bims-ershed Biomed News
on ER Stress in Health and Diseases
Issue of 2022–01–09
ten papers selected by
Matías Eduardo González Quiroz, Worker’s Hospital
  1. Structure-Based Drug Discovery of IRE1 Modulators.
  2. Assays to Study IRE1 Activation and Signaling.
  3. Drosophila Unfolded Protein Response (UPR) Assays In Vitro and In Vivo.
  4. Detecting the Non-conventional mRNA Splicing and Translational Activation of HAC1 in Budding Yeast.
  5. Detection of HAC1 mRNA Splicing by RT-PCR in Saccharomyces cerevisiae.
  6. In Vitro Stimulation of IRE1α/XBP1-Deficient B Cells with LPS.
  7. Analysis of XBP1 Contribution to Hyperosmolarity-Induced Lipid Synthesis.
  8. The Use of Fluorescent Protein Fusions to Monitor the Unfolded Protein Response and Protein Foldase-Substrate Interactions in Plant Protoplasts.
  9. Fluorescence-Based Biosensors for the Detection of the Unfolded Protein Response.
  10. Detection of PERK Signaling in the Central Nervous System.
  1. Methods Mol Biol. 2022 ;2378 293-315
    Structure-Based Drug Discovery of IRE1 Modulators.
    Diana Pelizzari Raymundo, Leif A Eriksson, Eric Chevet, Xavier Guillory.
      IRE1α (inositol-requiring enzyme 1 alpha, referred to IRE1 hereafter) is an Endoplasmic Reticulum (ER) resident transmembrane enzyme with cytosolic kinase/RNAse activities. Upon ER stress IRE1 is activated through trans-autophosphorylation and oligomerization, resulting in a conformational change of the RNase domain, thereby promoting two signaling pathways: i) the non-conventional splicing of XBP1 mRNA and ii) the regulated IRE1-dependent decay of RNA (RIDD). IRE1 RNase activity has been linked to diverse pathologies such as cancer or inflammatory, metabolic, and degenerative diseases and the modulation of IRE1 activity is emerging as an appealing therapeutic strategy against these diseases. Several modulators of IRE1 activity have been reported in the past, but none have successfully translated into the clinics as yet. Based on our expertise in the field, we describe in this chapter the approaches and protocols we used to discover novel IRE1 modulators and characterize their effect on IRE1 activity.
    Keywords:  Endoplasmic reticulum; IRE1; Structure-based drug discovery (SBDD); Unfolded protein response computer assisted drug design (CADD)
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_19
  2. Methods Mol Biol. 2022 ;2378 141-168
    Assays to Study IRE1 Activation and Signaling.
    Paloma Moraga, Raul Aravena, Hery Urra, Claudio Hetz.
      The endoplasmic reticulum (ER) stress sensor IRE1 is a a major player of the unfolded protein response (UPR), the main pathway driving adaptation processes to restore proteostasis.  In addition, overactivation of IRE1 signaling contributes to a variety of pathologies including diabetes, neurodegenerative diseases, and cancer. Under ER stress, IRE1 auto-transphosphorylates and oligomerizes, triggering the activation of its endoribonuclease domain located in the cytosolic region. Active IRE1 catalyzes the splicing of the mRNA encoding for the XBP1 transcription factor, in addition to degrade several RNAs through a process known as regulated IRE1-dependent decay of mRNA (RIDD). Besides its role as an UPR transducer, several posttranslational modifications and protein-protein interactions can regulate IRE1 activity and modulate its signaling in the absence of stress. Thus, investigating the function of IRE1 in physiology and disease requires the use of complementary approaches. Here, we provide detailed protocols to perform four different assays to study IRE1 activation and signaling: (i) Phos-tag gels to evaluate the phosphorylation status of IRE1, (ii) microscopy using TREX-IRE1-GFP cells to measure IRE1 oligomerization, (iii) conventional RT-PCR to assess XBP1 mRNA processing, and (iv) quantitative PCR to determine the levels of canonical UPR target genes and the degradation of several mRNAs that are target of RIDD. We propose to use these experimental strategies as "gold standards" to study IRE1 signaling.
    Keywords:  ER stress; IRE1 activation; IRE1 oligomerization; IRE1 phosphorylation; Regulated IRE1-dependent decay (RIDD); Unfolded protein response; XBP1 mRNA splicing
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_10
  3. Methods Mol Biol. 2022 ;2378 261-277
    Drosophila Unfolded Protein Response (UPR) Assays In Vitro and In Vivo.
    Hidetaka Katow, Deepika Vasudevan, Hyung Don Ryoo.
      Wildtype or mutant proteins expressed beyond the capacity of a cell's protein folding system could be detrimental to general cellular function and survival. In response to misfolded protein overload in the endoplasmic reticulum (ER), eukaryotic cells activate the Unfolded Protein Response (UPR) that helps cells restore protein homeostasis in the endoplasmic reticulum (ER). As part of the UPR, cells attenuate general mRNA translation and activate transcription factors that induce stress-responsive gene expression.UPR signaling draws research interest in part because conditions that cause chronic protein misfolding in the ER or those that impair UPR signaling underlie several diseases including neurodegeneration, diabetes, and cancers. Model organisms are frequently employed in the field as the UPR pathways are generally well-conserved throughout phyla. Here, we introduce experimental procedures to detect UPR in Drosophila melanogaster.
    Keywords:  ATF4 (crc); Drosophila melanogaster; ER stress; Eye discs; Fat body; IRE1; PERK; Unfolded Protein Response; Xbp1
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_17
  4. Methods Mol Biol. 2022 ;2378 113-120
    Detecting the Non-conventional mRNA Splicing and Translational Activation of HAC1 in Budding Yeast.
    Weihan Li, Robert H Singer.
      Protein-folding homeostasis in the endoplasmic reticulum (ER) is maintained by the unfolded protein response (UPR). UPR in Saccharomyces cerevisiae is regulated by a bZIP transcription factor, Hac1p. Under non-stress condition, HAC1 mRNA is translationally repressed. When un- or mis-folded proteins accumulate in the ER, HAC1 mRNA undergoes non-conventional mRNA splicing. The spliced HAC1 mRNA is translationally active and produces functional Hac1p, which initiates a transcriptional response that restores ER protein-folding homeostasis. Thus, the activation of yeast UPR is tightly regulated by HAC1 mRNA splicing. Here, we describe two methods that are used to monitor the splicing and translational status of HAC1 mRNA in budding yeast.
    Keywords:  Budding yeast; ER stress; HAC1; Non-conventional mRNA splicing; Unfolded protein response
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_8
  5. Methods Mol Biol. 2022 ;2378 101-110
    Detection of HAC1 mRNA Splicing by RT-PCR in Saccharomyces cerevisiae.
    Jagadeesh Kumar Uppala, Madhusudan Dey.
      HAC1 mRNA remains translationally repressed in the cytoplasm of the budding yeast Saccharomyces cerevisiae. Under conditions of cellular stress, a dual kinase RNase IRE1 (Inositol Requiring Enzyme-1) cleaves out an intervening sequence from the HAC1 mRNA. Cleaved mRNAs are then ligated by tRNA ligase, thus generating a spliced mRNA that translates an active transcription factor. This unconventional splicing of HAC1 mRNA in the cytoplasm is a molecular marker for various cellular stresses including oxidative stress and endoplasmic reticulum (ER) stress. This article describes a PCR-based protocol to detect the HAC1 mRNA splicing.
    Keywords:  HAC1; IRE1; Protein folding; Stress
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_7
  6. Methods Mol Biol. 2022 ;2378 221-231
    In Vitro Stimulation of IRE1α/XBP1-Deficient B Cells with LPS.
    Huabin Zhu, Chen Jiang, Randal J Kaufman, Honglin Li, Nagendra Singh.
      During immune responses, pathogen-specific B cells differentiate into plasma cells. Plasma cells synthesize and secrete large amounts of immunoglobulin (Ig) molecules which play a central role in immunity against pathogens. The synthesis, proper folding, and secretion of these Ig molecules require expansion of the extensive endoplasmic reticulum (ER) network. Accumulation of unfolded or misfolded proteins in the ER is sensed by three sensors: IRE1/XBP1, PERK, and ATF6, which coordinate with each other and initiate the unfolded protein response (UPR) pathway to expand the ER network and its protein folding and secretion capability. The expansion and maintenance of the ER network in plasma cells is triggered by activation of the IRE1/XBP1 branch of the UPR pathway. Here, we discuss the methods to stimulate the differentiation of B cells into plasma cells, measure the activation of the XBP1 pathway, and quantify the ER network.
    Keywords:  B cells; Unfolded protein response pathway (UPR); XBP1
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_14
  7. Methods Mol Biol. 2022 ;2378 169-187
    Analysis of XBP1 Contribution to Hyperosmolarity-Induced Lipid Synthesis.
    Cecilia I Casali, Leandro Parra, Luciana C Erjavec, María Del Carmen Fernández Tome.
      The unfolded protein response (UPR) is a complex network of intracellular pathways that transmits signals from ER lumen and/or ER bilayer to the nuclear compartment in order to activate gene transcription. UPR is activated by the loss of ER capacities, known as ER stress, and occurs to restore ER properties. In this regard, glycerolipid (GL) synthesis activation contributes to ER membrane homeostasis and IRE1α-XBP1, one UPR pathway, has a main role in lipogenic genes transcription. Herein, we describe the strategy and methodology used to evaluate whether IRE1α-XBP1 pathway regulates lipid metabolism in renal epithelial cells subjected to hyperosmolar environment. XBP1s activity was hindered by blocking IRE1α RNAse activity and by impeding its expression; under these conditions, we determined GL synthesis and lipogenic enzymes expression.
    Keywords:  Endoplasmic reticulum (ER) stress; Glycerolipid synthesis; Hyperosmolarity; Inositol-requiring enzyme kinase 1α (IRE1α); Unfolded-protein response (UPR); X-box-binding protein 1 (XBP1)
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_11
  8. Methods Mol Biol. 2022 ;2378 69-81
    The Use of Fluorescent Protein Fusions to Monitor the Unfolded Protein Response and Protein Foldase-Substrate Interactions in Plant Protoplasts.
    Rina Carrillo, Elizabeth Feldeverd, David A Christopher.
      Endoplasmic reticulum (ER) stress and the resulting unfolded protein response (UPR) are critical stress response pathways in eukaryotes. To study these types of interactions in plants, a wide range of methods have been used, including generation of transgenic plants, subcellular immunolocalization of protein foldases, and co-immunoprecipitation (co-IP) assays. Although these more time-consuming methods have been successfully implemented, there is a need for a versatile and rapid in vivo system to investigate ER stress and UPR. Here, we describe a transient expression system that uses plant protoplasts to define in vivo subcellular localizations and protein-protein interactions of protein foldases and their substrates fused to fluorescent protein reporters. This accurate and robust assay utilizes a variety of analyses, such as subcellular localization, FLIM-FRET, co-IP, mutagenesis, and RT-PCR in the genetically amenable Arabidopsis model system. We demonstrate the methodology by using the representative protein foldase, protein disulfide isomerase-9 (PDI9), as well as subcellular markers, secretory proteins, and dithiothreitol (DTT)-mediated induction of the UPR as monitored by RT-PCR. Together, these methods yield reliable high output results for investigating subcellular localization and protein-protein interactions in plants to decipher the UPR pathways.
    Keywords:  FLIM-FRET; Fluorescent protein fusion; Protein disulfide isomerase; Protein foldase; Protoplasts; Transient expression analysis; Unfolded protein response
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_5
  9. Methods Mol Biol. 2022 ;2378 19-30
    Fluorescence-Based Biosensors for the Detection of the Unfolded Protein Response.
    Heinrich Kroukamp, Kai Peng, Ian T Paulsen, Riaan den Haan.
      The unfolded protein response (UPR) is a highly conserved protein quality control mechanism of eukaryotic cells. Aberrations in this response have been linked to several human diseases, including retinitis pigmentosa and several cancers, and have been shown to have a drastic impact on recombinant protein yields in fungal, insect, and mammalian cell lines. Here, we describe the use of in vivo biosensors to measure and characterize this dynamic cellular response, specifically for detecting the UPR induced by protein overproduction stress in the model cell factory Saccharomyces cerevisiae.
    Keywords:  Biosensors; Protein folding capacity; Saccharomyces cerevisiae; Unfolded protein response
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_2
  10. Methods Mol Biol. 2022 ;2378 233-245
    Detection of PERK Signaling in the Central Nervous System.
    Zhixin Lei, Sarrabeth Stone, Wensheng Lin.
      In response to endoplasmic reticulum (ER) stress, activation of pancreatic ER kinase (PERK) signaling adapts cells to stressful conditions by phosphorylating eukaryotic translation initiation factor 2α (eIF2α). Phosphorylation of eIF2α inhibits global protein translation but stimulates the expression of numerous stress-responsive genes by inducing the transcription factor ATF4. A large number of studies have shown that activation of PERK signaling has beneficial or detrimental effects in various diseases of the central nervous system (CNS), including neurodegenerative diseases, myelin disorders, CNS injuries, among others. This chapter is devoted to describing the practical methods for the detection of PERK signaling in CNS diseases.
    Keywords:  ATF4; CHOP; GADD34; Immunofluorescence; Neuron; Oligodendrocyte; PERK; Phosphorylated eIF2α; Real-time PCR; Western blot
    DOI:  https://doi.org/10.1007/978-1-0716-1732-8_15
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