene expression profiling in Drosophila indicated that delta-family glutathione-S-transferases (gstD) are prominently induced by the UPR-activating transgene Rh1G69D. Perk was necessary and sufficient for such gstD induction, but ATF4 was not required. Instead, Perk and other regulators of eIF2a phosphorylation regulated Xrp1 protein levels to induce gstDs. The Xrp1 5' leader has a conserved upstream Open Reading Frame (uORF) analogous to those that regulate ATF4 translation. The gstD-GFP reporter induction required putative Xrp1 binding sites. These results indicate that antioxidant genes are highly induced by a previously unrecognized UPR signaling axis consisting of PERK and Xrp1.
    Keywords:  D. melanogaster; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.74047
  3. J Clin Invest. 2021 Sep 01. pii: e145472. [Epub ahead of print]131(17):
    Ubiquitination of ATF6 by disease-associated RNF186 promotes the innate receptor-induced unfolded protein response.
    Kishu Ranjan, Matija Hedl, Saloni Sinha, Xuchen Zhang, Clara Abraham.
      Properly balancing microbial responses by the innate immune system through pattern recognition receptors (PRRs) is critical for intestinal immune homeostasis. Ring finger protein 186 (RNF186) genetic variants are associated with inflammatory bowel disease (IBD). However, functions for the E3 ubiquitin ligase RNF186 are incompletely defined. We found that upon stimulation of the PRR nucleotide-binding oligomerization domain containing 2 (NOD2) in human macrophages, RNF186 localized to the ER, formed a complex with ER stress sensors, ubiquitinated the ER stress sensor activating transcription factor 6 (ATF6), and promoted the unfolded protein response (UPR). These events, in turn, led to downstream signaling, cytokine secretion, and antimicrobial pathway induction. Importantly, RNF186-mediated ubiquitination of K152 on ATF6 was required for these outcomes, highlighting a key role for ATF6 ubiquitination in PRR-initiated functions. Human macrophages transfected with the rare RNF186-A64T IBD risk variant and macrophages from common rs6426833 RNF186 IBD risk carriers demonstrated reduced NOD2-induced outcomes, which were restored by rescuing UPR signaling. Mice deficient in RNF186 or ATF6 demonstrated a reduced UPR in colonic tissues, increased weight loss, and less effective clearance of bacteria with dextran sodium sulfate-induced injury and upon oral challenge with Salmonella Typhimurium. Therefore, we identified that RNF186 was required for PRR-induced, UPR-associated signaling leading to key macrophage functions; defined that RNF186-mediated ubiquitination of ATF6 was essential for these functions; and elucidated how RNF186 IBD risk variants modulated these outcomes.
    Keywords:  Immunology; Innate immunity; Macrophages
    DOI:  https://doi.org/10.1172/JCI145472
  4. Neurochem Int. 2021 Sep 30. pii: S0197-0186(21)00244-8. [Epub ahead of print]150 105198
    Sevoflurane post-conditioning alleviated hypoxic-ischemic brain injury in neonatal rats by inhibiting endoplasmic reticulum stress-mediated autophagy via IRE1 signalings.
    Jiayuan Niu, Ziyi Wu, Hang Xue, Yahan Zhang, Qiushi Gao, Chang Li, Ping Zhao.
      Post-conditioning with sevoflurane, a volatile anesthetic, has been proved to be neuroprotective against hypoxic-ischemic brain injury (HIBI). Our previous research showed that autophagy is over-activated in a neonatal HIBI rat model, and inhibition of autophagy confers neuroprotection. There is increasing recognition that autophagy can be stimulated by activating endoplasmic reticulum (ER) stress. Herein, we purposed to explore: i) the association of ER stress with autophagy in the setting of neonatal HIBI; and ii) the possible roles of ER stress-triggered autophagy, as well as IRE1 signaling in the neuroprotection of sevoflurane post-conditioning against neonatal HIBI. Seven-day-old rats underwent ligation of the left common artery, and a subsequent 2 h hypoxia (8% O2/92% N2). The association of ER stress with autophagy was examined by ER stress inducer (tunicamycin), 4-PBA (ER stress inhibitor), or 3-MA (autophagy inhibitor). Rats in the sevoflurane post-conditioning groups were treated with 2.4% sevoflurane for 30 min after HIBI stimulation. The roles of ER stress-mediated autophagy, as well as the IRE1-JNK-beclin1 signaling cascade in the neuroprotection afforded by sevoflurane were explored by ER stress inducer (tunicamycin) and the IRE1 inhibitor (STF-083010). HIBI over-activated ER stress and autophagy in neonatal rats. HIBI-induced autophagy was significantly aggravated by tunicamycin but blocked by 4-PBA; however, HIBI-induced ER stress was not affected by 3-MA. Sevoflurane post-conditioning significantly alleviated ER stress, autophagy, cell apoptosis, and cognitive impairments, which were remarkably abolished by tunicamycin. Also, tunicamycin blocked sevoflurane-induced downregulation of IRE1-JNK-beclin1 signaling pathway. Whereas, IRE1 inhibitor could reverse the effects of tunicamycin. ER stress contributes to autophagy induced by HIBI. Furthermore, sevoflurane post-conditioning significantly protects against HIBI in neonatal rats by inhibiting ER stress-mediated autophagy via IRE1-JNK-beclin1 signaling cascade.
    Keywords:  Autophagy; Endoplasmic reticulum stress; Hypoxic-ischemic brain injury; IRE1; Sevoflurane post-conditioning
    DOI:  https://doi.org/10.1016/j.neuint.2021.105198
  5. Chembiochem. 2021 Oct 06.
    Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells.
    Di Shen, Yulong Bai, Yu Liu.
      Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel tools and methods to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnosis, and therapeutics. In this review, we summarized the recent progress on the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, chemical protein tags, and small molecule probes to visualize protein aggregation process, detect proteome stresses, and quantify protein homeostasis network capacity. Inspired by these seminal works, we generalized design principles to develop new detection methods and probes that illuminate this important biological process in the future.
    Keywords:  protein aggregation, fluorescent protein, AggTag, proteostasis capacity sensor, small molecule probe
    DOI:  https://doi.org/10.1002/cbic.202100443
  6. Arch Toxicol. 2021 Oct 05.
    Cell survival after DNA damage in the comet assay.
    Ezgi Eyluel Bankoglu, Carolin Schuele, Helga Stopper.
      The comet assay is widely used in basic research, genotoxicity testing, and human biomonitoring. However, interpretation of the comet assay data might benefit from a better understanding of the future fate of a cell with DNA damage. DNA damage is in principle repairable, or if extensive, can lead to cell death. Here, we have correlated the maximally induced DNA damage with three test substances in TK6 cells with the survival of the cells. For this, we selected hydrogen peroxide (H2O2) as an oxidizing agent, methyl methanesulfonate (MMS) as an alkylating agent and etoposide as a topoisomerase II inhibitor. We measured cell viability, cell proliferation, apoptosis, and micronucleus frequency on the following day, in the same cell culture, which had been analyzed in the comet assay. After treatment, a concentration dependent increase in DNA damage and in the percentage of non-vital and apoptotic cells was found for each substance. Values greater than 20-30% DNA in tail caused the death of more than 50% of the cells, with etoposide causing slightly more cell death than H2O2 or MMS. Despite that, cells seemed to repair of at least some DNA damage within few hours after substance removal. Overall, the reduction of DNA damage over time is due to both DNA repair and death of heavily damaged cells. We recommend that in experiments with induction of DNA damage of more than 20% DNA in tail, survival data for the cells are provided.
    Keywords:  Cell death and comet assay; DNA damage; DNA repair
    DOI:  https://doi.org/10.1007/s00204-021-03164-3
  7. Nature. 2021 Oct;598(7879): 129-136
    An atlas of gene regulatory elements in adult mouse cerebrum.
    Yang Eric Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Yunjiang Qiu, Olivier B Poirion, Bin Li, Joshua Chiou, Hanqing Liu, Antonio Pinto-Duarte, Naoki Kubo, Xiaoyu Yang, Rongxin Fang, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Michael Miller, Samantha Kuan, David Gorkin, Kyle J Gaulton, Yin Shen, Michael Nunn, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker, Bing Ren.
      The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2-6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.
    DOI:  https://doi.org/10.1038/s41586-021-03604-1
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