bims-ershed Biomed News
on ER Stress in Health and Diseases
Issue of 2021–09–26
twelve papers selected by
Matías Eduardo González Quiroz, Worker’s Hospital
  1. ATP-competitive partial antagonists of the IRE1α RNase segregate outputs of the UPR.
  2. Necroptosis activates UPR sensors without disrupting their binding with GRP78.
  3. Enhanced GRP78 protein expression via the IRE1α/ASK1/p38 MAPK pathway during As2O3-induced endoplasmic reticulum stress in BEAS-2B cells.
  4. Targeting the IRE1α/XBP1 Endoplasmic Reticulum Stress Response Pathway in ARID1A-Mutant Ovarian Cancers.
  5. ATF6 is essential for human cone photoreceptor development.
  6. Therapeutic Effects of Natural Compounds and Small Molecule Inhibitors Targeting Endoplasmic Reticulum Stress in Alzheimer's Disease.
  7. Elongin functions as a loading factor for Mediator at ATF6α-regulated ER stress response genes.
  8. The future in an RNA molecule: from mRNA vaccines to therapeutics - An interview with Drew Weissman.
  9. How COVID-19 changed scientific mentoring.
  10. Regulation of mRNA decay in E. coli.
  11. Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity.
  12. Substrate ubiquitination retains misfolded membrane proteins in the endoplasmic reticulum for degradation.
  1. Nat Chem Biol. 2021 Sep 23.
    ATP-competitive partial antagonists of the IRE1α RNase segregate outputs of the UPR.
    Hannah C Feldman, Rajarshi Ghosh, Vincent C Auyeung, James L Mueller, Jae-Hong Kim, Zachary E Potter, Venkata N Vidadala, B Gayani K Perera, Alina Olivier, Bradley J Backes, Julie Zikherman, Feroz R Papa, Dustin J Maly.
      The unfolded protein response (UPR) homeostatically matches endoplasmic reticulum (ER) protein-folding capacity to cellular secretory needs. However, under high or chronic ER stress, the UPR triggers apoptosis. This cell fate dichotomy is promoted by differential activation of the ER transmembrane kinase/endoribonuclease (RNase) IRE1α. We previously found that the RNase of IRE1α can be either fully activated or inactivated by ATP-competitive kinase inhibitors. Here we developed kinase inhibitors, partial antagonists of IRE1α RNase (PAIRs), that partially antagonize the IRE1α RNase at full occupancy. Biochemical and structural studies show that PAIRs promote partial RNase antagonism by intermediately displacing the helix αC in the IRE1α kinase domain. In insulin-producing β-cells, PAIRs permit adaptive splicing of Xbp1 mRNA while quelling destructive ER mRNA endonucleolytic decay and apoptosis. By preserving Xbp1 mRNA splicing, PAIRs allow B cells to differentiate into immunoglobulin-producing plasma cells. Thus, an intermediate RNase-inhibitory 'sweet spot', achieved by PAIR-bound IRE1α, captures a desirable conformation for drugging this master UPR sensor/effector.
    DOI:  https://doi.org/10.1038/s41589-021-00852-0
  2. Proc Natl Acad Sci U S A. 2021 09 28. pii: e2110476118. [Epub ahead of print]118(39):
    Necroptosis activates UPR sensors without disrupting their binding with GRP78.
    Wei Liang, Weiwei Qi, Yang Geng, Linhan Wang, Jing Zhao, Kezhou Zhu, Guowei Wu, Zairong Zhang, Heling Pan, Lihui Qian, Junying Yuan.
      Necroptosis is a form of regulated necrosis mediated by the formation of the necrosome, composed of the RIPK1/RIPK3/MLKL complex. Here, we developed a proximity ligation assay (PLA) that allows in situ visualization of necrosomes in necroptotic cells and in vivo. Using PLA assay, we show that necrosomes can be found in close proximity to the endoplasmic reticulum (ER). Furthermore, we show that necroptosis activates ER stress sensors, PERK, IRE1α, and ATF6 in a RIPK1-RIPK3-MLKL axis-dependent manner. Activated MLKL can be translocated to the ER membrane to directly initiate the activation of ER stress signaling. The activation of IRE1α in necroptosis promotes the splicing of XBP1, and the subsequent incorporation of spliced XBP1 messenger RNA (mRNA) into extracellular vesicles (EVs). Finally, we show that unlike that of a conventional ER stress response, necroptosis promotes the activation of unfolded protein response (UPR) sensors without affecting their binding of GRP78. Our study reveals a signaling pathway that links MLKL activation in necroptosis to an unconventional ER stress response.
    Keywords:  ER stress; IRE1α; PERK; UPR sensors; necroptosis
    DOI:  https://doi.org/10.1073/pnas.2110476118
  3. Toxicology. 2021 Sep 21. pii: S0300-483X(21)00284-5. [Epub ahead of print] 152962
    Enhanced GRP78 protein expression via the IRE1α/ASK1/p38 MAPK pathway during As2O3-induced endoplasmic reticulum stress in BEAS-2B cells.
    Jiaming Yuan, Chenjuan Yao, Jing Tang, Yingqi Liu, Chunyan Huang, Shali Yu, Haiyan Wei, Yu Han, Gang Chen.
      Inorganic arsenic is widely present in the environment. Exposure to moderate to high concentrations of arsenic from drinking water or air can cause various cancers and multisystem dysfunction. Glucose-regulated protein 78 (GRP78) is an endoplasmic reticulum (ER) stress sensor of unfolded protein response (UPR) under stress conditions and it enhances cell survival. The aim of this study is to investigate molecular mechanisms of arsenic-induced GRP78 expression in BEAS-2B cells model. We found that GRP78 protein expression was enhanced, while the level of GRP78 mRNA expression did not change under arsenic trioxide (As2O3)-induced ER stress condition in BEAS-2B cells. Cycloheximide, a protein synthesis inhibitor, completely inhibited As2O3-induced GRP78 protein expression. GRP78 mRNA expression was inhibited by actinomycin-D (Act-D). However, GRP78 protein expression was upregulated in the presence of Act-D under As2O3-induced ER stress condition. These data indicated that the upregulation of GRP78 protein under As2O3-induced UPR condition was possibly due to the increased biosynthesis of GRP78 protein. Moreover, both inositol-requiring enzyme 1α (IRE1α) RNase and kinase inhibitor KIRA6 and IRE1α kinase inhibitor APY29 completely inhibited As2O3-induced GRP78 protein expression and phosphorylation of JNK, ERK and p38 MAPK. Activation of apoptotic signaling kinase 1 (ASK1) is a downstream effector of IRE1α kinase. ASK1 inhibitor selonsertib and p38 MAPK inhibitor SB203580 partially inhibited As2O3-induced GRP78 protein expression, respectively. Our results suggested that As2O3 enhanced GRP78 protein expression in BEAS-2B cells via IRE1α kinase/ASK1/p38 MAPK signaling pathway. To our knowledge, this is the first report on illuminating the related mechanisms of increased GRP78 protein expression in As2O3-induced ER stress condition through a novel IRE1α pathway.
    Keywords:  arsenic trioxide (As(2)O(3)); endoplasmic reticulum stress (ER stress); glucose-regulated protein 78 (GRP78); inositol-requiring enzyme 1α (IRE1α); p38 MAPK
    DOI:  https://doi.org/10.1016/j.tox.2021.152962
  4. Cancer Res. 2021 Sep 21.
    Targeting the IRE1α/XBP1 Endoplasmic Reticulum Stress Response Pathway in ARID1A-Mutant Ovarian Cancers.
    Joseph A Zundell, Takeshi Fukumoto, Jianhuang Lin, Nail Fatkhudinov, Timothy Nacarelli, Andrew V Kossenkov, Qin Liu, Joel Cassel, Chih-Chi Andrew Hu, Shuai Wu, Rugang Zhang.
      The SWI/SNF chromatin-remodeling complex is frequently altered in human cancers. For example, the SWI/SNF component ARID1A is mutated in more than 50% of ovarian clear cell carcinomas (OCCC), for which effective treatments are lacking. Here, we report that ARID1A transcriptionally represses the IRE1α-XBP1 axis of the endoplasmic reticulum (ER) stress response, which confers sensitivity to inhibition of the IRE1α-XBP1 pathway in ARID1A-mutant OCCC. ARID1A mutational status correlated with response to inhibition of the IRE1α-XBP1 pathway. In a conditional Arid1aflox/flox/Pik3caH1047R genetic mouse model, Xbp1 knockout significantly improved survival of mice bearing OCCCs. Furthermore, the IRE1α inhibitor B-I09 suppressed the growth of ARID1A-inactivated OCCCs in vivo in orthotopic xenograft, patient-derived xenograft, and the genetic mouse models. Finally, B-I09 synergized with inhibition of HDAC6, a known regulator of the ER stress response, in suppressing the growth of ARID1A-inactivated OCCCs. These studies define the IRE1α-XBP1 axis of the ER stress response as a targetable vulnerability for ARID1A-mutant OCCCs, revealing a promising therapeutic approach for treating ARID1A-mutant ovarian cancers. SIGNIFICANCE: These findings indicate that pharmacological inhibition of the IRE1α-XBP1 pathway alone or in combination with HDAC6 inhibition represents an urgently needed therapeutic strategy for ARID1A-mutant ovarian cancers.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1545
  5. Proc Natl Acad Sci U S A. 2021 Sep 28. pii: e2103196118. [Epub ahead of print]118(39):
    ATF6 is essential for human cone photoreceptor development.
    Heike Kroeger, Julia M D Grandjean, Wei-Chieh Jerry Chiang, Daphne D Bindels, Rebecca Mastey, Jennifer Okalova, Amanda Nguyen, Evan T Powers, Jeffery W Kelly, Neil J Grimsey, Michel Michaelides, Joseph Carroll, R Luke Wiseman, Jonathan H Lin.
      Endoplasmic reticulum (ER) stress and Unfolded Protein Response (UPR) signaling promote the pathology of many human diseases. Loss-of-function variants of the UPR regulator Activating Transcription Factor 6 (ATF6) cause severe congenital vision loss diseases such as achromatopsia by unclear pathomechanisms. To investigate this, we generated retinal organoids from achromatopsia patient induced pluripotent stem cells carrying ATF6 disease variants and from gene-edited ATF6 null hESCs. We found that achromatopsia patient and ATF6 null retinal organoids failed to form cone structures concomitant with loss of cone phototransduction gene expression, while rod photoreceptors developed normally. Adaptive optics retinal imaging of achromatopsia patients carrying ATF6 variants also showed absence of cone inner/outer segment structures but preserved rod structures, mirroring the defect in cone formation observed in our retinal organoids. These results establish that ATF6 is essential for human cone development. Interestingly, we find that a selective small molecule ATF6 signaling agonist restores the transcriptional activity of some ATF6 disease-causing variants and stimulates cone growth and gene expression in patient retinal organoids carrying these variants. These findings support that pharmacologic targeting of the ATF6 pathway can promote human cone development and should be further explored for blinding retinal diseases.
    Keywords:  ATF6 signaling; achromatopsia; cone photoreceptors; retinal organoids; stem cell biology
    DOI:  https://doi.org/10.1073/pnas.2103196118
  6. Front Cell Dev Biol. 2021 ;9 745011
    Therapeutic Effects of Natural Compounds and Small Molecule Inhibitors Targeting Endoplasmic Reticulum Stress in Alzheimer's Disease.
    Xun Gao, Yuanyuan Xu.
      Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by progressive cognitive impairment and memory loss. So far, the pathogenesis of AD has not been fully understood. Research have shown that endoplasmic reticulum (ER) stress and unfolded protein response (UPR) participate in the occurrence and development of AD. Furthermore, various studies, both in vivo and in vitro, have shown that targeting ER stress and ER stress-mediated apoptosis contribute to the recovery of AD. Thus, targeting ER stress and ER stress-mediated apoptosis may be effective for treating AD. In this review, the molecular mechanism of ER stress and ER stress-mediated apoptosis, as well as the therapeutic effects of some natural compounds and small molecule inhibitors targeting ER stress and ER stress-mediated apoptosis in AD will be introduced.
    Keywords:  Alzheimer’s disease; apoptosis; endoplasmic reticulum stress; neuroprotection; unfolded protein response
    DOI:  https://doi.org/10.3389/fcell.2021.745011
  7. Proc Natl Acad Sci U S A. 2021 09 28. pii: e2108751118. [Epub ahead of print]118(39):
    Elongin functions as a loading factor for Mediator at ATF6α-regulated ER stress response genes.
    Yanfeng He, Shigeo Sato, Chieri Tomomori-Sato, Shiyuan Chen, Zach H Goode, Joan W Conaway, Ronald C Conaway.
      The bZIP transcription factor ATF6α is a master regulator of endoplasmic reticulum (ER) stress response genes. In this report, we identify the multifunctional RNA polymerase II transcription factor Elongin as a cofactor for ATF6α-dependent transcription activation. Biochemical studies reveal that Elongin functions at least in part by facilitating ATF6α-dependent loading of Mediator at the promoters and enhancers of ER stress response genes. Depletion of Elongin from cells leads to impaired transcription of ER stress response genes and to defects in the recruitment of Mediator and its CDK8 kinase subunit. Taken together, these findings bring to light a role for Elongin as a loading factor for Mediator during the ER stress response.
    Keywords:  Mediator; RNA polymerase II; enhancer; transcription
    DOI:  https://doi.org/10.1073/pnas.2108751118
  8. FEBS Lett. 2021 Sep 21.
    The future in an RNA molecule: from mRNA vaccines to therapeutics - An interview with Drew Weissman.
    Daniela Ruffell.
      
    DOI:  https://doi.org/10.1002/1873-3468.14190
  9. Nature. 2021 Sep 22.
    How COVID-19 changed scientific mentoring.
    Julie Gould.
      
    DOI:  https://doi.org/10.1038/d41586-021-02570-y
  10. Crit Rev Biochem Mol Biol. 2021 Sep 21. 1-25
    Regulation of mRNA decay in E. coli.
    Bijoy K Mohanty, Sidney R Kushner.
      Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed that most of the ribonucleases and accessory proteins involved in mRNA decay have been identified, our understanding of the regulation of mRNA decay is still incomplete. Furthermore, the vast majority of the studies on mRNA decay have been conducted on exponentially growing cells. Thus, the mechanism of mRNA decay as currently outlined may not accurately reflect what happens when cells find themselves under a variety of stress conditions, such as, nutrient starvation, changes in pH and temperature, as well as a host of others. While the cellular machinery for degradation is relatively constant over a wide range of conditions, intracellular levels of specific ribonucleases can vary depending on the growth conditions. Substrate competition will also modulate ribonucleolytic activity. Post-transcriptional modifications of transcripts by polyadenylating enzymes may favor a specific ribonuclease activity. Interactions with small regulatory RNAs and RNA binding proteins add additional complexities to mRNA functionality and stability. Since many of the ribonucleases are found at the inner membrane, the physical location of a transcript may help determine its half-life. Here we discuss the properties and role of the enzymes involved in mRNA decay as well as the multiple factors that may affect mRNA decay under various in vivo conditions.
    Keywords:  RNase E; RNase III; RNase P; exonucleases; polyadenylation; sRNAs
    DOI:  https://doi.org/10.1080/10409238.2021.1968784
  11. Exp Mol Med. 2021 Sep 21.
    Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity.
    Seo Yun Lee, Jae Jin Kim, Kyle M Miller.
      Endogenous DNA damage is a major contributor to mutations, which are drivers of cancer development. Bromodomain (BRD) proteins are well-established participants in chromatin-based DNA damage response (DDR) pathways, which maintain genome integrity from cell-intrinsic and extrinsic DNA-damaging sources. BRD proteins are most well-studied as regulators of transcription, but emerging evidence has revealed their importance in other DNA-templated processes, including DNA repair and replication. How BRD proteins mechanistically protect cells from endogenous DNA damage through their participation in these pathways remains an active area of investigation. Here, we review several recent studies establishing BRD proteins as key influencers of endogenous DNA damage, including DNA-RNA hybrid (R-loops) formation during transcription and participation in replication stress responses. As endogenous DNA damage is known to contribute to several human diseases, including neurodegeneration, immunodeficiencies, cancer, and aging, the ability of BRD proteins to suppress DNA damage and mutations is likely to provide new insights into the involvement of BRD proteins in these diseases. Although many studies have focused on BRD proteins in transcription, evidence indicates that BRD proteins have emergent functions in DNA repair and genome stability and are participants in the etiology and treatment of diseases involving endogenous DNA damage.
    DOI:  https://doi.org/10.1038/s12276-021-00673-0
  12. Cell Rep. 2021 Sep 21. pii: S2211-1247(21)01166-9. [Epub ahead of print]36(12): 109717
    Substrate ubiquitination retains misfolded membrane proteins in the endoplasmic reticulum for degradation.
    Zhihao Sun, Christopher J Guerriero, Jeffrey L Brodsky.
      To maintain secretory pathway fidelity, misfolded proteins are commonly retained in the endoplasmic reticulum (ER) and selected for ER-associated degradation (ERAD). Soluble misfolded proteins use ER chaperones for retention, but the machinery that restricts aberrant membrane proteins to the ER is unclear. In fact, some misfolded membrane proteins escape the ER and traffic to the lysosome/vacuole. To this end, we describe a model substrate, SZ∗, that contains an ER export signal but is also targeted for ERAD. We observe decreased ER retention when chaperone-dependent SZ∗ ubiquitination is compromised. In addition, appending a linear tetra-ubiquitin motif onto SZ∗ overrides ER export. By screening known ubiquitin-binding proteins, we then positively correlate SZ∗ retention with Ubx2 binding. Deletion of Ubx2 also inhibits the retention of another misfolded membrane protein. Our results indicate that polyubiquitination is sufficient to retain misfolded membrane proteins in the ER prior to ERAD.
    Keywords:  ERAD; Ubx2; chaperone; proteasome; protein quality control; ubiquitination; vacuole; yeast
    DOI:  https://doi.org/10.1016/j.celrep.2021.109717
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